Some lab-leakers try to downplay Chinese military involvement in the origin of Covid. They argue it’s speculative and a distraction from issues like biosafety and gain-of-function experiments. But it’s neither speculative, nor peripheral. The PLA have been at the forefront of coronavirus research in China - and even in the US. Why try to obfuscate this? Partly because lab-leakers are concerned for their image. They want to be taken seriously by “serious” scientists, and those scientists say that bioweapons are a “conspiracy theory”.

Ironically, many “serious” scientists owe their careers to the tsunami of funding that inflated the sector during the millennium-era panic over bioterrorism. After the costly failure to confirm BW in Iraq and Afghanistan, it seemed to some the threat had been over-hyped - perhaps even deliberately. A premature consensus formed among scientists that SARS had emerged naturally by zoonosis - even before the virus had been sequenced, let alone a zoonotic host identified. Their view was shaped by misconceptions about bioweapons and geopolitics rather than scientific evidence.

With the bioterrorism panic abating, scientists didn’t want to relinquish their lavish funding, so they inflated a new threat: disease emergence resulting from ecological wantonness. One Health became the mantra for a still thriving biodefense sector.

But they were wrong again. SARS was never scientifically proven to be natural, and bioterrorism is still a threat. Jihadists and Middle-Eastern “failed states” had been struck from the list of suspects, but China and Russia were never on it - and they are far more capable, if their motives less discernable. Conversely, nature is not the threat that some claim. Although bats certainly harbor dangerous diseases, they aren’t poised to ignite human respiratory pandemics. The ability to transmit between humans efficiently evolves in humans (or close relatives) gradually. But it can be conferred easily and instantly in a lab.

Soon after SARS, the PLA introduced new grey-zone tactics into doctrine known as the “Three Warfares”: Public Opinion Warfare, Psychological Warfare and Legal Warfare. These principles enshrine the use of deception, media manipulation and influencing global institutions - even outside wartime. They would prove extremely useful for concealing the origin of SARS.

This is a story of geopolitically naive western scientists: ecologists, zoologists, veterinary scientists - motivated by ideals like nature conservation, health equity, international development. They entered collegiate relationships with Chinese scientists in a spirit of trust and openness. They weren’t trained to sniff-out fraud and saw no reason to suspect it. Pitted against them were rat-cunning PLA bioweaponeers covertly engaged in unrestricted war with the West. They framed their involvement in soft terms the westerners could relate to, and even became China’s champions for One Health. They worked hand-in-glove with Chinese civilian institutions, whose roles under Military-Civil Fusion arrangements were even less transparent.

SARS came from civets, didn’t it?

Some lab-leakers point out that even though they believe SARS-1 is natural, that doesn’t rule out an artificial origin of SARS-CoV-2. There are important differences between the two e.g. after six years no-one has found an intermediate host for SARS-CoV-2, but during SARS-1, civets were identified within weeks. True enough, but few know how this unfolded and that the PLA was instrumental in forging the link.

At the time of SARS, China was in a leadership transition between Jiang Zemin and Hu Jintao. Hu became President on March 15th, 2003, but Jiang remained head of the Central Military Commission, so kept command of the PLA. Four weeks into his presidency, Hu called an emergency meeting of the politburo to demand a new approach to SARS. The PLA had been caught concealing case numbers from civilian authorities. Hu now demanded complete transparency. China was to mobilize all necessary resources to end the epidemic swiftly, it would be framed as a patriotic struggle. The PLA at first seemed reluctant to co-operate, until Jiang Zemin added his assent.

The day of the politburo announcement, Cao Wuchun's group from the Academy of Military Medical Science (AMMS) uploaded a sequence to GenBank which they claimed had been isolated from a patient early in the Guangdong outbreak. It had a unique feature - an extra 29-nucleotides inserted in ORF8. They published a paper which hypothesized this was an ancestral strain that had spilled over recently from an unknown animal host. They suggested the deletion of this 29-nt in other known sequences was an adaptation which allowed better replication in humans (this was eventually shown to be false).

Now if only someone could find a zoonotic strain with this extra 29-nucleotides…

They didn't have to wait long. Guangdong CDC claimed that several of the early cases they had managed to trace were in food handling occupations and floated a theory that the outbreak may have been related to the trade in wild animals sold for food. At the invitation of high-profile respiratory doctor and CPPCC delegate Zhong Nanshan, two scientists from Hong Kong University (HKU) - Bojian Zheng and Yi Guan, crossed into Shenzhen to assist the CDC in sampling live animal markets. Both scientists were born and educated in mainland China, Bojian Zheng was a Guangdong native who had previously studied at Zhong Nanshan's institution.

Soon they announced they had sequenced strains of SARS with the 29-nt insert in samples from six civets and a raccoon dog in a Shenzhen market. They announced their findings at a press conference months before publishing the paper and sequence data. For most of the public and media this evidence was enough. Case closed!

Well, for scientists…not quite.

Another group also sampled civets and many other mammals. Finding no evidence of any coronavirus, they questioned HKU’s results. Other scientists weighed in, suggesting it was possible the civets may have been infected by people, or other animals in the market, and perhaps weren’t the reservoir. WHO and UN representatives declared that further investigation was needed.

In December 2003, 7 months after SARS had been declared eradicated world-wide, four new SARS cases were announced in Guangzhou. The cases weren’t linked to each other and all had mild symptoms, so it is perhaps surprising they were detected at all. Fortuitously, one of the cases was a 20-year-old waitress who happened to work in a restaurant serving exotic animals. Once more, Bojian Zheng and Yi Guan raced to Guangzhou to help sample civets in the restaurant kitchen and a nearby market. This time they sequenced a strain in the civets that was an identical match to the waitress’ clinical samples - and all had the extra 29-nucleotides. This- they claimed - was evidence of a new spillover in progress - caught before the virus had time to adapt to humans. On this new evidence Zhong Nanshan recommended a mass culling of civets on farms and wildlife markets. Since then, no SARS cases have been detected in civets, humans or any other animal (excluding lab-leaks). Case closed - again!

Well, not quite…

The PLA papers over the cracks

Even before the civet evidence, US scientists favored a natural origin. They assumed China wasn’t the kind of place terrorists would target, but Guangdong was exactly the kind of place a novel virus might emerge. The consensus view comfortably aligned with President Bush’s wish to engage China as a partner in the war on terror, and corporations clamoring to do business. In the wake of SARS, governments raced to help China develop bioscience capability. Due diligence was neglected, the warnings of intelligence agencies and national security hawks went unheeded.

At WHO and UN urging, China allowed foreign scientists to assist with origin investigations (restricted to natural causes, of course). The most significant contributions came from Institut Pasteur, Australia’s CSIRO, and US-based EcoHealth Alliance. But they didn’t work alone. Most of the work of collecting samples and sequencing them was conducted by their Chinese collaborators. There is a crucial limitation that hasn’t been recognized: there is no way to independently verify sequence data is genuine, or that samples haven’t been tampered with. Not only is data inadequate for an investigation of possible bioterrorism, it doesn’t meet basic scientific criteria of reproducibility and falsifiability. To believe SARS was a natural phenomenon - you must trust the PLA.

Institut Pasteur was at the center of negotiations for the French Government to help design and build China’s first P4 lab. French intelligence agency DSGE had expressed concern about the PLA use of such a facility for biowarfare. To assuage their fears Institut Pasteur Shanghai (IPS) was founded in 2004. This was a joint venture with China’s Academy of Science. The intention was that IPS would host international scientists who would maintain some oversight of the lab (which was originally planned for Shanghai). China pushed back against this before the lab was even complete. Through its existence, IPS was largely staffed by Chinese scientists. France eventually dissolved the JV in 2021 for reasons that are unclear.

Institut Pasteur assisted Wuchun Cao’s AMMS group on the epidemiology of the Beijing outbreak. What was the point made by this work?

Most SARS cases from the international outbreak (excluding China) stem from the super-spreader incident which occurred at Hong Kong’s Hotel Metropole. The presumed index case, Dr Liu Jiunlun, was supposed to have stayed there, after being infected at a Guangzhou hospital at which he worked. One of many outstanding mysteries was why sequences descending from the Metropole had several different signature mutations to those from patients at the hospital. The AMMS/Pasteur paper claims that the same set of mutations evolved independently (convergently) during the Beijing outbreak, proposing these were strongly selected adaptations due to the recency of the spillover to humans.

The sequences supporting this were provided by AMMS, should they be trusted? Institut Pasteur obtained and transferred over 2000 patient samples back to Paris. Perhaps these could have been independently sequenced, but the samples disappeared in 2013, in a mysterious incident which remains unsolved.

Another super-spreader incident that lacks a plausible explanation is the Amoy Gardens, in which over 300 people were said to have been infected from a single index case transmitted via diarrhea aerosolized by a toilet flush. Although viral RNA had been detected in stool samples, attempts to culture live virus from them had failed. Again, it was the PLA who tied this loose end. The evidence for live virus in feces, and the possibility of transmission via this route comes from the PLA’s 302 Hospital.

Most research into SARS in civets comes from a group from the AMMS Military Veterinary Research Institute in northern China’s Jilin province, a group led by Tu Changchun. Tu’s papers provide the experimental evidence that civets can be infected with SARS, sequences that support the viral evolution between human and civet, and further evidence of civet infection in live animal markets.

Scientists from Australia’s CSIRO are listed as co-authors on Tu Changchun’s civet-related papers. The role CSIRO played, and extent of their involvement is unknown. Tu Changchun and his colleagues often publish using civilian affiliations and titles in order to obfuscate their military links.

Focus switches to bats

While Linfa Wang’s CSIRO team had pre-existing expertise in identifying and isolating bat viruses, Wuhan Institute Virology did not. At the time Zhengli Shi studied the viruses of marine crustaceans. Linfa Wang had an intuition that bats may be the reservoir host. Zhengli Shi expressed interest in this hypothesis. A collaboration formed that would last well over a decade.

They had early success finding bat coronaviruses that seemed closely related to SARS through much of the genome. But the all-important spike gene - which determines host tropism - was quite divergent. In particular, the region of spike which binds the host cell receptor - the RBM - had several amino acid deletions, which meant these viruses couldn’t bind human ACE2, nor even bat ACE2.

In 2008 a German group led by Christian Drosten isolated a bat virus from a sample collected in Bulgaria. Although very different from SARS through much of the genome, the RBM was much closer to SARS than any Chinese bat virus. Since then, many more related viruses have been discovered belong to this clade, spanning much of Europe and Africa. Some of these can bind ACE2, albeit weakly, they still have some amino acids missing.

SARS appears to be a recombinant - or chimera - having the "backbone" of a Chinese virus, but the spike (especially the RBM) is much more similar to an African or European virus.

The Bulgarian discovery reignited interest in finding a bat virus with SARS-like RBD, and also led people to experiment with artificial chimeras. Ralph Baric and Marc Denison showed you could replace the RBD of a Chinese bat virus with that of SARS and the resulting chimera was viable and able to infect human cells. WIV tried to engineer something similar, but weren’t able to recover and culture living virus - at least initially.

HKU strengthens ties to Beijing

HKU remained involved in the origin search, also switching their focus to bats. They quickly answered CSIRO/WIV's bat virus discovery with a similar one of their own (HKU3). CSIRO/WIV had also sequenced some variants from other provinces and bat species (Rm1/Rf1). HKU again responded with viruses similar to these (BtCoV279/BtCoV273). Both groups had matching sets.

In 2005, the HKU microbiology department of Bojian Zheng and Yi Guan, JS Malik Peiris and Kwok-Yung Yuen was designated State Key Laboratory for Emerging Infectious Diseases, and began to receive lavish funding from the PRC government. Later it began to collaborate - rather than compete with WIV, and established formal partnerships with other mainland institutions, such as a three-way collaboration with Zhejiang University and the Institute of Pathogen Biology in Beijing.

Bojian Zheng became a guest professor at AMMS Beijing lab, which at around the same time was designated the State Key Lab of Pathogen and Biosecurity. AMMS virologist Lanying Du moved from Beijing to Hong Kong to commence a PhD. Her thesis was on the structure and function of the SARS spike protein, Bojian Zheng was her supervisor. Du was married to senior AMMS officer Yusen Zhou until his death in early 2020 (reportedly from falling off a building). After completing her PhD, she moved to the US to continue researching SARS, and later MERS, under Shibo Jiang. Over the years she has authored several key papers on receptor binding and proteolytic cleavage of SARS and MERS.

Yusen Zhou remained in Beijing, where he collaborated with Tong Yi-gang developing synthetic biology techniques. They invented systems for assembling viral genomes seamlessly using DNA synthesis and PCR. This is an alternative approach to the restriction enzyme based "no see-em" system used by Baric et al, and has become the preferred method for many scientists, as the cost of DNA synthesis has fallen.

Zhou and Tong jointly developed other engineering techniques with possible relevance particularly to the FCS region.

They also used a directed evolution technique called phage display which is used to select variants of a protein which bind most strongly to another protein. This technique might be used to select from a library of millions of randomly generated variants, an RBM sequence that binds most strongly to hACE2.

The search heats up

In 2012 a group of epidemiologists from the 4th Military Hospital published a paper in a Chinese language journal suggesting SARS had an artificial origin. They pointed out some epidemiological quirks:

• Ten years on, no reservoir species had been identified.

• As suddenly as it appeared, SARS vanished without trace. No infections in humans or animals have been reported since early 2004 (aside from lab-leaks). Excepting smallpox (which took decades after the development of an effective vaccine) this is unprecedented.

• It has signs of reverse evolution. Adaptations thought key for its replication in humans/civets, reverted to less fit residues in some of the more recent sequences.

The leader of the group, Xu Dezhong, had been the senior epidemiologist working with China’s Ministry of Health during SARS. As a PLA(but not AMMS!) general Xu has been misrepresented in some media as a BW Dr Strangelove. However, he wasn’t promoting the use of BW, but edited a compilation of papers that gave an introduction and historical background. He noted the similarity of SARS to USAF Colonel Michael Ainscough’s depiction of a bioterrorist attack with a novel genetically engineered pathogen.

Having failed to interest the Chinese government in investigating an artificial origin, Xu tried unsuccessfully to get the group’s papers published in English language journals. He wrote to WHO Director-General Margaret Chan personally, asking her to open an investigation. She dismissed him curtly.

As Hong Kong Department of Health Director at the time of SARS, Margaret Chan had been chastised by the subsequent Hong Kong Legislative Council inquiry. She was accused of doing too little to press her Chinese counterparts for information about the situation in Guangdong, and of keeping discussions with them secret from her Hong Kong colleagues. Her counterpart in Beijing had been Liu Peilong, Director-General of International Cooperation at the Ministry of Health. In June 2003, Liu Peilong was appointed Assistant Director and Advisor to the incoming WHO Director-General, South Korean Lee Jong-Wook. In 2006, Lee died suddenly of a subdural hematoma after collapsing at a function held at the Chinese mission in Geneva. Chan, Liu and China’s Minster for Health Gao Qiang were all present at the time. There was no autopsy or inquest held. Following Lee’s death, China lobbied intensely at high level for Chan to be elected to the role.

But Xu’s ideas were attracting some attention in China. In a review published in August 2013, Ruiheng Xu, former Deputy Director of Guangdong CDC, who had led the epidemiological investigation in the province, gave some credence to his theory.

He also gently chided AMMS for keeping secret that they had identified, isolated and sequenced the virus long before the rest of the world. The possibility of further muckraking may have expedited a resolution to the origin.

Holiday in Yunnan

Baric’s human infectious chimera heightened US concerns over pandemic potential viruses in Chinese bats. The USAID-funded PREDICT program, led by UC Davis’s One Health Institute joined the search. PREDICT’s work in China was led by EcoHealth Alliance (EHA), which rebranded from Wildlife Trust under the slogan “Local Conservation, Global Health”. EHA subcontracted much of the fieldwork to WIV.

In October 2012, PREDICT and EHA organized a joint US-China workshop in Kunming, Yunnan. I recently obtained some FOIA documents about this period from UC Davis's Jonna Mazet - the Global Director of PREDICT. They contain a few insights, but what’s perhaps most interesting is what's not discussed and what’s not on the conference agenda.

Zhengli Shi gave a talk on general bat virus diversity. Cao Wuchun gave a talk on tick-borne viruses. Zhao Guoping, who led the SARS Molecular Epidemiology Consortium was also present. Zhang Shuyi had been involved in the earlier CSIRO/WIV bat virus discoveries. The Chinese contingent was packed with SARS origin expertise, but SARS origin wasn’t on the agenda, and the conference attendees weren’t even discussing it in emails between each other.

This is doubly surprising because a year later WIV would publish the first paper suggesting that SARS likely emerged in a cave just a short drive from the conference venue. They claim to have sampled and cultured bat viruses that for the first time had an almost identical RBM to SARS and were capable of binding hACE2. The first of these was collected in April 2011, they should already have sequenced it by the time of the conference.

What’s more, the "Mojiang miners" incident is also said to have happened recently in Yunnan. This was deemed important enough that three teams of Chinese scientists made multiple trips to the mine to collect samples. But again, the incident isn’t mentioned by the conference attendees. It seems that the choice of conference location was pure co-incidence.

There’s also no mention that in January 2013, WIV joined a Chinese state funded program, with a similar objective of collecting novel pathogens. This 5-year program brought together WIV (led by Zhengli Shi), AMMS (led by Cao Wuchun) and the CDC lab of Zhang Yongzhen (Eddie Holmes collaborator). Either WIV didn’t disclose this to EcoHealth, or EcoHealth didn’t disclose it to PREDICT, but it seems a serious conflict of interest.

Myth of the Mojiang Miners

The tale of the Mojiang Miners is well known in lab-circles. In an abandoned mine-shaft, in Mojiang county, Yunnan, six miners clearing guano fell ill, and three died. In this mine-shaft, WIV claims to have discovered RaTG13 - the virus which for a time was the closest to SARS-CoV-2. Some lab-leakers speculate that WIV may have sampled other viruses in the mine, kept them secret and one of these may have been the precursor to SARS-CoV-2. That isn’t my view though - I think the miners’ story is fiction.

There are no official records or local media articles about the incident, it is mentioned only in three student theses and one published paper. Between these sources, important details (such as dates and test results) differ or are unclear. WIV seems to be the source of the claim some clinical tests were positive for SARS - but they later recanted and said that the disease was fungal, and that all tests had been negative. According to Zhengli Shi, it was just a co-incidence that hearing of these sick miners guided them to the place they discovered the first SARS-CoV-2 related virus. So these student theses contained false information:

Zhong Nanshan was said to have been involved in sampling.

In late 2012 a pre-print about the origin of SARS was posted by a group led by Zhong Nanshan. The paper was accepted for publication, but never published. The pre-print has a strange annotation.

This pre-print explains the emergence of SARS as being from bats via civets in Guangdong, and also claims SARS still circulates in humans in mild form. It doesn’t mention Yunnan at all. This suggests Zhong Nanshan hadn’t heard of the Mojiang miners - or WIV’s hACE2 binding viruses either.

The first mention of the hACE2 binding viruses in Jonna Mazet’s emails isn’t until August 2013, after the paper has already been accepted for publication by Nature.

CSIRO have been unable to find any documents about the work, but UC Davis has a couple that suggest they had little involvement in the “discovery”.

While the ABC and BBC played up CSIRO’s role, the Guardian may have the correct nuance. WIV used a technique pioneered by CSIRO. Aside from reading the draft paper, CSIRO may have had nothing to do with it.

The first author of the paper, Xinye Ge, had recently complete his PhD jointly between WIV and Institut Pasteur (Paris). His work at WIV involved isolating bat viruses, but at Pasteur he learned skills in synthetic virology: reverse genetic systems, phage display, protein-protein interactions. He may have succeeded where his WIV colleague Zhang Huajun failed, successfully engineering chimeras which were passed off as natural.

As WIV’s Nature paper was being finalized, Tu Changchun’s AMMS group uploaded sequences for a similar virus (LyRa11) they claim to have sampled in another part of Yunnan (also in 2011). Lyra11 is from a different bat species R. affinis, while WIV's are from R. sinicus. The significance is that while R. sinicus is largely confined to China, R. affinis has a range that extends deep into South-East Asia - where it is possible for it to encounter a Malayan pangolin. R. affinis is also the host of RaTG13.

One Health infects China - or vice versa?

Xu Dezhong didn’t back down. He responded to WIV’s new discoveries with further reasonable objections. But it became impossible to get heard by western scientists, or the WHO. I’ve since shown that Ge et al appears to be a work of fraud (for other reasons).

Former US Navy Captain Gregory Gray had a long and distinguished career as an epidemiologist at the Naval Health Research Center where he led programs and centers funded by GEIS, the DoD’s infectious disease surveillance program. After transitioning to civilian academia, in 2002 he became interested in One Health, and championed its international spread.

Gray became involved in China and started collaborating with Wuchun Cao and AMMS. Together they published a military-themed call for Chinese institutions to adopt One Health.

Gray proposed holding a symposium to promote the One Health approach in China. The first of these was held in 2014 in Guangzhou, and was sponsored by Sun Yat-Sen University (SYSU), South China Agricultural University (SCAU) and AMMS. Participants included key SARS origin figures Nanshan Zhong, Guoping Zhao. Xu Jianguo - the leader of the joint pathogen discovery project, was also present.

Gray and AMMS produced papers highlighting risks posed by live animal markets and proposing more active surveillance - a theme echoed by the PREDICT/EHA group.

Today, One Health reigns supreme in academia and global institutions and is enshrined in the recent WHO treaty. All disease outbreaks are automatically declared natural, bioweapons are a “conspiracy theory”, no effort is expended to investigate the possibility. It is likely that there have been other disease outbreaks - impacting not only humans, but livestock and crops - that are misattributed as natural and touted as further support for One Health. And no-one questions the role of the PLA’s biowarfare unit in promoting this belief.

Gray even spent time at USAMRIID, if he couldn’t conceive of a realistic threat from offensive bioweapons - which US scientists could? In an early 2020 interview, Gray seemed appalled that people would accuse China of even an accidental lab leak. The people he dealt seemed professional and open - had western standards. The mastermind of the deception - Cao Wuchun - is well-educated and traveled, has worked and studied at Cambridge, Karolinska and Erasmus. But the PLA is steeped in ethno-nationalist, expansionist ideology of a type that many westerners wrongly assume went extinct last century. And deception is embedded in their doctrine.

What of the WIV?

WIV’s relationship with AMMS becomes clearer when reading the scientific literature and analyzing sequence data. In a future article I’ll explain the relationships between their respective “discoveries”. WIV’s primary role has been to build credibility and relationships with foreign institutions and influential scientists, so as to disseminate false science and sequence data. This is most evident in the composition of their scientific advisory committee.

It’s clear that most western scientists are no wiser to WIV’s manipulations, and some prefer to blame our free press and open political discourse for Zhengli Shi’s discomfort. These are the strengths of our system. Attempts to stifle debate are signs of the erosion of liberal values within our institutions as China’s influence grows.

It’s also clear that many scientists place more weight on collegiate relationships and institutional reputations, than science. They’re unable to explain why certain sequences appear to violate established principles of molecular evolution. Nor are they bothered that they can’t reproduce results. They’ve made the mistake of trusting the scientist - not the science.

Even before 9/11 there was heightened interest in bioterrorism. In June 2001, CSIS and JHU ran "Operation Dark Winter", which simulated a terrorist attack on the US with smallpox. The CDC was stockpiling smallpox vaccines and training responders to prepare for an attack.

A book about biowarfare by New York Times journalists was released on October 2nd, 2001, the same day as the first anthrax victim was hospitalized. A major theme of the book was how the US was unprepared for an inevitable bioterrorist attack. They got lucky with the timing, it quickly became a best-seller.

In 1999, Ken Alibek, the former deputy head of USSR bioweapons program (who had defected to the US in 1991), published “Biohazard”. The extent of the Soviet program, and advancement of their weapons, had been gravely underestimated by the US. Alibek also claimed scientists from the program were being recruited by other countries, and potentially trans-national terrorist networks.

Alibek described Soviets experiments to genetically engineer novel bioweapons in various ways e.g. by making them express peptides from human regulatory proteins or by combining gene fragments from different viruses.

Another area of intensive research was aerosolization. Bioweapons need an effective delivery system. The USSR developed aerosolization technology on many scales - from low-flying cruise missiles capable of infecting entire cities, to miniaturized gadgets.

In April 2002, US counter-proliferation expert Colonel Michael Ainscough predicted a possible terrorist attack with a genetically engineered bioweapon. He depicted a scenario in which the unknown pathogen had a delayed onset of symptoms. This allowed it to spread quietly unnoticed. It could be carried internationally by unwitting airline passengers. Hospitals would become paralyzed as healthcare workers became infected. Diagnosis would be difficult for a novel pathogen with no tests available.

This is uncannily similar to the way SARS would soon play out.

In the wake of the 1996 Taiwan Straits crisis - which resulted in a huge loss of face for the PLA - China raised military spending, purchasing most weaponry from Russia. The 2001 Treaty of Friendship brought China and Russia still closer. The focus shifted to military technology transfer and joint weapons development.

Military aspects of the “Treaty of Friendship” were negotiated by China’s Defense Minister Chi Haotian.

Chi had fought in World War 2 in Shandong peninsula where up to 200,000 died from cholera - which has been attributed to Japanese biowarfare attacks. In the Korean War he received the top award for valor, involved in a successful attack against a far better equipped US regiment at Chosin. He was primarily a “political officer” responsible for indoctrinating troops with CCP ideology. He rose to be head of the PLA at the time of the Tiananmen Square massacre, gaining a reputation as a hard-liner for pushing a harsh crack-down in the aftermath. In 1993 he was appointed defense minister.

During the Korean War, North Korea, China and Russia conspired to make fraudulent accusations that the US was using bioweapons against them and their civilian populations. Their collusion was revealed in documents released after the USSR dissolved, and others from China which have been leaked by former officials. But such claims still circulate within the PLA and are widely believed - partly due to Chi Haotian.

Most alarmingly, a secret speech attributed to Chi before his retirement in 2003, promotes the use of bioweapons to “clean up America” so it may become a lebensraum for Chinese people (although he advises against using the term).

The 1999 PLA manual Unrestricted Warfare recognized the US remained militarily unassailable and looked to unconventional tactics pioneered by a variety of non-state actors - including terrorists, hackers, financial speculators - to strategically weaken the west. Al-Qaeda and Aum Shinrikyo were recognized for their “achievements” in the domain of terrorism.

In October 2002, Russia put its aerosolization expertise to use against Chechen terrorists who were holding over 900 hostages in the Nord-Ost theater in Moscow. The agent used wasn't a real gas, but an aerosolized fentanyl derivative (which is solid at room temperature). Unfortunately, 40 hostages died from its effects.

With dark humor, Alibek relates a conversation with a KGB colleague about developing miniaturized gadgets for aerosolizing viruses for the purpose of assassination.

Using an agent in the form of dry powder adds some complexity, but aerosolizing liquids is straightforward - even with cheap consumer gadgets. Ultrasound nebulizers (such as those used to dispense a room fragrance, humidify, or create a decorative mist effect) are ideal, but even a basic atomizing spray bottle or can, might be effective. Aum Shinrikyo, when attacking the Tokyo subway, used sarin unheated, in plastic bags which they pierced before alighting from trains. The high volatility of sarin was sufficient even at room temperature. The Russians developed more complex hybrid techniques whereby volatile liquids would vaporize and carry fine solid particles in suspension.

Cynics claimed bioterrorism was over-hyped by the Neocons to build support for the Iraq invasion they had long planned. Just a week after 9/11, anthrax-laced letters were sent to US media outlets. They reference the date 9/11 and contain crude Jihadist tropes in an apparent attempt to misattribute. Though only 5 deaths resulted, the attacks stoked disproportionate panic, causing social and economic disruption.

Some even claimed the letters may have been a “false flag” plot. Doubts remain over the quality of scientific evidence the FBI gathered against their “lone wolf” suspect.

President Bush tried to foster personal friendships with China's leaders, seeing China as an ally in the Global War on Terror. Others in his administration (e.g. Donald Rumsfeld) were far less trusting. Jiang expressed solidarity with the US after 9/11, claiming that China also had problems with terrorism. Bush accordingly added Xinjiang separatist groups to the US list of terrorist organizations.

Falun Gong charged that the Chinese government was falsely accusing them of anthrax attacks in China, an attempt to have them also listed as a terrorist organization. Chinese propagandists who had been labeling them an “evil cult” sharpened their rhetoric. Acts of self-immolation in Tiananmen Square were denounced as terrorism.

Many countries introduced new security laws, protocols and agencies in the wake of 9/11. Inevitably, authoritarian states would also seek to exploit the opportunity.

In China, the PLA authors of “Unrestricted Warfare” promoted a body that would take control during any national or international emergency. With the PLA at the core, it would control the media and be in charge of international liaison.

After SARS, PLA doctrine was amended to include what they termed the “Three Warfares”: public opinion warfare, psychological warfare, and legal warfare.

In September 2002, pro-China legislators in Hong Kong introduced a national security law that created crimes of sedition, treason and espionage against the PRC. Although some form of security law was required under the “one country, two systems” Basic Law, the timing was opportunistic and critics claimed it went beyond what was required and would undermine human rights and freedoms. It encountered huge opposition and was ultimately enacted only in 2024. It was recently used to jail Jimmy Lai.

On Feb 6th, 2003 Colin Powell addressed the UN to present the case for the Iraq invasion. With war imminent, terror alert levels were raised worldwide. Hong Kong was no exception. Although deemed an unlikely target, someone appeared to be trying to inspire fear of Jihadist terror.

A few days later HK media reported on a panic in neighboring Guangdong province, rumors of an unknown and fatal respiratory disease were spreading.

One specific rumor relayed was that hundreds of people had fallen ill at once at the Guangzhou World Trade Center - twin-tower style office buildings with a high-end shopping complex. There were whispers of bioterrorism.

No-one really knows what happened in Guangzhou. The media was barred from reporting for much of the time. Officials also stayed silent. Disease outbreaks had been designated a state secret.

Rumors were primarily spread via an organized mass SMS campaign. Tens of millions of identical text messages were sent each day.

WHO sent a team to China, but they were barred from entering Guangdong for several weeks. They stayed in Beijing where their Chinese counterparts refused to discuss anything of substance. The US Secretary of Health and Human Services offered to send a CDC team to Guangdong but was rebuffed. Hong Kong health officials were unable to contact their counterparts across their shared border.

The Guangzhou outbreak was retrospectively blamed on a super-spreader dubbed the “Poison King” who was reportedly transferred between 3 hospitals, infecting dozens of staff at each. When WHO staff were eventually allowed to enter Guangdong, he evaded their attempt to interview him. He also eluded the press.

Epidemiologically, SARS in Guangzhou was unlike a typical respiratory outbreak spreading widely across the city. A couple of hundred cases were sent to four designated hospitals. According to officials 95% of hospitals remained unaffected. For a province the size of Guangdong (some 80 million people at the time), the case numbers are small for a respiratory outbreak. Why was SARS a concern at all - why was it even detected?

Worst hit was the 8th Hospital, 3 minutes from the World Trade Center. But at another hospital which was reportedly overrun with SARS, a journalist found no patients.

According to the official account, one Guangzhou hospital that was stricken by the “Poison King” is the link to the global pandemic. The presumed index case was a doctor from Sun Yat-Sen No.2 Hospital who traveled to HK for a wedding.

But the doctor wasn’t in a front-line emergency role. He was a retired professor of nephrology (kidneys), who was said to have been volunteering in an outpatient clinic. The Poison King's stay at that hospital was short - 18 hours by one account (details are inconsistent across different sourses). A paper describing the outbreak at that hospital says that 96 people became infected at that hospital. But most cases were mild, and only one died - why was that doctor so unlucky?

The doctor caught a bus to Hong Kong for a nephew’s wedding - A full 3 weeks after the Poison King’s visit - and he was feeling fine. He checked into the Kowloon Hotel Metropole (which is owned by a Chinese SOE) at 5p.m. He stayed just one night. In that time, he purportedly infected over 20 other guests on the floor. But how? The incident remains unexplained, despite a WHO forensic investigation.

Is it significant that he stayed in room 911? The hospital had 487 guest rooms, so if a co-incidence, it’s an unlikely one. A terrorism scenario could explain all the anomalies - if it had been contemplated.

The majority of SARS cases stem from this one super-spreader incident. Some who stayed on the 9th floor went on to seed new clusters in hospitals in Singapore, Vietnam, Canada and at Hong Kong’s Prince of Wales. But most others who were infected at the Metropole transmitted to only one or two others, or no-one else at all.

These downstream hospital outbreaks also have a mysterious epidemiology - doctors and nurses who had early and close contact with an index case from the Hotel Metropole suffered the most severe illness or death. But those who had secondary infections from other staff had generally mild illness, and ICU nurses who treated the patient were relatively unaffected. What could explain this?

I speculate that these people carried something physical (perhaps a complimentary toiletry) from the Hotel Metropole, which traveled with them in their luggage or clothing, to hospitals at their destinations. This was adulterated with SARS coronavirus in an aerosolizable form.

A later super-spreader incident happened on Flight CA112 on 15th March - the day of the pre-ordained election of new President Hu Jintao. The presumed index case somehow infected 22 people on the short flight between Hong Kong and Beijing. Some of those infected were seated several rows away from the index case, but only two of the eight seated directly around him were infected. This pattern can only plausibly be explained by aerosol transmission.

The WHO retrospectively identified 35 other flights on which SARS cases flew, but there were only 5 suspected transmissions on these other flights combined.

Interestingly, 112 is the ITU approved alternative to 911. In most countries if dialed from a mobile it will divert to local emergency services. Uncanny, but perhaps this reference was too indirect and obscure. Unlike room 911, no-one seems to have remarked on it. Most airlines had stopped using 911 as a flight number as it made passengers and crew nervous. It wasn’t just irrational superstition, but commercial reality, recognizing the number had become associated with terrorism in the public mind.

The largest super-spreader event was at Hong Kong's Amoy Gardens. The official story is that a SARS case had diarrhea. When he flushed the toilet, it aerosolized virus-laden feces. Due to a poorly designed and faulty plumbing system the plume of aerosols was able to enter neighboring units.

OK, but he supposedly infected around 330 people, in 15 different towers - up to 100 meters apart! It sounds ludicrous. Even if SARS could transmit through feces, how could such quantities of aerosol be generated that could survive a 100m journey outdoors and enter so many units? There were many doubters, but this remains the official explanation. Other possibilities such as transmission by rats and/or cockroaches have also been refuted.

Terrorism might have offered a more parsimonious explanation - if it had ever been contemplated. Alibek’s former colleagues in the USSR had envisioned such attacks.

The needed rooftop was on an adjacent construction site, where industrial spraying machines wouldn’t be out of place. This style of attack would resemble one carried out in 1994 by Aum Shinrikyo in the town of Matsumoto. An improvised aerosolization device was deployed from the back of a truck upwind of a group of apartment blocks.

SARS occurred during a leadership transition in China. Outgoing President Jiang Zemin was popular with the PLA and remained in command for some time after Hu Jintao became president. There was tension between the PLA and government over how to manage SARS. The PLA hid the true case numbers even from the Ministry of Health, concealing patients in hospitals controlled by them. They initially ignored the new President Hu Jintao’s command that stopping the spread of SARS was a priority.

Ultimately Hu prevailed. The attempt to manufacture terror now needed to be covered up. It is bizarre that those prosecuting the Global War on Terror in the US saw no signs of it in SARS. The head of US CDC, Julie Gerberding, on one occasion responded to a journalist that they were “keeping an open mind” to the possibility of terrorism, but in later appearances would speak of SARS and bioterrorism in the same breath without connecting the two. Congress and think-tanks discussed SARS as a “wake-up call” or a “dry-run” for a terrorist attack, but never the real thing.

The US saw stability in China as essential and baked the new leadership, who they perceived as moderate. Financial and technical assistance was offered to help develop China’s healthcare systems and scientific expertise. US corporations slavered over commercial opportunities in China. Hank Paulson (who would become Bush’s Treasury Secretary) flew to Beijing even before SARS was eliminated, to buy Chinese government debt on behalf of Goldman Sachs.

Biodefense scientists continued to fret about the bioterrorism risks of smallpox and anthrax, but hastily declared SARS natural - well before there was any zoonotic evidence - even before the virus had been sequenced!

The only substantive scientific argument among these opinions is that recombination is frequent in coronaviruses, and that might allow them to jump species.

But had scientists ever witnessed this in nature? No. It was a hypothesis they had shown to work in a lab with genetic engineering. They then shared their methods with the world. It is in fact *extremely unlikely* it would happen in nature (for reasons discussed elsewhere on this site).

US institutions made the mistake of assuming all biological research is peaceful unless proven otherwise. Alibek’s warnings fell on deaf ears.

There's another dangerous mantra, chanted by One Health adherents.

"Assume all disease outbreaks are natural unless proven otherwise."

But then no serious efforts are made to investigate prove otherwise. Those who so much as suggest otherwise are smeared as “conspiracy theorists”.

The unclassified version of the State Department WMD Compliance report of 2005 (the first report to cover the SARS period) added references to PLA interest in aerosol technology. Does the classified version contain something more?

The intelligence community has shown remarkable reticence to show its hand, and even signs of obstruction. Are they protecting sources and methods? Should they also be protecting the public? Are they colluding with China to cover-up as part of some 4D geopolitical chess game? Or are they simply clueless?

The 2005 table-top exercise Operation Atlantic Storm again imagined smallpox dispensed by terrorists, but this time the outbreak went international and was spread by terrorists using handheld dry-powder sprayers - noting that “a number of these devices are commercially available”.

The US still has a (diminished) conventional military advantage, but decades after Alibek's warnings, is as vulnerable as ever to biological attack. The PLA is paying attention. Iran shows the importance of manufacturing to replenish munitions. Bioweapons are cheap and easy to manufacture secretly and, once deployed, can be self-sustaining. It's a dimension of war few in the west have even contemplated, but China has direct experience - both as victim and aggressor.

Most readers will be familiar with Yusen Zhou, the PLA scientist who died in May 2020. The manner of his death - it was rumored he fell (or was pushed) off a roof - and the fact he had patented a SARS-CoV-2 vaccine with remarkable speed, has led to justified speculation about his role in its origin. Zhou and his US-based wife, Lanying Du, have been involved in several important papers on the proteolytic cleavage and receptor binding of the highly pathogenic human coronaviruses SARS and MERS.

Tong Yi-gang is not quite so widely known. His group, also based at the AMMS Beijing Institute for Microbiology and Epidemiology, was also able to quickly propose therapeutics for SARS-CoV-2. They claim to have isolated a pangolin coronavirus (GX PCoV) in 2017 from pangolins seized from smugglers in Guanxi. In early 2020, Tong claimed it to be useful as a model for developing therapeutics for SARS-CoV-2 - thanks to its high similarity, but inability to infect humans.

Yigang Tong (left) with Wuchun Cao (right). His epaulettes indicate a rank of Major General

No need for “No see-’em”

Long before Covid, Zhou and Tong had co-authored papers on genetic engineering techniques, that although generic, are applicable to the enhancement of viruses. A particular focus was techniques based on assembly PCR. These methods avoid the use of restriction enzymes to splice genetic fragments together, relying instead on overlapping sequences at each end. The fragments can be designed in a computer (perhaps based on results of directed evolution experiments) and synthesized. There is simply no need for the techniques like Baric’s, that some still believe to be state of the art.

Zhou and Tong were using PCR assembly, and even writing high profile papers on new techniques as early as 2007.

Although this paper doesn’t describe, per se, a reverse genetic system, it demonstrates prowess with overlapping PCR to stitch together genes produced synthetically. It also mentions DNA shuffling. In a previous article I showed evidence this technique may have been used in engineering SARS-1 and MERS.

In 2009 another group invented circular polymerase extension cloning (CPEC), which did away with the need for restriction enzymes and ligation when inserting into a plasmid.

In 2014, another group exploited the cell’s own repair mechanism, joining fragments of synthetic viral DNA with overlapping ends, to produce live virus. This technique, Infectious Subgenomic Amplicons (ISA), is more suited to smaller genomes with fewer fragments, as recombination isn’t assured.

By 2017, CPEC was being applied to synthesizing viruses straight from sequence data. Zika was the first published example, followed by Dengue and other flaviviruses.

With the pandemic, several groups applied the technique to rescuing SARS-CoV-2, claiming various optimizations to the protocol.

The main advantage of Baric’s No See-’em technique in its time was that it was high-fidelity, the resulting sequence should contain few or no errors - even the handful of synonymous mutations needed to create restriction sites are avoided. The point wasn’t to hide evidence of manipulation, but to avoid errors that could make the resulting genome non-viable, and to properly understand the virus in as close to its natural form as possible.

In the early days at least, PCR based techniques could introduce errors, particularly when working with large fragments. However, this may not be a consideration for an engineer who is intentionally introducing mutations using directed evolution techniques - it may even be desirable. The result is a quasi-species swarm which are then subjected to a series of selection tests. It doesn’t matter if some species are non-viable, only the fittest will be selected.

Chimeric Structure of SARS-CoV-2

SARS-CoV-2 spike appears to be a chimera with the NTD derived from one virus, and the RBM another. Although RaTG13 (or a virus similar to it) has been proposed as the “backbone” into which a novel RBD was inserted, I believe it is a fabricated sequence, invented post-facto to misattribute the origin.

The likely precursors are the Guanxi pangolin coronavirus (GX PCoV) and the Guangdong pangolin coronavirus (GD PCoV), although neither likely came from pangolins (at least not the spike), and are already heavily engineered. The GX PCoV was isolated by Tong Yigang by his own admission, and the GD PCoV is clearly linked to a virus (ZC45) from another PLA group who are also linked to the “PLA Logistics Department” (later known as the Join Logistics Support Force, this is the unit who implemented the lockdown of Wuhan).

The relationship between these viruses, and chimeric structure of SARS-CoV-2 should be evident from the alignment below.

The GD PCoV is most similar to SARS-CoV-2 in the RBM - there’s just one amino acid difference between them but - bizarrely - 26 silent mutations. That’s an extraordinary ratio for what should be the most variable part of the genome, and a change in host species. The GX PCoV has 16 amino acid differences, but the important structural peptide TEIQAGST (described in a previous article) is conserved.

Engineering an FCS cassette

Comparing the three sequences in the region flanking the FCS insert there is just one nucleotide where SARS-CoV-2 doesn’t follow the GD PCov sequence, an A→G mutation, which is synonymous, doesn’t change the amino acid encoded.

But it does make a difference to a genetic engineer. If they wanted to insert a four amino acid FCS, and perhaps try a few different versions, or create multiple variants by some directed evolution technique, they need an easy way to cut the RNA nearby to make the insert. Commercial restriction enzymes are the most popular method.

The GD PCoV sequence already has some well-place Type IIS cut sites on the 5' side, but there are none immediately upstream.

A single nucleotide change A→ G creates two that are well placed.

The SARS-CoV-2 genome has many restriction sites, including some more that exist only due to the A→ G mutation.

Some have suggested that the FCS sequence may have been encoded the way it is, so as to deliberately introduce a restriction site FauI.

This may have been intended to give the engineer an easy way to test for the presence of the FCS sequence using gel electrophoresis. This provides a quick way to estimate sizes of the various DNA fragments present. Cutting the genome at the FauI site using its restriction enzyme will result in a recognizably different pattern from a similar genome without the FCS.

Interestingly this technique was invented by Tong Yi-gang and Yusen Zhou in 2009.

When they employed this technique, they use Phusion DNA polymerase which has a very low error rate of just 4.4×10−7 bases per cycle.

This should result in just ~0.015 errors in a 30kb coronavirus genome per PCR cycle. Noting that any PCR based procedure might require 20-30 cycles, and they may perform several PCR procedures in the course of manipulating a genome, it is still possible to employ these techniques to achieve a high-fidelity result - if that’s what is desired.

Reagents like Phusion aren’t cheap, but it’s important to understand the AMMS is no poor cousin to its civilian counterparts e.g. WIV, that are better known internationally. Military doctors and scientists are among the elite in their professions, and AMMS are the elite of the elite. They are well paid, well-trained, well-equipped, able to study and attend conferences internationally (pre-pandemic). The synthetic biology techniques they employ are way ahead of WIV, and even Baric. The downside is the risk of falling from a building in case of failure - or treason.

Tong’s SADS says so much

Tong Yigang’s grant for his secret project for the PLA Logistics Department amounts to ~US$4.5 million over 4 years - a large sum for China. For comparison, WIV received a combined US$1.7 million from PREDICT and NIH over a decade. What did Tong’s group “produce” in that time?

A pangolin coronavirus that appears to be one of the precursors to SARS-CoV-2 and wasn’t reported until the outbreak. But there’s more…

There’s been renewed interest in a pig coronavirus, SADS, that first struck China in 2017. The interest is because former WIV scientists are involved, and the work is only being done at BSL-2 level. It seems to fit the “risky research/poor biosafety” narrative. Zhengli Shi protege Peng Zhou is the first author on a 2018 paper describing the outbreaks, and the discovery of novel bat coronaviruses suspected to have been the precursor. It is a star-studded cast, many of which will soon go on to play leading roles in the SARS-CoV-2 cover up.

But once again I found the viruses behind SADS to have weird evolutionary relationships to one another - bafflingly recent recombinations, bizarrely high proportions of synonymous mutations, long regions with no mutations. I believe SADS is also artificial.

For once, I’m not alone in having suspicions. Hassanin et al made some different observations which led them to similar conclusions.

Once again, Tong Yigang avoided the limelight. SADS wasn’t WIV’s discovery, it was his. It seems odd for a scientist working on a secret military project in Beijing to take an interest in an outbreak of enteric pig disease in Guangdong. Such outbreaks aren’t uncommon, and have a variety of causes - including other coronaviruses. As with SARS-1, AMMS identified it first and passed it to WIV to find the origin. WIV already had all the samples they needed in their freezer. Their run of incredibly good fortune in finding exactly what was needed continued.

The apparent point of SADS was to emphasize that coronaviruses are frequently jumping into (non-bat) mammalian animals, and to set expectations for a future outbreak of a human coronavirus. It also seems to have been a team building exercise/dry run between the bioweapon designers (AMMS), the civilian origin hunters (WIV and SCAU), and the international scientists who would sell the story to the world - Peter Daszak and Linfa Wang.

More from Tong Yigang’s recruitment ad - for qualified applicants

Professor and doctoral supervisor, with a bachelor’s degree in genetics from Fudan University, a doctorate from the Academy of Military Medical Sciences, and postdoctoral research at UBC, Canada. Formerly a researcher in molecular microbiology at the Academy of Military Medical Sciences, and director of the Omics and Bioinformatics Research Laboratory of the State Key Laboratory of Pathogenic Microbiology Biosafety at the Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences. His research focuses on biosafety, microbiology, genomics, high-throughput sequencing, bioinformatics, and bacteriophage science. He has published over 300 papers in Chinese and English in journals such as Nature, PNAS, The Lancet Infectious Diseases, Journal of Virology, and Journal of Biological Chemistry, including over 180 SCI papers, with a total citation count exceeding 2500. He has led more than ten projects, including major military biosafety projects, national key projects in synthetic biology, national major science and technology projects for infectious diseases, national major projects for new drug development, key projects for biosafety technology research and development, national 863 projects, and National Natural Science Foundation of China projects. He serves as the chief expert for both the national major infectious disease project and the national key project in synthetic biology. Chief Scientist of the Chinese Medical Team to Sierra Leone (Third Batch) in the Fight Against Ebola. Chinese Representative at the UN Biological Weapons Convention Conference. Leading domestic researchers in high-throughput microbial sequencing and bacteriology. Published three research papers in Nature (first author and corresponding author) on emerging infectious disease outbreaks, including a paper on the evolution of the Ebola virus, which was selected as one of the top ten scientific advances in China in 2015. In early 2017, when a large-scale outbreak of diarrhea and death in piglets occurred in Guangdong, the research group discovered the virus immediately and traced its origin to a bat host. This article, published in Nature, attracted widespread attention both domestically and internationally. Completed the first whole-genome sequencing of imported Zika virus in China and discovered the first imported Rift Valley fever case in my country through high-throughput sequencing…

…Job responsibilities

Main research areas are as follows:

1. Optimization of the coronavirus GX_P2V virus infection system.

2. Screening, evaluation and mechanism research of antiviral drugs.

3. Research on important viral invasion mechanisms

In previous articles I’ve documented the deceptive nature of WIV’s claims to have discovered bat viruses with human pandemic potential in Yunnan. Initially this seemed to be about laying a false evidentiary trail for a natural origin of SARS-1. But with the “discovery” of RaTG13 they moved on to preparing the cover-up of a future bioweapon.

Throughout their endeavors WIV were shadowed by Tu Changchun, of the AMMS Institute of Military Veterinary Medicine (IMVM). The IMVM is based in the city for which Tu is named: Changchun, capital of Jilin province, in northern China formerly known as Manchuria. Though Tu doesn’t have a high profile, he has a central and recurring role in the SARS origin saga. Wherever there’s a gap in the evolutionary evidence, Tu has an uncanny knack of being in the right place and time to sample/sequence precisely what is needed.

Of the many teams who joined the search for SARS-related coronaviruses other than WIV, only Tu Changchun’s group claimed to have found any with a SARS-like RBM i.e. one that is capable of efficiently binding human ACE2.

Tu’s discovery LyRa11 was published to GenBank around the same time as WIV’s discovery was announced in Nature in 2013. While Tu stayed out of the limelight, Lyra11 provided necessary corroboration of WIV’s discoveries - which have flaws pointing to their artificial origin.

LyRa11 was purportedly found on the other side of Yunnan, near the town of Baoshan. Baoshan was the site of a horrific Japanese biological warfare attack in May 1942. LyRa11 was sampled from a different horseshoe bat species: R. affinis, whereas WIV’s “discoveries” had all been in R. sinicus. At that time R. affinis wasn’t known to host any SARS-related virus, but soon it would become known as the host of RaTG13. The significance of the host species is that R. affinis has a range that extends deep into South-East Asia, while R. sinicus prefers cooler climes in China. Due to host species, and a more southerly site, RaTG13 is within range of Manis javanica, the Malayan pangolin.

Early in the pandemic, the recombination of a Malayan pangolin coronavirus and a RaTG13-like bat virus was, for a time, the preferred explanation of natural evolution of SARS-CoV-2. But the evolutionary puzzle was still missing some pieces.

ZC45 and suppressed sequences

ZC45 was the first member of the SARS-CoV-2 clade to be published, by a group from the PLA’s Nanjing Command Medical Research Center. It was published on March, 28th, 2018, coincidentally (perhaps) the day after a consortium including Ralph Baric, Linfa Wang, Zhengli Shi, Peter Daszak submitted the notorious DEFUSE proposal. In the proposal, Baric stated they wanted to find viruses approximately 20% different to SARS. ZC45 is 19.4% different. What’s more, its PLA discoverers had already shown it could infect suckling mice. It would have made an ideal case study for DEFUSE.

Curiously, WIV also had viruses with spike sequences 99% similar to ZC45. These were purportedly found in Guangdong province, some 1200km away. But WIV kept these hidden from the public, and don’t seem to have disclosed them to their DEFUSE collaborators either. They uploaded them to GenBank in July 2018 but kept them in suppressed mode. They were briefly made visible when a pre-set embargo expired in July 2022, but they immediately asked NCBI to hide them again.

These ZC45-like sequences don’t seem genuine. There are far too few amino acid differences between them for viruses that evolved so far apart, but there are many silent mutations. The abnormal ratio of these types of mutations is a sign of likely fraud. Also their RdRp sequences place them nowhere near ZC45 in the phylogenetic tree. What game were WIV playing?

Unlikely recombination

ZC45 has an interesting relationship with the coronavirus purportedly sampled from sick pangolins captured in Guangdong (MP789). There is very high homology in the spike NTD (green). But in the RBD, ZC45 is more like a genuine SARS-1 related bat virus (e.g. Rp3), while MP789 is suspiciously close to SARS-CoV-2.

The NTD is usually one of the most variable parts of the spike and genome as a whole. It has surface loops that are tolerant of mutation, and it's highly exposed to the immune system at the tip of the spike. Given also that these two viruses were sampled far apart and in different host species, we should expect many more amino acid differences between them.

ZC45 was found in Zhoushan, an archipelago off the port of Ningbo, in Zhejiang province. It was hosted by R. Pusillus - which is known as the least horseshoe bat as it measures just 3-4cm in length and flies only short distances.

MP789 was sampled in Guangdong, from pangolins seized from smugglers and held in a wildlife rescue center. Some scientists suggested the pangolins may have been infected at their origin in South-East Asia, or by the smugglers, or other animals they were smuggled alongside. This may have deviated from the original script prepared by the PLA.

On January 20th, Shi Zhengli submitted a paper proposing an origin based around a ZC45-like virus - while omitting to mention that she had a much closer sequence (RaTG13) or that she had ZC45-like sequences sampled in Guangdong. This was no mistake, but more deception. To what end?

Just two days later pangolin data was uploaded to GenBank, and WIV submitted the pre-print about RaTG13, a virus far closer to SARS-CoV-2 (if it is genuine). Attention was drawn away from ZC45.

“In war, no plan survives first contact with the enemy”.

On 19th January, with indications an epidemic was spreading uncontrolled in Wuhan, HKU virologist Dr Li-Meng Yan appeared on a popular Chinese language livestream to publicize the PLA connection to ZC45, and the official cover-up of transmission between humans. This brought an immediate response. China admitted to human transmissibility the next day. Three days later a harsh lockdown was imposed on Wuhan.

With these events, some started talking about the outbreak becoming “China’s Chernobyl”, a prediction it might lead to the communist regime’s demise, as had happened to the USSR. Connections to the PLA, had to be obfuscated.

WIV’s lab was commandeered by the AMMS. Some believe Shi Zhengli erratic disclosures were made under duress, or that she had defied orders and been punished. Having investigated her past work, I doubt she was so heroic. But with whistleblowers being punished and threatened, it should have been obvious that it wasn’t an environment conducive to open independent science. Data about the origin should never have been trusted.

PLA fingerprints on pangolin data

In 2022, Adrian Jones, Daoyu Zhang et al took a deep dive into pangolin sequencing data. Some of this data had been shared between multiple groups, and its provenance remains unclear. Jones et al looked at all available datasets, used in several different papers, including a more recent one with pangolins sampled after the outbreak.

They found:

• Very little RNA from pangolin coronavirus overall, and only in a handful of samples. There were more reads from non-pangolin viruses.

• Only 9 coronavirus reads in total covering the RBM (the key link to SARS-CoV-2).

• Insufficient read coverage to assemble the complete MP789 genome.

• Contigs with highly structured repeats at each end, suggestive of cloning in a circular plasmid.

• Reads that matched synthetic DNA cloning vectors.

• In the more recent dataset, reads from an unpublished coronavirus closely related to ZC45, which was not identified by the paper’s authors.

Novel virus - or evidence of artifice?

While Jones et al did some excellent analysis, I disagree with their conclusion these reads came from an unpublished coronavirus.

The reads together cover only ~9% of a coronavirus genome, and read depth is very uneven, high over one end of the RdRp, but much lower over the catalytic core (typically the most conserved region, commonly used as a “genetic fingerprint”). There is a large gap with no coverage between nsp4 and the RdRp. Jones et al point out that while an assembled sequence aligns best to ZC45 in the RdRp, it is closer to the Guanxi (GX) pangolin coronavirus in the nsp4 region. N.B. GX is a different pangolin virus to the GD virus discussed above. There is low homology between them in some regions (e.g. S1).

There is far too much genetic diversity between the individual reads for them to have come from a single virus. Some reads in the RdRp have 100% identity to ZC45, but many are ~95% identical, and some are as low as 75%. Blasting those with lower identity shows them to be closer to other coronaviruses e.g. HKU3, Anlong-89, SARS-1, than they are to ZC45.

Of the reads in nsp4 the highest is ~98% identical to the GX pangolin coronavirus, but only ~85% identical to ZC45. Again, there is too much genetic diversity for them to have come from a single virus.

My interpretation is that this is evidence of genetic engineering - a directed evolution experiment intended to generate random chimeric sequences. This was likely done with techniques such as DNA shuffling and error prone PCR as described in a previous article. The nsp4 reads are likely from a similar but separate experiment. The purpose of these experiments could be to support fraudulent studies on coronavirus evolution, distribution, host switching - in which often only the RdRp is used. Alternatively, they may have been intended to become part of novel viral genomes, assembled from individually optimized genes.

Whose fingerprints are on the data?

Jones et al highlighted several other contaminating viruses that might offer clues to the provenance of the datasets. Among others, they identified African Swine Fever Virus and Porcine circovirus type 2.

Porcine viruses like African Swine Fever are commonly studied by agricultural universities in China, but also by the IMVM, particularly in 2018-19.

I found the Porcine circovirus 2 reads noted by Jones et al, to be from an unpublished species which is less than 80% identical to any species in GenBank. Finding novel circovirus genotypes was a focus for IMVM during 2017-19, with Tu Changchun’s involvement.

In a subsequent paper, Jones et al found a novel MERS-related virus in reads from a different dataset published by a similar group of authors. The authors claimed the dataset was derived from pangolin samples, but Jones et al determined it was from wild boar. Tu Changchun and IMVM also surveyed wild boar in 2017-19.

Some of the sequencing data was uploaded by Nanjing Agricultural University (NJAU). According to documents obtained by Colonel Lawrence Sellin, NJAU virologist Shuo Su has been funded by the IMVM. The director of IMVM, General Xia Xianzhu, is an alumnus of NJAU. It seems likely that the pangolin samples and/or read data were provided to the group via Tu Changchun. Tong Yi-Gang of AMMS Beijing Institute of Microbiology and Epidemiology (BIME) claims to have isolated and sequenced the GX pangolin virus in 2017, his group may be the original source.

The pangolin trail leads back to Zhejiang

Interestingly, the Manis Javanica pangolin samples analyzed in this paper were all said to have been found in Jinhua, Zhejiang province (~200km from Zhoushan) in the wild. Although there is a Chinese pangolin species (Manis pentadactyla) which is native to the region, it is far from the range of Malayan pangolins. How did they get there?

In June 2019, an article appeared in an international conservation magazine about the practice of releasing seized smuggled Malayan pangolins into the wild. Some local authorities were apparently unable to distinguish between the species.

This in turn cites a Chinese article from October 2018, which discusses specific cases of this occurring. One such incident apparently occurred in Zhejiang, but similar incidents were also reported in Yunnan and Guangdong.

The article also mentions the smuggled pangolins from which Tong Yi-gang’s group claimed to have isolated the GX pangolin coronavirus.

The “Game Animals” paper used data from both Malayan and Chinese pangolin (M. pentadactyla) samples - all collected in Zhejiang.

The paper infers that the two species can pass pathogens between each other. This seems unlikely to happen in the wild as they are both solitary species. Chinese pangolins are rare, and released Malayan pangolin rarer still.

The group also published a new ZC45-like bat coronavirus from Guangdong (GD/L102.18). It has 108 synonymous mutations, but only 2 amino acid differences in the spike compared to one of WIV’s secret Guangdong sequences. This is the most extreme ratio of synonymous to non-synonymous mutations I’ve coming across, having compared thousands of pairs of viruses. I can confidently say these sequences aren’t genuine. But WIV’s sequences are needed to compare it to. These were still hidden at the time, it might have been assumed they would stay hidden.

PLA pangolin wrangler Tu Changchun

Before and during World War 2 the broader region formerly known as Manchuria, was occupied by Japanese colonial forces known as the Kwantung Army. It was the locale for the bioweapon experimentation and other atrocities committed by the infamous Unit 731 based in Harbin. Unit 731 wasn’t the only such unit. The city of Changchun housed Kwantung Army Unit 100, also known as the Warhorse Disease Prevention Unit. This unit produced offensive bioweapons targeting horses and livestock, some of which (e.g. glanders) could also infect humans. Experiments on human subjects (usually Chinese prisoners) were common. Post-war Changchun under the CCP retained an institution with similar focus (although China would claim for defensive purposes only) the Military Horse Health Research Institute, which later became the IMVM of the AMMS.

Tu Changchun is a protege of General Xia Xianzhu, who joined the Military Horse Health Research Institute after graduating from Nanjing Agricultural University, later becoming director of IMVM. Xia emphasizes building “Military-Civilian Fusion” links with civilian institutions, such as Harbin Veterinary Research Institute. Many of these also have a focus on zoonotic pathogens with biowarfare potential. This is partly a legacy of the Japanese colonial period. For years after World War 2 there were sporadic epidemics of diseases like plague linked to wartime Japanese bioweapon releases which persisted in environmental and animal reservoirs.

During the Korean War, the CCP claimed the US was deploying biological weapons near its border. This is unproven and likely just propaganda, but US failure to prosecute Japanese biowarfare criminals, and USAMRIID’s appropriation of Unit 731’s research data fueled suspicion and resentment. At the time the US and other western powers still had offensive biowarfare programs.

Tu Changchun’s contributions to the origin saga include:

• In May 2003, he was involved in sampling civets to ascertain a connection to SARS. The paper was a collaboration with CSIRO’s Gary Crameri.

• In 2004 he conducted animal experiments infecting civets with different strains of human SARS.

• In 2009 he worked closely with Trevor Drew (then of the UK’s Animal and Plant Health Agency) to develop a reference lab for rabies in Changchun. In September 2018, Drew became head of CSIRO’s AAHL lab.

  

  

• In August 2013, as WIV and CSIRO were publishing the first viruses with SARS-like RBM, Tu Changchun’s IMVM group published Lyra11, as evidence to support the existence of a SARS-like RBM in bats.

• In 2016, Tu’s group claimed to have found a SARS-like virus with a distinctive 579-nucleotide deletion seen only twice before. Once in a late-stage human SARS patient, and once by WIV.

• In April 2020, journalist Sharri Markson wrote a piece exposing the relationship between Trevor Drew and Tu Changchun. The piece lacked any incriminating substance. Drew in media interviews didn’t disclose CSIRO’s work with WIV and AMMS on SARS origin.

• Later in 2020, Tu collaborated on a paper with Linfa Wang, CSIRO’s Gary Crameri, which claims to have sequenced a SARS-CoV-2 related coronavirus from Thai bats. They also claim a pangolin tested positive for SARS-CoV-2. They refer to “historical data” which shows a pangolin tested positive for SARS in May, 2003 but provide no reference for this.

Shame and striving

In an interesting coincidence the release of the smuggled Malayan pangolin in Zhejiang province happened near the city of Jinhua. This region was the site of Unit 731 bioweapon attacks, Chongshan Village, a few km from where the pangolin was released now hosts a memorial and center of research into Japanese biowarfare atrocities.

The port of Ningbo, off which the islands of Zhoushan sit, was the site of another notorious attack in which a Japanese plane dropped plague infected fleas, killing over 1500 people from disease and forcing the destruction of houses. Today the site is marked with a monument bearing a plaque which reads: “Never forget our national humiliation, strive to strengthen the nation”.

The PLA Eastern Theater Command (formerly Nanjing Command) today occupies the former site of Japanese Unit 1644 in Nanjing. Unit 1644 was responsible for deploying the bioweapons developed by Unit 731 in Zhejiang.

Symbolism is particularly important to the PLA and the CCP. The CCP’s domestic propaganda still emphasizes historical “humiliation” dealt to China, by Japan and western powers. But the age of imperialism is over. In the present zeitgeist, it’s the CCP’s bioterrorist aggression that will bring the shame.

Increasingly I use AI to research topics related to the genetic engineering of viruses. As I’ve delved deeper into it, I started to see this message more frequently:

“I’m sorry, I cannot assist with that request as it involves restricted subject matter.”

The information I’m seeking isn’t restricted or secret. It’s in the public domain, many papers I reference are 25-30 years old. These techniques have applications which can greatly benefit human health. But, as with any technology, it can also be turned to nefarious purpose.

I doubt these techniques are accessible to amateurs. I think the risk of a competent, well-equipped, but reckless scientist causing such a catastrophe is also overstated. SARS-CoV-2 isn’t simply a bat virus with an FCS insert, as many have been led to believe (thanks to fraudulent sequence data). It was the work of a sophisticated state actor, with access to unpublished viral genomes, biosecurity labs, animal testing/passage and genetic engineering expertise - and crucially they needed to have the intent to design a bioweapon.

The debate over the origin of SARS-CoV-2 has so far barely touched on the possibility it may have been engineered for nefarious purposes. The public has been kept in the dark about what is possible for humans to engineer. The threat posed by nature has been vastly exaggerated. It’s possible for humans to engineer more potent pathogens than nature, because we can do so without the challenges natural evolution presents: the trade-offs needed to evade host immune systems, the time needed to mutate and adapt. Genetic engineers have learned to mimic evolution, but in a fraction of the time and with a specific goal in mind - directed evolution. We can’t detect, let alone stop people engineering novel bioweapons. So we must learn to attribute - to discern between artificial and natural pathogens.

SARS-CoV-2 emerged in a time when most scientists agree that genetic engineering techniques and understanding of coronaviruses were sufficiently advanced for humans to have engineered it. Mechanisms of coronavirus infection such as receptor binding and cleavage by proteases had been well studied, reverse genetic systems (RGS) were established and in routine use. But what was possible in 2002 when SARS-1 emerged? And what evidence of engineering can we find in the genome?

Switch the spike to switch the host

A seminal advance in coronavirology was a paper published in early 2000, in which researchers substituted the spike of mouse coronavirus MHV, for that of feline coronavirus FIPV. They found the new chimeric virus could infect cat calls, but not mice.

Kuo et al. used a technique called targeted recombination. Cells are first infected with mouse hepatitis virus (MHV), then transfected with a synthetic mRNA carrying the region to be swapped - in this case, the spike protein from FIPV. For recombination to happen, the mRNA also needs matching MHV sequences at both ends. Only a small fraction (<~1%) of the resulting virus particles end up with the FIPV spike. These recombinants can then be isolated by growing them in feline cells, which those retaining the MHV spike are unable to infect.

More complex reverse genetic systems (RGS) - such as Ralph Baric’s “no see-em”, divide the genome into smaller fragments so that they are easier to grow in bacterial plasmids. These were also developed and published in the early 2000s. But the long-established targeted recombination technique of Kuo et al was likely sufficient for engineering SARS-1.

Recombinant structure of SARS

SARS genome appears to be a recombinant based around a Chinese lineage “backbone”. Chinese bat viruses have been discovered with a genome that is 90-95% identical to SARS. But the S1 domain of spike is quite divergent, identity drops to ~70%. The RBM of the Chinese lineage has large deletions such that these viruses are unable to bind ACE2 - even bat ACE2.

On a SNAP diagram comparing SARS to its overall closest known sequence Anlong-112, it seems likely from the change in rate of total mutations (the slope of the purple line) that there is a recombination breakpoint near the start of spike, and another a little way into ORF3. The rest of the sequence is very similar (particularly in amino acids), suggesting that only the spike differs from a natural virus, and the technique of Kuo et al is applicable. To separate recombinant SARS from natural bat coronavirus, a cell culture that expresses ACE2 (e.g. Vero E6) may have been used.

Shuffling the spike

Curiously, the RBM of SARS’ spike is far more closely related to the Afro-European lineage of sarbecovs, than to the Chinese lineage. In a previous article I showed how SARS’ sequence before the RBD mostly agrees with the Chinese lineage (highlighted in cyan), then switches to following the Afro-European lineage (pink), then back again.

But that was a simplification, to explain how it may have appeared to researchers like Baric and WIV, that SARS was a recombinant with breakpoints around the RBM (or RBD).

In fact both, upstream and downstream of the RBD, there is more switching back and forth between the two lineages as illustrated in the next alignment of the NTD. It seems as if there’s not been just one recombination, but several. Note in the NTD particularly there are also many residues shared with neither lineage (orange).

How might this have happened? A natural explanation of multiple recombinations seems unlikely, given there is at least 7000km between the locations which these lineages have been sampled to date. My speculation is that the spike has been engineered using a technique called DNA shuffling, also known as molecular breeding.

DNA shuffling is a form of directed evolution, a type of technique in which multiple variants of a sequence are generated and then selected for desired attributes. DNA shuffling was first described in 1994. It works by first creating random fragments of two or more DNA regions or entire genes. These must be somewhat homologous so that they can join to each other where the ends are conserved. They are then annealed resulting in a multitude of “mix and match” chimeric variants.

They can then be selected for desired traits (such as ability to infect human cells), and the process can then be repeated iteratively if desired. The power of the technique is that a vast library of hybrid candidates can be created and tested simultaneously.

By August 2000, this technique had been extended so that it could be applied to breeding RNA viruses, and specifically their attachment genes (e.g. spike). The selection criteria in this example is resistance to centrifugation, but this could easily be replaced by a selection filter of more relevance to a bioweapon designer (e.g. infection of human cells).

Could MERS also be artificial?

In 2005, while hunting for SARS-like coronaviruses, scientists from HKU discovered two bat coronaviruses from a different family: HKU4 and HKU5. Viruses of this clade (now known as merbecovs) have turned out to be widespread, they’ve since been found in many parts of Europe, Africa, Asia and recently the Americas.

The merbecov that most resembles the backbone of MERS was discovered in South Africa and sequenced in 2011 by a team led by Christian Drosten. They named it NeoCoV (after the presumed bat host Neoromicia capensis).

But the all-important S1 domain of MERS spike is quite divergent from NeoCov, being only 45% similar in amino acid sequence. Interestingly, the Chinese viruses HKU4 and HKU5 are more similar in S1 than NeoCov, each have around 60% amino acids the same as MERS. But that is still too distant to be regarded as a pre-cursor.

Or is it?

On an alignment of the spike it can be seen that MERS actually has much in common with both. It appears to agree with HKU4 (blue) in some regions and HKU5 (pink) in others. Occasionally it agrees with the more divergent NeoCoV (green), and sometimes it agrees with none of these (orange).

As with SARS, this seems consistent with DNA shuffling. MERS seems to alternate between the component sequences more frequently than SARS, suggesting perhaps more than one round of shuffling.

In the S2 of spike there are many point mutations that agree only with NeoCoV, indicating a breakpoint near the start of S2 and the possibility that the genome is mostly natural thereafter.

A SNAP chart confirms the recombination breakpoints are likely located near the start of spike, and near the S1|S2 junction.

The RBD also seems to alternate between HKU4, HKU5 and shared homology:

Some minor contributions appear to have come from NeoCoV.

The S1|S2 junction also seems to be a bit-of a mash-up. It isn’t clear where the interesting leading Proline has come from, and there are several other residues of unexplained origin. HKU5, NeoCoV and MERS have furin cleavage motifs, HKU5 does not.

Point mutations

While the S1 of both SARS and MERS alternate between related but divergent lineages, they also contain several point mutations unique to themselves. Another directed evolution technique often used in conjunction with DNA shuffling and developed in the early 1990’s is error prone PCR (epPCR). All PCR introduces some errors, but polymerases have usually been designed to try keep the error rate very low. Genetic engineers using directed evolution wanted to introduce random mutations deliberately so that they were able to test many possibilities at once. This can be done simply by using a low-fidelity polymerase which has a higher error rate. The error rate might be up to 3% per PCR cycle vs <0.01% for a high-fidelity polymerase.

This technique can be used conjunction with DNA shuffling without adding to the workload, as PCR is already a part of the process. It’s a simple matter of choosing a low-fidelity polymerase.

Random peptide insertion

As well as single point mutations, there are several short sequences of 5-9 consecutive amino acids in the spike of MERS, SARS and SARS-CoV-2 that aren’t conserved in their related bat viruses. These are mostly located in flexible surface exposed loops (particularly in the NTD). These NTD loops gained notoriety early in the pandemic, when Indian researchers from IIT claimed they had identified peptides from HIV. I disagree on the HIV source, but agree that these inserts appear very suspicious.

SARS-1 also has peptides at these sites which resemble none of its bat relatives, or SARS-CoV-2 either. Even without resolving the 3D structure, it’s clear these regions are tolerant of variation. As they’re poorly conserved, they don’t play an essential role in viral replication - but might be useful to enhance transmissibility or pathogenicity. In several coronaviruses the NTD is a secondary binding domain, using sugar (sialic acid/heparan) as a receptor.

The first time I blasted this particular peptide GFHTINHT, one of the top results was a human adenovirus. A paper from 2001 described a particularly virulent form of adenovirus that caused an epidemic of keratoconjunctivitis, where the cornea can also be infected.

The peptide isn’t described, but is at an interesting location in the protein associated with virulence, at the very start of the NTD (after the signal peptide is cleaved).

Curiously, when I blasted the peptide again a year later, I found other sequences were now ahead of it in the results - including one from a WIV/Institut Pasteur collaboration. I suspect they may have been trying to bury the adenovirus result by making the peptide appear common.

Random peptide insertion is another commonly used directed evolution technique. Appropriate sites are identified - usually surface exposed loops which can be safely modified without making the structure unviable. A library of peptides is prepared by adding flanking sequences to match the sites. Random permutations of peptides and sites are created and tested for fitness.

Inserting a peptide at random, might carry low expectations of success, but if it is inserted at an appropriate site there’s little risk of creating a non-viable protein. With a conventional RGS workflow, having to painstakingly reassemble the genome after each speculative insert might not be worth the effort. The power of directed evolution is in allowing all permutations of sites and peptides to be tried and tested simultaneously, those that enhance fitness can be selected without it being necessary to fully understand why.

Serendipitous SARS becomes human infectious

One small but important difference between SARS and most related bat viruses is that it has 3-5 residues inserted at the start of its RBM sequence, which are absent in both the Chinese and Afro-European bat covs. While the bat viruses have 2-3 Tyrosine (Y) residues, SARS has 4, and they are interleaved with other residues, rather than adjacent to each other. The extra residues extend the ACE2 binding interface so that it has more contacts with the receptor, forming a much stronger bond. Tyrosine is versatile in the types of bonds it can form.

Interestingly the sequence YNYK that comprises the apparent insert is repeated a short distance upstream. The sequence is low complexity, comprised entirely of A/T bases and incorporates repeats which are also palindromic (read the same on both strands of DNA). There are 15 identical nucleotides between the 2 sites, making unlikely to be a random co-incidence.

In many of the bat viruses the downstream site is also low complexity, A/T rich, and the sequence partially matches the upstream site (ATTATA).

This suggests the possibility the duplication arose by an error which resulted in a fragment from downstream to be ligated into the wrong site in some variants created by a directed evolution method. Such mutants would have a strong advantage if selected by infecting cells expressing ACE2. It’s possible this serendipitous “error” is how SARS came to be human infectious.

Growing backbones in the brain

Where did the source viruses to engineer SARS come from?

Bats have been of interest to virologists long before SARS. Ebola, Nipah and Hendra like viruses are hosted by fruit bats, rabies and other lyssaviruses by fruit bats and vampire bats. But SARS was the first known human disease known to be hosted by tiny insectivorous horseshoe bats. There’s no record of people sampling them for viruses before SARS - they had a virgin virome, ideal source material for a bioweapon engineer.

With the publication of ZC45/ZXC21 in 2018, the PLA gave us an inkling of how they may have obtained live virus. Tissue of an infected bat was ground up and injected directly into the brain of immune deficient suckling mice - a technique called intracerebral inoculation. At this stage the bat virus can’t bind ACE2, won’t infect VERO E6, or even bat cell cultures.

Intracerebral inoculation bypasses the blood-brain barrier which keeps most pathogens from the central nervous system (CNS). The immune response within the CNS is less robust, so that once infected, that infection may persist giving the virus time to adapt to the new host. This technique is very old, being used as far back as the 1930s to infect mice with yellow fever.

With the ability to culture a virus, microscopy can be used to determine the class of virus, allowing RNA to be amplified, isolated, sequenced. AMMS demonstrated their prowess to a visiting WHO virologist Klaus Stöhr in the aftermath of SARS. They admitted they had cultured and isolated SARS coronavirus from patient samples weeks before international groups succeeded, but - they kept it secret.

Did they perhaps have a head start?

On a sequence alignment of representatives of these two lineages, SARS spike sequence seems to alternate between agreeing with the Asian clade (blue), then the Afro-European clade (pink) in the RBD then returns to following to the Asian clade (blue). There are also several residues unique to SARS (orange).

This is somewhat simplified…a more detailed discussion in a future article.

Once BM48-31 was published, it would have been possible to interpret that a recombination with another bat virus happened with breakpoints located somewhere on either side of the RBD. This RBD region has far closer resemblance to BM48-31 than the Chinese clade. Crucially, members of the Afro-European lineage have since been shown to bind ACE2 (though not as well as SARS), while the Chinese lineage cannot. This is because the Chinese lineage has many deletions, it’s RBM is shorter. The Afro-European lineage has fewer deletions, but SARS is still longer by 3-5 amino acids.

The intuition that the RBD had been acquired by recombination led WIV to experiment with chimeric spike proteins. They inserted regions of the RBD of SARS into Rp3, using various breakpoints, to determine the minimal region required to make Rp3 infectious to human cells. Ralph Baric and Marc Denison independently experimented. They went a step further than WIV, making a live clone. More about this in previous article below.

Drosten’s discovery re-ignited interest in hunting for novel bat CoVs in China. Before that the source of the RBD had remained a mystery, some had even suggested the source might be a bird or rat virus. There was still no explanation of how the RBD most similar to a bat virus from Bulgaria (some 8000km away) may have ended up in a Chinese backbone. It suggested there must be some missing link bat virus somewhere in China.

Starting in 2010, teams that included China’s central and provincial CDCs and the Institute of Pathogen Biology in Beijing (CAMS) collected thousands of bat samples across China.

Also in 2010 (according to former EcoHealth executive Andrew Huff) Peter Daszak was approached by the CIA, who wanted to “keep an eye on things” in China. EcoHealth received funding under the PREDICT program to sample bats within China. But they didn’t work independently, much of the work was performed by WIV. Over the next 5 years the collaboration sampled over 13,000 bats. In late 2019, they published 600 novel bat coronavirus species, of which 90 are SARS related. The resulting paper (published March 2020) is referred to as Latinne et al.

It can be difficult to sequence a full genome, and at the time it was unrealistic to generate a full sequence for every virus. Usually as a first pass, a short “fingerprint” is sequenced - a partial RdRp. This can be used to identify close relatives and ancestors and position the virus in a phylogenetic tree. When evolution is as normal, this is useful for identifying samples of interest for follow-up sequencing. But evolution in sarbecovs is far from normal - if WIV’s claims are to be believed. Frequent recombination might mean separate regions like RdRp and spike are related differently, they may come from different sources.

That implies two viruses closely related by RdRp, might have different ACE2 binding capability, so the spike gene should be sequenced to properly determine this. The vast majority of sequences in Latinne et al have not had their spike sequenced. Unfortunately, the thousands of samples collected remain stored at WIV, so there’s no possibility of independently confirming the existence of any ACE2 binding spikes. But it is clear from RdRp alone that none of these viruses belong to the SARS-CoV-2 clade.

Discovery of the Magical Cave of Recombination

From a table of the many bat coronavirus surveys, it’s clear that some groups had better luck than others. Altogether over 26,000 bats were sampled across China and South-Asia. Eleven viruses with a SARS-like RBD were sequenced. All but one of these were discovered by WIV at a single site, Shitou cave near Yunnan’s capital, Kunming. The other was found by an AMMS Institute of Military Veterinary Science group led by Tu Changchun, who had been previously involved in WIV/CSIRO’s investigations into civets.

Some scientists have suggested to me that the reason no-one else managed to sequence a virus SARS-like RBD (or even a close relative) is because some viruses can be very localized, evolving in a geographically isolated bat colony. But Tu Changchun’s discovery was made 500km away, on the other side of Yunnan, in a different bat species, so they ought to be more widespread. WIV and AMMS weren’t the only groups to sample in Yunnan either - as the table above indicates.

And if the colony was truly isolated - how did RsSHC014 evolve this homology to a virus from Bulgaria - 8000k away?

Absence of evidence isn’t necessarily evidence of absence. We can’t be 100% certain similar viruses don’t exist, no matter how much sampling is done. But this violates a tenet of the scientific method - falsifiability. WIV’s claims aren’t falsifiable, so they need further corroboration. There are a handful of Latinne et al sequences that are closely related by RdRp - but that we don’t have spike sequences for. These might have been used to confirm WIV’s results, even if impossible to refute them.

But we can surely say that outside of this cave, such viruses must be very rare. How did WIV stumble upon this “rich gene pool”, what led them to Yunnan in the first place?

In 2010, a WIV/HKU collaboration announced they had discovered 2 new viruses (Rs672 and Rs806) from samples WIV collected in 2006. This paper is unusual in several ways. Firstly, they only had samples from 24 bats, yet managed to extract two complete sarbecov genomes. Other groups needed hundreds of samples for each genome sequenced. This is partly because bats infected with a similar virus are relatively rare, and because RNA breaks down rapidly in feces, often only small parts of a genome can be obtained from a single sample. But once again, WIV got lucky.

Rs672 has a 579-nucleotide deletion in sp3 - a distinguishing feature it shared only with a human patient from the late phase of SARS. The late phase occurred several months after SARS had been thought eliminated, and consisted of just four cases. Crucially, the same strain was sampled from civets at the same time. This was the key evidence in favor of civet to human spillover and led to the mass slaughter of farmed civets. Rs672 now seemed to offer a further clue linking bats to SARS. Among all viruses subsequently sequenced, this 579-nt deletion has only been found once more (coincidentally by Tu Changchun’s AMMS group).

WIV’s earliest discovery, Rp3, at the time closest to SARS “backbone” had been sampled from bat species R. pearsoni. But they had already shown R. pearsoni ACE2 was incapable of binding SARS RBD. If two viruses can’t co-infect the same host cell, recombination is impossible. So WIV announced they had previously misidentified Rp3’s host - it had actually come from R. sinicus, they now claimed. Shortly after this they announced they had discovered that R. sinicus ACE2 could bind SARS. Problem solved.

Rs672 was sampled in Guizhou province, further west from Rp3 and other discoveries. A map indicates that the same clade of R. sinicus bats inhabits Guizhou and Yunnan. This points to where they will go next, though there was no evidence of SARS-related CoVs in Yunnan at the time. WIV commenced a 12-month survey in Shitou cave apparently on a hunch. And again luck was with them, they found the viral mother lode. the cave, they claimed, contains all the genetic “building blocks” of SARS, which are frequently recombining into new mix-and-match viruses, some potentially human infectious.

Mojiang mojo

In April 2012 (according to a master’s student thesis) Kunming Hospital treated 6 artisanal miners who were apparently clearing guano from an abandoned mine-shaft when they became ill with a respiratory disease. Three eventually died. WIV were reportedly sent some of their clinical samples and at one time claimed they were positive for SARS antibodies. In an early 2020 interview, Zhengli Shi denied this, claiming they had caught a fungal disease, not a SARS-like virus.

Reports of the incident sent at least 3 teams of scientists scurrying to the mine to sample. Once again WIV succeeded where groups from China CDC and the Institute of Pathogen Biology found little of interest, despite repeat visits. WIV traveled to Mojiang three times in 2012-13, and sampled 276 bats. They only reported one SARS-like virus, but it is of special importance. It would become the first member of the SARS-CoV-2 clade: RaTG13. Despite their interest in the cave, WIV claimed to have not fully sequenced RaTG13 until 2018, and it wasn’t made public until late January 2020.

Some lab-leakers have proposed that perhaps WIV found other viruses in the mine that were even closer to SARS-CoV-2. Another intriguing hypothesis is that the miners themselves became incubators for the virus that eventually became SARS-CoV-2 (possibly with some extra engineering). Prolonged infection and suppressed immune response may have given the virus time to become better adapted to the human respiratory tract.

But I suspect the incident may never even have happened. The master’s thesis is the only primary source. Its submission date is given as June, 2013, but though it contains all the known clinical detail, it isn’t cited by others. Were the claims made verbally by WIV? Basic details are stated inconsistently by secondary sources. The date of the incident is variously documented as 2011, April 2012, June 2012, and November 2012, even the number of deaths is uncertain, some sources said only 2 had died, others said 3. Importantly, the type of clinical tests WIV claimed to perform, and the results obtained are inconsistent. WIV didn’t mention the incident at all in their 2016 paper describing their sampling at the mine. More recently WIV seemed to deny the miners tests were ever SARS-positive, offering no explanation for why it attracted the interest of multiple groups.

The thesis also claims that famous Guangdong doctor Zhong Nanshan, who was closely involved in all aspects of SARS: treatment, epidemiology, origin - was asked to advise on the miners’ case. Interestingly, in October 2012, Zhong had a paper accepted for publication by PLoS One, but a month later the acceptance was rescinded. The group posted their pre-print to ArXiv with a bizarre statement hinting that someone had intervened to have publication canceled.

Zhong’s pre-print proposes that SARS originated as a spillover in Guangdong, as early as 1998. It spilled directly from bats to humans, and evolved into two strains - one virulent (SARS), and one mild. Humans later infected civets with the mild strain. The authors also believed the mild strain is still circulating in Guangdong, 20% of samples of children they tested were seropositive. This is a very different origin narrative to the one WIV were proposing. Zhong’s paper doesn’t mention Yunnan at all. If Zhong had heard of the miners’ incident, he hadn’t thought it significant.

So RaTG13 - the only true SARS-CoV-2r from 26,000 bats sampled before the pandemic - was found because miners caught a fungal disease, which co-incidentally had similar symptoms to SARS? Serendipity strikes again for WIV. Zhengli Shi later said that while the miners’ disease was fungal, if the mine had stayed open any longer they would have caught a coronavirus. So there’s that.

In late 2020, WIV revealed 8 more viruses from the same mineshaft. Based on RdRp these aren’t closely related to SARS-CoV-2, but closer than the SARS-1 clade. They’re meant to be an evolutionary intermediate. WIV claim they sequenced these only after linking RaTG13 to SARS-CoV-2 in 2020.

This is false, and not an innocent mistake. The thesis of WIV student Yu Ping completed a year earlier (obtained by Drastic) utilized the full 2757-nt RdRp sequence. What’s more the full spike, RdRp and ORF8 sequences of these viruses had been uploaded to GenBank in July 2018 - but they remained “suppressed”, hidden from public sight. They were briefly exposed to public view when an automatic embargo they had set expired, and quickly returned to “suppressed” mode at WIV’s request.

As with RaTG13, Yu Ping, and supervisor Jie Cui were again left off the author list when the paper was published in August 2021. Cui had by then transferred to Institut Pasteur Shanghai. Although sampled in 2015, these sequences weren’t provided to EcoHealth/PREDICT. Clearly some sequences WIV decided to keep to themselves. Do they even represent real viruses, or were they fabricated to support a phony natural origin?

My view is that there are no bat coronaviruses with human pandemic potential in nature. The myth of the Mojiang miners was confected to suggest that spillovers from bats to humans had already occurred from a virus similar to - but not - RaTG13. A persistent infection starting in the lungs might plausibly result in a bat virus gaining human respiratory tropism. This backfired when WIV and RaTG13 became the focus of lab-origin allegations.

Though unlikely, a virus similar to RaTG13 might hypothetically be transformed into SARS-CoV-2 by recombining with a coronavirus purportedly found in Manis javanica - the Malayan pangolin. M. javanica doesn’t inhabit Yunnan, so this detail was likely intended to point to an origin outside China’s borders. The choice of bat host also seems intentional. R. affinis’ range extends deep into South-East Asia unlike R. sinicus, which is largely confined to China. Before RaTG13, WIV had made no discoveries in R. affinis. There was only Tu Changchun’s LyRa11.

This left the question of how did a SARS-like RBD travel from Europe to Yunnan, given that neither R. sinicus, or R. affinis are found anywhere close to Europe or Africa. Once again Tu Changchun came to the rescue. In 2016 he claimed to have sampled JTMC15 (the 3rd virus with the 579nt deletion) in R. ferrumequinum. A larger bat, its range extends from Japan to the UK.

The provenance of pangolin coronaviruses is also murky. The AMMS are intimately involved in their discovery (or invention), claiming to have first isolated one in 2017. They were unknown by others until they appeared in a low-key paper in September 2019. But even then, their sequence data was unpublished until WIV simultaneously released the RaTG13 sequence around 22nd January, 2020. Later in 2020, EcoHealth analyzed samples from 334 pangolins collected between 2009 and 2019, and detected no coronaviruses. Another example of the different fortunes of virus hunters.

In 2015 Vineet Menachery and Ralph Baric made a synthetic virus using the spike gene of RsSHC014, which WIV claimed to have sampled from a bat in a Yunnan cave in 2012. My previous work suggests WIV’s claim is fraudulent and RsSHC014 is not a natural virus. Unfortunately, Menachery et al didn’t consider this possibility. But they did demonstrate that it was capable of infecting human airway cells and causing pathogenesis in mice.

This was an interesting finding because RsSHC014’s RBM is quite different from SARS’, with only ~50% amino acids the same. There are 30 amino acid differences, including 7 of the 14 residues that make contact with the ACE2 receptor. This shows that the RBM is able to accumulate many mutations, and still bind human ACE2 efficiently.

If my claim is correct that RsSHC014 is artificial how might its RBM have been designed?

In 2008 a team led by Christian Drosten discovered a bat virus, BM48-31, which had (at the time) the closest RBD to SARS. This is surprising because BM48-31 was sampled from bats in Bulgaria, 8000km from Guangdong where the SARS outbreak started.

Interestingly, RsSHC014 shares several residues with BM48-31, that weren’t in SARS or any other known bat CoVs. How were they conserved between different bat species, viral lineages, 8000km apart and perhaps thousands of years evolved from a common ancestor?

I postulate RsSHC014 has a chimeric RBM: residues from BM48-31 were selectively introduced to create an RBM somewhat divergent from SARS, but still able to bind hACE2.

So, what about SARS-CoV-2?

A chimeric design for SARS-CoV-2’s RBM

Chimeric RBMs were of interest to scientists researching broad spectrum coronavirus vaccines, like this team featuring AMMS officers Wanbo Tai and the mysteriously deceased Yusen Zhou. They took mutations from various MERS strains, including camel variants and combined them into more divergent RBDs. Antibodies against wild-type MERS worked well, but these new RBDs have only a handful of mutations from that strain.

In contrast, Menachery et al found that antibodies to SARS don’t neutralize RsSHC014 effectively, there are too many differences between them. One solution is to use a chimeric RBM that combines short, surface-exposed amino acid sequences (epitopes) from both. It could also include other divergent SARS-related viruses deemed spillover risks. A vaccine based on this chimeric RBM could hopefully guard against the emergence of even unknown SARS-like viruses, as Baric describes:

Approximately 50% of amino acids are conserved between the RBM of SARS-1 and SARS-CoV-2. Could SARS-CoV-2 RBM also be chimeric? What viruses, other than SARS, might be used to construct it?

RsSHC014 was already known to bind hACE2 so it would be an obvious candidate. As it happens, RsSHC014 shares several residues with SARS-CoV-2 that aren’t in SARS-1.

Another virus that was known and is divergent from these is PDF-2386. This was discovered by the PREDICT consortium in Uganda and is similar to other African viruses (e.g. BtKY72). PDF-2386 and RsSHC014 were the subject of proposed experiments by Ralph Baric and Fang Li in 2017-18, which were stalled due to the Gain of Function moratorium in place at the time. It isn’t clear if they ever went ahead.

Had this experiment gone ahead as described, it wouldn’t have resulted in SARS-CoV-2. Only one of the 12 mutations specified is present in SARS-CoV-2, and that is also found in other human SARS strains.

Nonetheless, PDF-2386 has other RBM residues shared with SARS-CoV-2 that aren’t in SARS or RsSHC014.

SARS-CoV-2 also many have inherited some residues from Chinese lineage SL-CoVs, of which HKU3 is representative.

A larger alignment using only SARS-1 related sequences shows that all but 5 residues have a match somewhere. Conversely, viruses from all regions and lineages have epitopes represented in the SARS-CoV-2 RBM.

This is not a sequence nature would have evolved by mutating residues one at a time - but it is one that humans would have devised!

However not all the sequences in this alignment were published before the SARS-CoV-2 outbreak. The region in the cyan box shows particularly close homology between SARS-CoV-2 and bat viruses from the UK (e.g. RhGB02). But no UK viruses were sampled or published before the outbreak. At least, none were known to have been discovered. This suggests viruses might have been sampled but not disclosed. Based on other documentary evidence this is almost certainly the case in South-East Asia and China, but perhaps also further afield.

An alien peptide?

One region (in the red box above) stands out as having especially low homology with most sequences (with RsSHC014 being an exception).

Compared to SARS-1, SARS-CoV-2 has 9 consecutive amino acid differences. Nucleotide conservation is also poor. If this evolved naturally it must have been by a process other than regular substitution. The changes have an important effect on structure and function.

The SARS-1 sequence has a remarkable 5 Proline residues in a region of 12. Proline adds structural rigidity that can reduce binding affinity. In SARS-CoV-2, only one Proline is conserved, while two Glycines are gained (Glycine is small and flexible). This creates a much more flexible structure in this loop, allowing closer contacts, stronger bonds to form with the ACE2 receptor.

Curiously, when I blasted this peptide I got an unlikely match to a peptide from a bat adenovirus - WIV17/WIV18.

Ordinarily this might seem spurious- adenoviruses are DNA viruses unrelated to coronaviruses, any peptide of this size can be found in many organisms in GenBank. But WIV17/WIV18 were (purportedly) discovered in 2012 in Mojiang County, Yunnan - the same time and place as RaTG13. It’s quite a remarkable co-incidence given the far smaller pool of sequenced organisms in this one cave.

But - stranger still - an earlier WIV PhD student’s thesis stated WIV17/18 were collected in a cave near Kunming, not Mojiang, which is 300km and 5 hours drive away. So they seem to have changed the sampling location so that it corresponds to RaTG13.

WIV may also have intended RaTG13 itself to have originated in the Kunming cave, rather than the Mojiang mine. In the PLoS paper “A rich gene pool…” single virus said to have been sampled from R. affinis in the Kunming cave, was never sequenced, and it doesn’t appear in phylogenetic trees. They were perhaps keeping their options open.

If intended for vaccine research, why plan a cover-up?

Although a chimeric RBM may have some legitimate use in vaccine research, WIV seem to be engaged in something quite different - planning the cover up of an outbreak that was yet to happen. And SARS-CoV-2 is certainly not a vaccine - not even a failed attempt at one. - there is no evidence of an attempt to attenuate it as would be expected in a LAV. Quite the contrary, it seems engineered for human transmissibility and pathogenicity.

A figure at the center of coronavirus research and intersecting networks of Chinese and US researchers is Fang Li. He is a close collaborator with Baric, but also with WIV, where he was a visiting fellow in 2016-17. He studied the remarkably similar MERS FCS with AMMS’ Yusen Zhou and his widow Lanying Du. Over the years his lab has hosted several postdocs from the State Key Lab of Virology (which connects Wuhan University and WIV scientists) and it is these students who have done most of the hands-on lab work on coronavirus structure and entry mechanisms. In 2018 he collaborated with WIV’s Shi Zhengli and Jie Cui on a paper about the origin of SARS and MERS. The resulting paper published in December 2018, suggests an origin scenario for SARS similar to that initially proposed for SARS-CoV-2 (substituting pangolins for civets).

Jie Cui, and his doctoral student Yu Ping were responsible for sequencing RaTG13 - (although curiously their names aren’t listed as authors on the eventual paper). In July 2018, they uploaded partial sequence data to GenBank for RaTG13, and many other viruses, but they omitted the all-important spike gene. In Yu Ping’s thesis there is an alignment of the RBDs of these new viruses, but RaTG13 was again omitted.

Interestingly, the RBD is the region of RaTG13 which is notably different to SARS-CoV-2, while the Guangdong pangolin coronavirus has a close RBD, but is divergent elsewhere in the genome. An early hypothesis was that SARS-CoV-2 was formed of the recombination of the two.

FOI documents acquired by US Right to Know show Fang Li’s proposed work would have determined the crystal structure of bat coronaviruses in complex with ACE2 of various species. This work might be useful in informing the design of a chimeric RBD. It’s unclear if this work was ever done, no results have been published.

Fang Li shares common interests with Baric in receptor binding and protease cleavage. Unlike Baric, he is also interested in the spike NTD as a potential sugar binding domain (“sugar” includes sialic acids, heparan sulfate, other glycans). This interest is perhaps vindicated by the recent pre-print from NIH scientists suggesting that heparan sulfate - not ACE2 - is the primary receptor for SARS-CoV-2 (the NTD will be the subject of a future article).

I don’t mean to imply that Fang Li had any direct or willful input into the design of SARS-CoV-2 - but someone with such expertise and connections should not have been overlooked by investigations such as the Covid Select Subcommittee.

From the start, the Furin Cleavage Site has attracted more attention than any other genomic feature as pointing to an artificial origin. It isn’t simply that all of SARS-CoV-2’s close relatives (even the fakes) lack an FCS motif, it’s also that it occurs as an insert. It didn’t evolve one mutation at a time, it happened in an instant - RNA from an unknown foreign source somehow got injected due to an error during replication. Although such a phenomenon isn’t regarded as impossible, it is exceedingly rare. Even more improbable that the RNA randomly acquired would form a valid cleavage motif, and in the precise location the S1/S2 junction is cleaved. If a detailed calculation multiplying these minuscule probabilities had been made, the debate over an artificial origin should have ended in February, 2020.

Yet it continues. “That’s not how I would have designed an FCS - it’s sub-optimal” they say, “other coronavirus families have an FCS”, “the S1|S2 junction is a hotspot for inserts”, “we don’t know what else may be out there” etc. This shouldn’t be difficult to counter - but for an uneven balance of academic credentials. A cabal of former Oxford Zoology Department professors (Holmes/Worobey/Rambaut/Robinson et al) refuse to engage in serious debate, but recite these same talking points ad nauseum to any media still interested. It perhaps doesn’t help that lab-leakers indulge in speculating on artificial sources it may have come from e.g. “a Moderna patent”, “the human Enac sequence” etc. This shifts the debate from the infinitesimally small chance of it ever having happened, to having to defend a specific source. In an artificial origin, the FCS needn’t match anything, it could easily have been derived from undocumented experiments.

Still, knowing the pitfalls, I’m going to weigh in again anyway…

CpG depletion

SARS-CoV-2 - and particularly the spike protein is extremely depleted in CpG dinucleotides (all this means as a C followed by a G in the nucleotide sequence). This has been hypothesized to be due to the virus evolving to evade the host immune system, by taking on the hosts own nucleotide bias (human and bat genomes are also CpG depleted). To an extent this is true of all coronaviruses, CG is usually in a range 1.5-3% of all nucleotide pairs, whereas if random, we’d expect 6.25%.

But SARS-CoV-2 is exceptional in that:

• the depletion is particularly pronounced in spike (at only ~0.7%). There’s no obvious natural explanation for this. Host factors that seek out CpG don’t know which region of viral RNA corresponds to which gene/protein.

• this depletion is also evident in the 3 Banal sequences closest to SARS-CoV-2, RaTG13 and pangolin CoVs, but not in most other bat CoVs. The Banal sequences have an extended region straddling the RBD, where there are no CG at all.

There are many potential causes of CpG depletion in a lab environment. Cytosine deamination causes C→T mutations, so CG becomes TG. This can result from heating (e.g. during PCR), sequencing, irradiation, long-term storage, UV light, exposure to enzymes and other reagents.

But if SARS-CoV-2 spike is depleted in CpG overall, why does the FCS have three CG pairs in such a short segment (it is coded CCT-CGG-CGG-GCA-CGT)? The codon CGG is rare in coronaviruses making up ~3% of Arginine codons, or ~1 in 1000 of all codons. This suggests a source other than a coronavirus. Humans have a higher preference for CGG codons (~20% of Arg or ~6 in 1000 of all codons), but the human genome is also overall CpG depleted (~1%), as are those of bats. The chance of two CGG codons in a row is still only 0.0035% (if random).

So, what might be the source?

If you read my previous article, you’ll know about my woes FOI-ing documents from CSIRO. Almost all documents relating to SARS have disappeared. But they did manage to dig up some documents relating to other projects. I had requested all correspondence from Zhang Huanjun, the WIV intern who was running gain of function experiments in CSIRO’s BSL-4 lab. As a side project, he was sequencing a bat herpesvirus, and exchanging sequence data with CSIRO staff via email.

Not expecting much, I searched anyway for CGGCGG. To my surprise it was everywhere, over 1000 instances, and extending up to 10 nucleotides from the FCS. The explanation is that unlike coronaviruses, this herpesvirus is CpG enriched (~9% of nucleotide pairs). This WIV/CSIRO work resulted in a paper, and a complete herpesvirus genome (>200k bases) posted to GenBank. Blasting it results in longer FCS matches up to 12nt.

Further, they were trying to sequence another herpesvirus from a different bat species that was even more CpG enriched, but they may not have succeeded (I’ve been unable to find it in GenBank).

Herpesviruses can survive for decades in the host as a circular DNA dormant inside a cell. They can later be reactivated and replicate when another virus infects the cell. This sounds like a scenario that could plausibly result in recombination, although it is unknown for a DNA virus to recombine with an RNA virus. I don’t believe that happened, but it might be that’s what the engineers of SARS-CoV-2 want us to think, hence the peculiar codon choice.

In similar fashion I found what appears to be a peptide from a WIV discovered bat adenovirus (WIV17) substituted into the SARS-CoV-2 RBM. Adenoviruses are also DNA, and some utilize similar strategies to herpesviruses. More in a future article.

Have MERSy

There is an obvious explanation for the derivation of the amino acid sequence of the FCS, which recently became more obvious. All its reputedly problematic characteristics: the leading Proline, the suboptimal cleavage efficiency, O-glycosylation sites, the extended loop, can be easily explained by looking at the MERS FCS - which indeed most scientists interested in SARS were also looking at.

Recently A.M. Lisewski noticed in GenBank a sequence for a variant of MERS which had been passaged in mice over 30 times. This passaging resulted in only two spike mutations one of which was added an extra Arginine in the FCS.

Although only a single amino acid is different, it is in the non-canonical position, the same as SARS-CoV-2. This in another extremely unlikely coincidence, an R in that position is rare. If the similarities to MERS weren’t enough already, this should have sealed it. Lisewski presented to the WHO group investigating the origin - SAGO, who weren’t persuaded.

There is only one remaining amino acid difference between MERS MA30 and SARS-CoV-2, and that V→A is a mutation a scientist would be likely to introduce in order to isolate the contribution of individual residues (a very commonly used technique Alanine scanning which replaces residues one at a time with A).

The first author on this paper was Kun Li, based in Stanley Perlman’s lab at University of Iowa - but formerly of the Wuhan Institute of Virology. His work caught the eye of Ralph Baric who sought approval to make these mutations himself and assess the effect on virulence.

I don’t subscribe to theories Baric was directly involved in engineering SARS-CoV-2, but he was being circled by people with connections to WIV and AMMS. While he wasn’t working directly with Zhengli Shi, he was a collaborator and confidante of Fang Li who, though US based, has strong ties to Wuhan. Fang Li and Zhengli Shi were in turn collaborating on a review paper with Jie Cui - who was responsible for sequencing RaTG13, and I think central to a pre-planned cover-up.

From a public health perspective, it makes little sense that there should have been such interest in SARS or MERS. The last SARS case was over 20 years ago. Despite briefly causing some localized panic, there were only ~800 deaths worldwide. A trickle of MERS cases continues, such that it has now killed more than SARS (957 at last count) but human-to-human transmission is rare. In contrast, seasonal respiratory diseases kill up to a million people every year. The scientific interest in SARS and MERS was only because they were seen as potential (or already proven) biological weapons.

If this possibility was foreseen, why is there such a taboo around asking whether SARS-CoV-2 may have been developed for that purpose?

Exercise for the statistically minded

Please feel free to weigh in with a comment especially if there are other factors needing consideration.

Calculate the probability that a four amino acid sequence…

• should create an FCS motif (when inserted) and…

• that motif closely resembles the one most studied by coronavirologists and…

• has a rare, non-canonical Arginine residue…

• is composed of rare codons and…

• it somehow comes to cohabit a cell that a coronavirus infects and…

• a replication error takes place such that…

• it becomes inserted at just the right location in the S1|S2 junction of the spike gene to complete an FCS motif…

• it survives, replicates, becomes dominant in the swarm and transmits to a new host species?

I know, right? “Nature is big - there’s a lot of dice being rolled”.

I asked Grok to help, taking into account the points above.

It’s answer: 10⁻³⁴. I don’t agree with some of its reasoning, but will try to work through it. In any case it’s small, very small.

I’ve spent 3 years battling CSIRO for FOI access to documents related to their long engagement with Wuhan Institute of Virology. This collaboration, which also included EcoHealth Alliance, was convened by WHO in the aftermath of SARS in 2003 to help China search for its origin. Over the next decade Linfa Wang’s CSIRO group jointly produced 15 papers with WIV related to SARS origin, 11 on other bat-borne viruses and bat immunology, and a further 4 with the PLA’s Academy of Military Medical Science (AMMS).

The apotheosis was the announcement in a 2013 Nature paper, of the discovery of bat viruses with a SARS-like receptor binding domain (RBD) which - they claimed - definitively proved SARS originated in bats. But for the 7 FOI applications I’ve made - and hounded them over - and their extensive trawling through back-up systems, CSIRO have been unable to locate a single document to show the work of sampling bats, isolating and sequencing these viruses ever happened. Alarmingly, CSIRO’s archives appear to have been systematically erased. The only correspondence remaining with WIV is about unrelated side projects and small talk. Other documents and data (such as sequencing reads) that might support their claims are non-existent. When it comes to AMMS - there are no documents at all.

WIV’s gain of function experiments at CSIRO

Even as WIV claimed to be hunting in caves for bat viruses, they had also been learning to engineer artificial ones - with the assistance of Linfa Wang’s group at CSIRO’s biosecurity lab in Geelong, which hosted WIV interns such as Peng Zhou, Shi Zhengli and Zhang Huajun.

In 2007 the collaboration engineered artificial chimeric spike proteins by taking segments of SARS spike of different lengths, using them to replace the equivalent region of a bat coronavirus (Rp3) spike. From this they determined a minimal region of SARS RBD that could confer the bat virus with the ability to infect human cells. They also noted that these chimeric viruses were unable to infect bat cells.

They had rivals. Ralph Baric of UNC and Mark Denison of Vanderbilt went a step further in 2008, engineering a live coronavirus from a full-length bat virus genome (synthetic, but based on HKU3), with its RBD replaced by that of SARS. They went on to show this could infect several types of human/primate cells and mice.

The WIV/CSIRO group had also wanted to make a full-length live virus, but had been unsuccessful.

The likely reason Baric/Denison succeeded, while WIV/CSIRO didn’t, is because Baric used human/primate/mouse cell lines. WIV/CSIRO were trying to use bat cell lines. SARS is a human virus and the RBD is the key determinant of host species it can infect. Still, if a virus is able to cross from one species to another, the RBD should be expected to attach to both to some degree. Linfa Wang’s reasoning was sound.

They didn’t give up. Another FOI email I obtained shows a WIV intern, Zhang Huajun, trying to engineer live chimeric viruses in the Geelong lab, with help from CSIRO staff. At this time, they were still trying to use bat cells, and were again unsuccessful.

But if they didn’t succeed in the lab - nature had already provided them what they were trying to engineer. Or had it?

Why did WIV succeed in Yunnan, where others failed?

In April, 2012 there was an incident in Mojiang County, Yunnan in which 6 miners clearing bat guano from an abandoned mineshaft were taken ill and hospitalized, 3 later died. Some of their samples were sent to WIV for testing. Shi Zhengli initially claimed one of their samples was seropositive for SARS. She later retracted this, instead agreeing with the medical staff who treated them that the disease was fungal. But the initial claim aroused interest, it seemed a clue in the search for SARS origins. Three groups including WIV visited the mine to sample bats and other wildlife. But WIV was the only one to claim the discovery of a SARS-related virus there - that virus is now known as RaTG13.

As if to explain the failure of the other groups to confirm their discovery, WIV hypothesized that coronaviruses were highly seasonal. They had encountered up to 50% seropositivity for alphacoronaviruses on one occasion, and as low as 7% on another. Of 276 bats sampled over all the trips, only one had a beta-coronavirus - a needle in a haystack. This makes confirmation by other scientists near to impossible. A core principle of the scientific method - reproducibility - is absent.

Curiously, in the 2013 paper WIV claimed they had already nearly completed a 12-month longitudinal survey in Yunnan. They retrospectively claimed had started this in April 2011, but at a different location - a cave near Kunming. It isn’t clear why they chose Yunnan for a longitudinal survey, since as of 2011 no SARS-related coronaviruses had been found there, and the miners’ incident was yet to happen. Were they acting on a hunch? Or did they invent this detail?

If it was prescience, it paid off. They soon announced 3 new virus discoveries - RsSHC014, Rs3367 and WIV1. RsSHC014 was (purportedly) collected in April, 2011 on the first excursion - so its sequence should have been known by the time of the miners’ incident.

SHC014 has a has an RBD that is somewhat divergent to SARS’, but similar in being of extended length, without the deletions that characterize other bat coronaviruses. This is key to conferring human and mammalian tropism. A 2015 Baric paper confirmed SHC014 is potentially human infectious. It was the closest known bat virus to SARS, but WIV hadn’t disclosed it. WIV1 and Rs3367, have an identical RBD, almost the same as SARS. These were collected in March and September 2012.

WIV’s claimed “discoveries” appear to be artificial chimeras

In the wake of SARS-CoV-2, I compared these viruses using SNAP diagrams. These provide more information visually than the more commonly used Simplot. They separate synonymous and non-synonymous mutations and indels, and they don’t use sliding window averaging. This makes changes in variability clear and allows visual identification of recombination breakpoints. Using SNAP it is immediately obvious there is an unusual relationship between the viruses.

SHC014 and Rs3367 are 99.9% identical for most of the genome, excluding the RBD, which has many mutations. Non-synonymous mutations (those that result in a different amino acid) are all within the surface loop (RBM) that makes contact with the ACE2 receptor. While this region is expected to be more variable, the distribution is a surprisingly neat - there are no amino acid changes at all outside this zone. But most bizarrely, the breakpoints of the variable region are almost precisely at the locations WIV had identified in the 2007 experiment described above.

There is nothing magical about the numbers WIV derived in this experiment, they are just approximations of where a functional segment of protein begins and ends. But recombination happens during replication. The replication apparatus reads RNA and writes RNA - it has no knowledge of the protein structure or function that RNA might encode. Recombination occurs at locations in the genome that are effectively random* - and most often there is just one. A map of breakpoint locations in recombinant SARS-CoV-2 variants illustrates this.

*This is somewhat of a simplification. For a more extensive nuanced discussion on this subject please see my pre-print and/or leave me a comment below.

WIV’s viruses apparently won the genetic lottery by not only having two breakpoints, but at precise locations that they had predicted would be ideal for conferring human infectivity. If it came to be widely accepted that natural evolution is capable of this it there are some important - and dangerous - ramifications.

Rewriting the science of viral evolution and disease emergence

The implication is that rather than requiring gradual adaptation one mutation at a time (as was the understanding of spillovers historically) the ability to infect and a much harder feat - to transmit efficiently between humans - could be transferred from one virus to another instantaneously. This represents quite a challenge to any conventional model of viral evolution. Although recombination is an accepted phenomenon, no-one imagined it could happen so precisely and efficiently in nature - though it had long been demonstrated in the lab.

Surely this would be controversial, skeptical scientists would contest these results?

WIV seem to have avoided debate by:

1. Simply not mentioning it in the paper. Although the paper has a paragraph about recombination, it relies on software and finds different breakpoints that are far less obvious, if they are even breakpoints.

2. Co-opting influential western scientists e.g. Ralph Baric who had been postulating recombination as a mechanism for species jumps since the 1990s, and was amenable to the idea.

3. Publishing in the most prestigious of journals, Nature, with co-authors from Australian government agency CSIRO and the US government supported EcoHealth Alliance.

4. Following up quickly with more discoveries, such that the original would be supported by other sequences. The next “discovery” with a SARS-like RBD, LyRa11, was already in GenBank by August, 2013. It was “discovered” by Tu Changchun from AMMS, a collaborator of CSIRO, and a member of WIV’s advisory board.

   

More biowarfare applications

WIV followed up their claimed discovery with further viruses which purport to show that bat coronaviruses are frequently swapping functional protein domains at other genomic locations which might facilitate the instantaneous transfer of function and host tropism. This is a claim that nature engages in the same practices a bioweapon engineer might. A harmless zoonotic virus can instantly become human infectious by acquiring a new RBD. This is exactly what was proposed for the emergence of SARS-CoV-2 - a bat virus (similar to RaTG13) acquired the RBD from a pangolin virus (which had recently been discovered by the AMMS).

Another strange feature of WIV’s 2013 discoveries is a mysterious gene called ORFX. WIV1 and Rs3367 are over 99.9% identical, just a handful of mutations between them. Except that WIV1 has an entirely new accessory gene inserted. Accessory genes aren’t involved in replication, and they don’t form part of the virion structure. In a sense they are optional though they often have effects on the immune response, and they can be toxic. Thus, they may be of interest to a bioweapon engineer e.g. to carry a encode a “payload” protein, with little risk of making the virus replication incompetent. ORFX was previously unknown to science and has no close matches in GenBank. It appears in just one other of WIV’s many “discoveries” (WIV16).

Soviet defector Ken Alibek who rose to be deputy head of the bioweapons program described how their scientists had in the early 1990’s genetically engineered bacteria to express human regulatory peptides, short proteins that have can have great impact on the human body.

The protein encoded by ORFX is likely just a made-up “nonsense” protein. It has been shown to have only a minor immune modulatory effect. But it has the correct format (with a TRS) for it to be translated as a protein. The precedent of coronaviruses naturally acquiring entire novel protein coding genes in a modular way, is very dangerous. What if the gene instead encoded a toxin, or a regulatory peptide homolog as described by Alibek? This might be used to create far more dangerous pathogens than nature could ever evolve - and to misattribute the origin as natural.

WIV later extended this concept to include the immaculate transfer of a gene. In a Chinese language publication they claim another viral discovery Rs4084 has two variants which are all but identical - except for their ORF8 genes. One variant shares it’s sequence with several other viruses, and one is unique. This suggests a mechanism where a more pathogenic “payload” could be exchanged with the accessory gene of an otherwise mild, human endemic virus. SARS-CoV-2’s ORF8 is highly variable, and some variants are known to be more pathogenic.

What is the real purpose of this work?

It is my contention that WIV isn’t a scientific research organization, so much as an agency of espionage and scientific disinformation. I doubt their capability in bioweapon design, rather I suspect their primary role is in misattribution - through disseminating scientific disinformation including fabricated sequence data, also acquiring intellectual property and isolates from foreign partners. Unfortunately, many western scientists and institutions have fallen for their ruse, and have become “useful idiots”, adding credibility and amplifying WIV’s claims with little skepticism.

AMMS, on the other hand, are more technically capable, more secretive, if somewhat less trusted by foreign institutions. Still, even though AMMS are consistently named on Bioweapons Convention compliance reports, and now blacklisted by the US State Department, this hasn’t deterred international institutions (e.g. CSIRO, Institut Pasteur and NIH) from collaborating with them.

And what of CSIRO and EcoHealth? To me, Peter Daszak appears to be most credulous, but lacking the technical competence to fully understand the work that bears his name. In contrast, Linfa Wang has considerable expertise (much of which he has transferred to WIV). It is most curious that he left Australia around the time of the 2013 publication (while retaining a CSIRO email account) and that all of his correspondence and records have since vanished. An unexplained China-related data breach also occurred at the time.

Unfortunately, CSIRO executives have been uncooperative and dismissive of my claims. Although their FOI staff have made considerable efforts to find documents, there is no interest in investigating why hundreds or thousands of documents that clearly should exist, do not. EcoHealth is a private institution, not subject to FOIA. Although documents are surfacing via leaks and subpoenas, there is little that relates to scientific work. Possibly their main role was only administrative. From WIV and AMMS of course we can expect nothing.

Even without these documents, the science ought to speak for itself. WIV claims to have discovered extraordinary evolutionary mechanisms, that contradict conventional scientific understanding. These are apparently unique to a small subclade of bat viruses found in a handful of locations. No-one outside China has access to the caves. None of this work is reproducible. There is no documentation to support it, no truly independent corroboration. Western scientists, seemingly oblivious to the security context, have accepted WIV’s claims on faith in fellow scientists. Faith is not the essence of science, this puts us all at risk.

After these 6, the next closest is RaTG13, which has 17 amino acid differences. Curiously there is no sequence with between 3 and 17 differences. Is this unusual distribution due to insufficient sampling? It seems unlikely - thousands of bats have now been sampled.

On September 20th, 2021, China’s National Health Commission lab submitted a preprint to ResearchSquare. This was a comprehensive survey, for which they had taken 17,000 samples from more than 13,000 bats at 703 locations across China between 2010 and 2021. Stunningly, they reported finding no trace of SARS-CoV-2 related viruses. They even returned to the abandoned mine in which WIV claimed to have found RaTG13, and declared it was no longer present. It appears part of a coordinated attempt to confine the origin of Covid-19 (whether natural or artificial) to be outside China - and was likely timed to coincide with the announcement of the Banals, coming just one day after they were published.

This pre-print upset some Western scientists who had previously collaborated with Chinese state and military groups on the pangolin coronaviruses and RmYN02. These results seemed to contradict their own.

But it seems the Propaganda Department relented, perhaps judging it wiser to keep their Western collaborators/promoters and prestigious science journals on-side. Soon after the controversy blew up in Science, a group from Sun Yat-Sen University reported sequencing another SARS-CoV-2 like virus, BtSY2, from Yunnan bats. Eddie Holmes got his name on another Nature paper.

BtSY2 has serious deficiencies with its data. The genome can’t be assembled from the sequencing reads. There is no read coverage at all of the RBM.

Meanwhile, the NHC’s comprehensive survey was resubmitted to a low-profile journal in which they defended their work somewhat meekly. The contradiction was never resolved.

Hughes and Holmes seem well aware that this paper likely has a propaganda purpose. They also understand that Chinese scientists are compelled to follow an official narrative. But they are unable to recognize that their own collaborations with Chinese state institutions might similarly be tainted by fabricated data. They haven’t been involved in generating that data (i.e. sequencing), merely helping to interpret it. While Hughes collected samples in Yunnan, she sent them to Shandong for processing - to a scientist who works closely with AMMS. There is no way for her to know what her samples really contained. But their names lend the papers credibility and help get them published in prestigious western journals.

The success rate for sampling SARS-CoV-2rs varies dramatically. WIV claimed to have found RaTG13 in one bat in a Mojiang mine shaft, but several other surveys reported nothing of interest at the same site. Institut Pasteur found 7 SARS-CoV-2rs (2 are incomplete and unpublished) in one cave in Laos, but none at another 3 sites. In Vietnam, Laos and Cambodia, Institut Pasteur has reported discoveries at a number of sites - some very close to the Chinese border. Why were none found in the first 15 years of hunting for bat sarbecovs, but since 2020 they have been reported across a vast expanse of China and South-East Asia?

My suggestion is there may be no such thing as a natural SARS-CoV-2 like virus. Every set of sequences presents evolutionary anomalies and/or has issues with sequencing data. Most have links to the same closely related parties - WIV, AMMS, Institut Pasteur. We should not unquestionably trust any sequence related to these events.

More batshit examples…

The locations of the 6 viruses with RBM closest to SARS-CoV-2 are plotted below (GD pangolin cov is excluded as its origin is unknown). There is ~900km between Banal-52 and BtSY2. That’s a long distance for tiny horseshoe bats to fly, they typically migrate distances of 20-30 kilometers. Given the RBM is expected to be the most variable region of the genome, there are astonishingly few differences between the bat viruses, and also human and pangolin viruses.

Banal Sequences

The 5 Banal viruses can be divided into three groups:

SARS-CoV-2 like: Banal-52 (which was described in an earlier article).

GD Pangolin CoV-like: Banal-103 and Banal 236. These are 98.4% identical to each other through the genome.

RmYN02-like: Banal-116 and Banal-247 which are 99.9% similar to each other, but hint at some interesting evolution.

Banal-52 and Banal-236 are very similar for much of the genome, aside from an apparent recombination in which the NTD of spike is replaced.

The bat/pangolin connection

Banal-236 is closer to the GD pangolin coronavirus in the NTD. The ratio of synonymous to non-synonymous mutations at ~9 is extremely high between Banal-20-236 and MP789 particularly considering a host and system tropism change.

Banal-20-103 and Banal-20-236 are very similar in the spike, partly because of another apparent recombination. This can be inferred visually by a clear change in the rate of mutations. A sharp change in gradient of the synonymous (green) line is most telling. The slope of the non-synonymous (red) line often changes because of differences in selection pressure in different regions, and may not always point to recombination.

There are several possible recombination points in the full-length genomes.

RmYN02 also validated?

Banal-116 and Banal-247 are a different species to the other Banals, though extremely closely related to each other with ~99.9% nucleotide identity. They are also closely related to RmYN02 and a coronavirus from Thailand, RacCS203. Although most authors are from Thailand, Tu Changchun from AMMS and Linfa Wang were also involved in sequencing these viruses.

RmYN02 and Banal-20-247 have no amino acid differences in the RBM, or extended RBD although there are 13 synonymous mutations in that region.

Banal-247 and RacCS203 have just 1 amino acid change in an extended region around the RBD, while there are 55 synonymous mutations.

Banal-247 was sampled approximately 500km distant from RacCS203, RmYN02 is 1000km distant from RacCS203. Interestingly, while sampled much further apart, the latter pair are closer in spike sequence with 206 total mutations vs 220.

Filling in the gaps - Hassanin et al.

Interestingly BtSY2 is claimed to have Tyrosine at 501 which is a most significant RBM mutation in human SARS-CoV-2 variants, having emerged independently several times. BtSY2 also has doubts over its provenance, it isn’t possible to assemble the genome from the raw read data provided. More about this in a future article.

Nonetheless BtSY2 has a curious recombinant relationship with Rp22DB159, another of the set from Vietnam sequenced by Institut Pasteur. These were collected four years apart (2018 and 2022), but also at a considerable distance (~400km). The N501Y mutation is the only amino acid difference in a region over 850 amino acids.

Frozen evolution

Cambodian virus RshSTT200 from Institut Pasteur Cambodia has a very odd relationship with a virus discovered recently in Vietnam, Ra22QT137 part of a set which were also sequenced (mostly) by Institut Pasteur. These two samples were collected ~450km and 12 years apart (in 2010 and 2022). In the first 450 amino acids of spike there are just 5 silent mutations and no amino acid changes - an extremely slow rate of mutation given there is a bare minimum of 12 years since they split from a common ancestor. In the middle of the RBM the rate of mutation increases substantially, suggesting a recent recombination with a species with a divergent S2. But how - since one of them was stored in a freezer?

An RBD frozen for 18 years

Another virus from this Vietnamese set Rt22CB395 is unusually close in amino acid sequence to Rp3 (the first SARS related virus discovered by WIV in 2004). The samples were collected 18 years apart - in 2022 and 2004 respectively, yet the RBD is unchanged. The ratio of S/N mutations is also very high.

But if we compare Rp3 to another virus collected in 2004, HKU3-1 it is not only overall more distant but has much lower S/N ratio and has 14 mutations in the RBM.

And comparing to another virus Rm1, also collected in 2004.

And another:

How is it that viruses collected 18 years apart in different species are more similar than those collected at the same time? Why is there no evolutionary pressure on the RBM of Rt22CB395 such that it is identical to Rp3 after 18 more years evolving?

Hyper-recombination

Another bizarre pair from two separate Institut Pasteur related groups, both sampled in Vietnam. In this case the samples were collected only 20km and 1 year apart in the same species R. thomasii. If they were close in sequence, it shouldn’t be too surprising. But the detail still appears quite unusual. There is just 1 synonymous mutation in the first 500 amino acids. Then the rate picks up a little, flattens out again, before a flurry of only synonymous mutations - 30 in total - at the 3’ end.

The full-length genome shows the main region of amino acid divergence is in ORF3a, which is very unusual.

But this isn’t a simple continuation of the previous recombined region, because the divergence only start after amino acid 12.

Discussion

Many sequences published since 2020, which purport to explain the evolution of SARS-CoV-2 do not conform to a conventional model of viral evolution in bats.

Common discrepant characteristics of these viruses are:

• An extremely high rate of recombination. Occasionally there appear to be even more recombination breakpoints than regular amino acid substitutions.

• An extremely low rate of mutation in the RBM. The RBM is expected to be a region of hypervariability as:

  • immune-exposed, surface location at tip of spike forces mutation to avoid antibody recognition

  • protein structure accommodates mutations - flexible, disordered loops

  • where host species changes, RBM need to adapt to better bind to new receptor variant

• Inconsistency in the rate of mutations over different time periods and distances.

• Host species and tissue tropism changes aren’t reflected in S/N ratio. Most pairs have an unrealistically high proportion of synonymous mutations even when the species hasn’t changed. The range of normality in other bat viral families is between 0.7 to 5.

These sequences should not be automatically accepted as evidence for SARS-CoV-2’s natural origin, or that unusually features such as the human-adapted RBM and NTD are natural. We need to have genuinely independent confirmation of the existence of similar viruses in nature and that the extraordinary evolutionary dynamics implied are valid.

Even some natural origin proponents were unconvinced by this hypothesis. Pangolins are solitary by habit, not an ideal host environment for a virus to evolve respiratory transmission. Recombination also requires that the bat and pangolin virus must infect the same host. A survey of 340 pangolins by EcoHealth found no evidence of a coronavirus, while another paper showed they weren’t for sale at Huanan market.

Lab-leakers were justifiably suspicious of both RaTG13 and the PCoVs. RaTG13 was sequenced by WIV perhaps as early as 2017, but they kept it secret. Some partial sequences were uploaded to GenBank in July, 2018 but they were hidden from public view, and the all-important Spike gene was missing. Even after the outbreak it was weeks before WIV admitted they had the closest zoonotic sequence by far to the novel coronavirus. It was shifty behavior from Shi Zhengli, already under suspicion due to the location of the outbreak.

On September 20th, 2019, two scientists from Guangdong Institute of Applied Biological Resources (GIABR) set up a GenBank repository for pangolin metagenomes, which included reads from a novel coronavirus. They wrote a paper in a low-profile journal announcing this discovery, but didn’t upload the data until four months later (at the same time WIV made RaTG13 public). The GIABR scientists hadn’t sampled any pangolins themselves. The data was given to them by a 3rd author, Chen Wu, a vet from Guangzhou Zoo. Chen later provided this same data to other institutions who claimed their own discoveries. It was unclear for a long time who was responsible for the sampling, and whether there were multiple virus discoveries, or just one.

Behind the scenes it was apparent that the PLA’s Academy of Military Medical Science (AMMS) was distributing pangolin samples and data to select civilian research groups. It was later revealed that AMMS had been experimenting with pangolin coronaviruses as far back as 2017. AMMS scientist, Tong Yi-gang, was working on a secret military research project when his group claimed to have first isolated a PCoV.

Although the PCoV genomes are overall quite distant from SARS-CoV-2, one of them (the Guangdong or GD PCoV) has an RBD which is remarkably similar. To complement this RaTG13 has a genome that is overall very similar to SARS-CoV-2, but the RBD is different. A recombinant of the two taking the backbone of RaTG13, and substituting the RBD of GD PCoV, is indeed very close to SARS-CoV-2. But lab-leakers pointed out that even if RaTG13 and PCoVs were themselves natural, this “recombination” could have happened in a lab. It would be of similar design that WIV and others (e.g. Ralph Baric) had already used several times for artificial chimeras - there are even patents covering it.

However, neither the PCoVs nor RaTG13 had the furin cleavage site (FCS) insert, and this remained a focal point of suspicions. At the same time the RaTG13 and the PCoVs were published, British zoologist Alice Hughes was contacted by Shandong University’s Shi Weifeng. Hughes had been working in Yunnan collecting samples from bats. In 2018 she was approached by Shi Weifeng to send his team bat fecal samples, and they would sequence them. In January 2020, he informed her that his group had sequenced SARS-like coronaviruses from samples she had sent. One of those viruses - RmYN02 - doesn’t quite have an FCS, but has a sequence suggestive of a possible evolutionary step to (or from) one. Although a civilian, Shi Weifeng and his team have collaborated often with AMMS over the years. He is particularly close to Tong Yigang, with whom he jointly led China’s mission to Sierra Leone during the Ebola epidemic of 2014. Since Alice Hughes had no involvement in the sequencing, she has no way to be sure such a virus came from samples she collected.

In July 2020, with the artificial origin controversy not subsiding, Institut Pasteur launched an expedition to sample bat caves in Laos. Curiously, they had only recently sampled these caves on a project funded by the US Department of Defense. On that occasion they collected over 500 samples from bats - but hadn’t sequenced any of them. These sat untouched in a freezer in Paris while they embarked on a new field trip. Why would they do this? Possibly because this time they intended to involve Institut Pasteur Shanghai (IPS) in sequencing the samples. IPS is a joint venture with China’s Academy of Sciences (WIV’s parent entity) and is staffed mostly by Chinese scientists. It may have been unacceptable to the US DoD to share samples with an institution so close to WIV.

The Banal sequences weren’t published for another 15 months after the samples were collected. In the meantime, other related sequences had been announced, but none were any closer to SARS-CoV-2, and all lacked the RBD and FCS.

When the Banals were announced, they were hailed by some as definitive proof SARS-CoV-2 was natural. Surprisingly, they weren’t rejected by lab-leakers either. Partly because they added to the growing pile of viruses that were related, but did not have an FCS. This might be interpreted as not diminishing, and perhaps even increasing the likelihood of a lab origin. The senior author of the Banal paper, Marc Eloit, went on the record saying he thinks an artificial origin is possible and should be investigated. Such public statements ingratiated him to lab-leakers.

The Banals don’t conflict with a simple “experiment gone wrong” scenario, in which an FCS was artificially inserted into an otherwise natural bat virus. But they do suggest many of its unusual features critical for transmissibility, pathogenicity and tropism are natural - including the RBD, which seemed already well-adapted to humans. Starting from a precursor similar to Banal-52, far less engineering is needed, making it unlikely SARS-CoV-2 was deliberately and extensively engineered for human infectivity and transmission.

Another implication of the Banal discovery is that the earlier sequences (PCoVs and RmYN02) that could have aroused suspicions of a military plot to misattribute an unnatural origin, are more likely genuine. In a remarkable stroke of luck (for the AMMS) the 5 viruses found in a single cave not only support the natural evolution of SARS-CoV-2, two of them share important features of RmYN02, and two are similar to the PCoVs.

More dangerously, the Banals support WIV’s claim that SARS-like coronaviruses evolve by an apparently unique mechanism based on recombination. This differs from a conventional understanding of recombination in that viruses exchange functional domains with one another as if they were discrete components or modules (WIV has called these genetic “building blocks”). This mode of evolution has so far only been observed in this viral family, in which it happens that WIV, AMMS and associated Chinese state institutions have published the vast majority of sequences.

If WIV’s proposed novel mechanism of evolution gains widespread acceptance among scientists, it makes it easy for future bioweapons to be misattributed as natural. It is crucial that such extraordinary claims be subjected to proper scientific scrutiny and debate, but this has not happened. Because to challenge it, is to make an implicit accusation of fraud. While the earlier “discoveries” from Chinese institutions drew limited attention from skeptics, few have questioned the Banals.

No Pressure Evolution

Banal-52 has both the SARS-CoV-2-like backbone and RBD making the need for the recombination of a pangolin and bat virus redundant. It challenges the conventional understanding of evolution in other ways.

Why would an RBD that enables efficient respiratory transmission in humans evolve in an enteric horseshoe bat virus? Why would a nearly identical spike work so well in what are physiologically very different species? Some claim that the FCS confers this capability. But it isn’t the FCS alone. The FCS helps present the RBD to the receptor, but the RBD needs a complementary structure and contact residues to form strong bonds with the receptor. An RBD would be expected to evolve a different form in adapting to human or pangolin airways vs it’s ancestral environment in a horseshoe bat’s gut.

It makes little sense intuitively, but there is a precedent: SARS-1, its civet variant, and the SARS-like bat viruses WIV claimed to have discovered a decade later. Unfortunately, this episode has also had little scientific scrutiny or debate outside a close-knit circle. I’ve recently shown it appears to be based on fraud.

Unfortunately, there’s been little interest in revisiting SARS-1, which was twenty years ago and had far less global impact. Distinctions can be made between SARS-1 and 2. It isn’t strictly necessary to show SARS-1 is unnatural for SARS-CoV-2 to be, so many lab-leakers prefer to assume it is natural. But it should raise eyebrows that the same people and institutions are proposing a very similar origin narrative on the basis of that dubious precedent. There is much to be learned from this not-so-distant history.

Measuring evolutionary pressure

This section is a simplified background for readers unfamiliar with the concept of evolutionary pressure and how it can be measured (skip ahead otherwise).

Consider a virus that infects two bats, which then become isolated from each other as one bat migrates to join another colony. The strains then start to diverge from each other, as they evolve through different mutations. Mutations happen more-or-less randomly - they can be caused by chemical reaction, or unpredictable events like cosmic rays. Most mutations don’t propagate, but occasionally they do. They may even become dominant in the strain circulating in the colony - particularly if the improve the virus’ fitness in some way. A count of the total mutations between the two strains provides an approximation of the amount of time since they split from a common ancestor.

There are two types of mutations. Synonymous (S) or silent mutations don’t change the amino acid coded. Non-synonymous (N) mutations cause an amino acid change, so change the protein structure and possibly impact some viral functional. Generally synonymous mutations don’t greatly affect a virus’ chances of surviving and replicating, while non-synonymous mutations often do.

Ratios of the two types of mutations - synonymous to non-synonymous (or vice versa) - can tell us about the evolutionary pressures faced. If a virus has spent millennia evolving in a single host species, it should already be highly adapted, it doesn’t need to change to be able infect other members of the species- in fact such changes often reduce its fitness. In this scenario, non-synonymous (amino acid changes) are disfavored, and synonymous mutations propagate more frequently. The ratio of Synonymous (S)/ Non-synonymous (N) is >1 and the virus is said to be under negative (or purifying) selection pressure. Nonetheless there will always some amino acid changes that are beneficial, the virus is never perfectly adapted.

In a scenario where a virus has jumped into a new species (e.g. from a bat into a human or pangolin) the virus needs to adapt rapidly to its new host environment. Cellular receptors are different, body temperature is different, the immune system reacts differently, tissues and organs are arranged differently, pH is different. Not adapting is not an option. In this scenario we should expect non-synonymous mutations to be favored over synonymous. The ratio S/N is expected to be <1 and the virus is under positive selection pressure.

There is an additional selection pressure even on viruses that have been evolving in the same host species for millennia. It comes from the host immune system which tries to recognize the virus and generate antibodies to disable it. The virus has to change the sequence of the regions most exposed to the immune system more frequently to evade recognition. These regions are the receptor binding motif or RBM (the part of the RBD that is exposed on the surface), and the NTD, which together comprise the tip of the spike. We should always expect these regions to undergo some non-synonymous mutations over time, regardless of how well-adapted the virus is.

Observations

We can see that in human SARS-CoV-2 variants the RBM is indeed the most variable region and some surface loops in the NTD are also hyper-variable.

SARS-CoV-2 variants have very few synonymous mutations in the Spike, perhaps fewer than might be expected. The combined pressure from adaptation to humans and immunity is very strong. Comparing a Delta variant sequence to the first Wuhan sequence there are over 4 non-synonymous mutations for each synonymous, and in the spike gene the ratio is 10:1. The ratio is likely also affected by unnatural immune pressures from vaccines and monoclonal antibodies. We should keep an open mind to the possibility some variants are also genetically engineered and deliberately introduced but that is for a separate post.

Comparing just the Spike gene of a recently circulating variant JN.1 to the first Wuhan sequence, demonstrates that the RBM is usually one of the most variable regions. Here there the ratio is 19N to 1S in the RBM. Again, part of this is likely the result of unnatural pressures from antibodies induced by vaccines, forcing the virus to adapt or go extinct.

But comparing the spike of bat virus Banal-52 to the original Wuhan human sequence, the situation is reversed. In this case there are 9 times as many synonymous mutations to non-synonymous in the spike. The virus appears to have been under very little pressure to adapt to the new host. In fact, the S/N ratio of 9 is extremely high, even for a pair of well-adapted viruses evolving in the same species of bats. I have looked at many families of bat viruses and found a ratio of between 0.6 and 5 seems to be the range of normality. Many more comparisons are in my pre-print.

How can this be explained? Perhaps the virus was very well adapted to a species of bat and evolved for a long time under negative selection in Laos. It then infected a human almost immediately before the Wuhan sample was taken, giving it little time to adapt. But this doesn’t fit the circumstances of the outbreak well, and the S:N ratio is still too extreme.

What if we created a hypothetical sequence consisting of the RBD of the GD PCoV, embedded in RaTG13, as according to the original recombination hypothesis? This means simply taking the first 310 amino acids of the RaTG13 sequence (unchanged) then from 310 to 518 of the PCoV, then from 518 to the end of RaTG13.

Curiously, that sequence is even closer to SARS-CoV-2 in amino acids and the S/N ratio is even higher with almost 16 synonymous mutations to each non-synonymous. This is strange because there are 3 different species involved, why is there so little evidence of evolutionary pressure to adapt?

Most bizarrely - if we compare Banal-52 to this hypothetical recombinant, it is closest of - with just 9 amino acid differences. And there are over 24 synonymous mutations for each non-synonymous - this is an absurd number.

This is evolutionary nonsense. The RBM and NTD should be the most variable parts of the genome regardless of the host species, yet their evolution appears to have been all but frozen. I’m yet to receive a plausible explanation for this from biologists on the natural origin side. One attempt to explain it has it that the RBM had evolved into an optimum for binding the ACE2 variants of all 3 species (and perhaps others), therefore any mutations to it are deleterious and aren’t selected. This is evidently false. The RBMs in recent circulating human variants have over 20 amino acid mutations from the original Wuhan strain. Many of these variants are as good, if not better at binding ACE2. Bat coronaviruses also have diverse and variable RBMs. Rather than reaching a stable optimum, the RBM has been observed and modeled to accommodate mutation.

Aside from adaptation, the RBM must mutate to evade recognition by antibodies. I’ve also heard arguments that “the immune system of bats is more tolerant of pathogens, reducing selection pressure on the RBM”. I accept that the immune system of bats may be different - but it is not non-existent. Bats do produce antibodies to infection, so immune-exposed regions of viruses should mutate to evade them. This extreme reticence to evolve seems unique to a handful of recent SARS and SARS-CoV-2 related viruses. Other viruses carried by bats don’t demonstrate this lack of selection pressure.

To summarize, there are 3 reasons why the RBM and NTD should be hyper-variable in theory, and indeed usually are observed to be:

1. They are the most exposed to the immune system, being located at the tip of the spike, so must constantly mutate to evade recognition by antibodies.

2. Their protein structure is tolerant of mutation as they are comprised of flexible disordered surface loops.

3. Where there is a host switch: receptors often have host-specific variants, so attachment regions (particularly the RBM) should adapt for stronger binding.

If not a unique exception to laws of evolution, what could explain this?

If a nefarious actor was trying to create a false evolutionary trail to cover up an artificial pathogen, they want to show that certain features evolved naturally - but - they don’t want the sequence to be so close overall that it appeared they were in possession of the direct precursor. They need to fabricate a new sequence with some extra mutations for distance. But if they add non-synonymous mutations, they change the protein structure. This risks creating a structure that might be non-viable if someone were to attempt to synthesize it. It also might change the function of a feature they were trying to demonstrate evolved naturally. It is generally safe to add synonymous mutations which don’t change the protein encoded. Of course it would be suspicious to only add synonymous mutations, but a disproportionate number might pass unnoticed.

Banal-52 spike gene can be easily fabricated by starting from the RaTG13/PCoV sequence and adding 24 synonymous mutations for each of 9 amino acids changed. All but one of these amino acid differences are conservative substitutions in which a residue is exchanged for another with very similar properties, having only minor effect on the protein structure and function. The RaTG13 and PCoV sequences may have been fabricated in a similar way. After 5 years, we are no closer to discovering whether they are viable or can infect their putative host species (despite Ralph Baric having been approved to do this work in early 2020).

I suspect laypeople would be horrified if they knew that there is no effective way to validate sequence data. Worse, scientists almost always place blind trust in the GenBank data and incorporate it data into their studies without questioning its provenance or the reliability of the submitter. When we are breathlessly informed by the media that “scientists have discovered a new virus in bats similar to…which could cause the next pandemic”, there is no advertising of the scientists’ possible connections to the PLA’s biowarfare unit, and no disclaimer that the discovery hasn’t been independently confirmed. Peer review is often cited to assure us that work has been checked, but this misunderstands what reviewers are able and expected to do.

The reason modern progressive people like to declare that they “trust science” over faith-based belief systems is because we understand the scientific method to mean findings are independently reproducible, so verifiable. If we can’t do this ourselves because we lack expertise and resources, we assume there will be others who can - and will. In some sciences this is true. If someone claims to have invented cold fusion or a room temperature superconductor, skeptics in physics departments the world over will immediately try to debunk them.

This is not always the case in biology. In sampling pathogens from wildlife in remote areas - replication is extremely difficult to impossible. Several different groups sampled the Mojiang mine where WIV claimed to have found RaTG13, but only WIV has ever reported finding SARS-like coronaviruses. When WIV revisited the mine later they weren’t able to find it again. A massive survey of over 13,000 bats by China’s National Health Commission claimed that SARS-CoV-2 related bat viruses were no longer found in China - conveniently shifting the origin to South-East Asia.

What many assume to be science turns out to be another faith-based system, which (like religion) is open to exploitation by charlatans. It’s a safe bet that bioweaponeers aren’t of the highest integrity and are motivated and well-resourced to avoid attribution. Simply “taking their word” for it or applying a presumption of innocence is unacceptable given the dreadful toll of the pandemic, and the potential for more.

Banal-52 wasn’t the end of it. More sequences have since appeared with a very similar RBM - most of these have also been collected by or sequenced by Institut Pasteur. These will be explored in another article in very near future.

For more background on the history of French involvement with WIV and the AMMS, please see my earlier article “French complicity in the origin and cover-up of Covid”.

Just months before SARS broke out, USAF Colonel Michael Ainscough warned of the threat of “next generation bioweapons” that have been enhanced by new genetic engineering techniques. He envisaged how a bioterrorist attack might play out.

His depiction is uncannily similar to the way the SARS epidemic unfolded just a few months later - to a degree it could have been inspired by his work. SARS is, to this day, believed to transmit only in close contact situations, via large respiratory droplets or fomites but there are a handful of “super-spreader” incidents in which SARS can only have transmitted by aerosol. These might more readily be explained as terrorism.

• The early spread in Guangdong in which 150 million bulk text messages were sent over 3 days, warning of a mysterious disease causing many deaths and infecting staff in hospitals. Online rumors told of an incident at Guangzhou’s World Trade Center in which hundreds of people were infected at once causing 30 deaths.

• In the 3 days Guangdong was being terrorized by a largely phantom epidemic, Hong Kong police investigated leaflets being distributed near the Kowloon mosque that declared support for Bin Laden and a “terrorist new era”.

• The international outbreak had its epicenter in Room 911 of Hong Kong’s 500 room Hotel Metropole. Over twenty guests were infected on one floor - who then carried it to several other countries. But no-one, including staff, were infected anywhere else in the hotel.

• On the day of the confirmation of China’s new President Hu Jintao, 24 people were infected on Flight CA112 from Hong Kong to Beijing (a 3-hour flight). Investigators later identified 35 flights on which known SARS cases had traveled and only found 5 infections resulted from all the other flights combined.

• At the Amoy Gardens high-rise estate over 320 people were infected at once, in 15 separate tower blocks up to 100m apart. HK authorities blamed it on a visitor to the estate who had diarrhea - combined with faulty plumbing.

Some of these incidents not only look as though they may have been deliberate, but that the perpetrators wanted them seen to be terrorism and to have them associated with 9/11 - like the anthrax killings a year earlier. It is likely that stoking psychological terror - rather than maximizing lethality - was the main objective, echoing “Unrestricted Warfare”:

“If terrorists confined their operations to traditional approaches: bombings, kidnappings, assassinations, and hijackings, this would instill less than the maximum degree of terror. What really strikes terror into people's hearts is the melding of terrorists with new technologies that may evolve into superweapons. We already have a hint of what the future may hold. When Aum Shinrikyo discharged Sarin gas in a Tokyo subway, the casualties from the poison accounted for just a small portion of the terror. This event put people on notice that modern biochemical technology had forged a lethal weapon for terrorists whose ambition was the mass destruction of humanity.”

The speed with which the narrative of SARS natural origin via animals gained acceptance is baffling. At the time there was very little evidence available. Nonetheless stories in two influential newspapers of record in late April made it appear the case was all but settled. The Times on 26th April:

They were outdone the next day by the New York Times’ graphic depictions of wildlife markets.

What was the basis of this confidence in an animal origin? What were the preliminary studies they referred to?

At this time there was no evidence of an animal host of SARS. The first SARS coronavirus sequence was made public on April 16th, by a Canadian group, followed in quick succession by HKU. At a press conference, HKU’s J.S. Malik Peiris asserted there was no chance the novel virus was man-made: "The whole genome is new" he said "Nature has been the terrorist throwing up this virus.". While it was true at this time no-one had published a closely related virus, it isn’t possible to discount that someone had discovered one - and not disclosed it. This same false reasoning has recently been applied to the origin of SARS-CoV-2. It should be obvious that one reason for not announcing such a discovery is if it was intended to be used for terrorism or warfare. But this argument has been off-limits as any suggestion of bioterrorism has become taboo.

The next day the PLA’s AMMS published a SARS sequence from a patient which had an unusual genetic feature: an extra 29 nucleotides. A paper describing the sequence claimed the patient was linked to one of the earliest cases in Guangdong. They speculated this variant had only recently transmitted from an animal, the extra nucleotides hindered replication in humans, so had been deleted in later cases. This speculation was eventually shown to be false (in 2018 by a German team led by Christian Drosten).

The only data available at the time that suggested an animal origin came from Guangdong CDC, but it wasn’t especially compelling. Their data showed that of the earliest 23 cases they had identified, 9 were in people who were in food handling jobs. Even if we consider Guangdong CDC trustworthy, this is a tenuous connection. The official record has it that the first SARS case was in Foshan on 16th November 2002 (the day after Hu Jintao’s election as CCP General-Secretary). But this was 5 months before tests would become available, and the pathogen was still unknown. Diagnosis was on the basis of symptoms, sometimes supplemented with radiography, but it is difficult to distinguish SARS from other respiratory illnesses objectively. A doctor alert to its peculiarities might be able to diagnose it, but the earliest SARS cases were diagnosed retrospectively, scored on a spreadsheet.

Guangdong at the time was a province of 85 million people. Over half a million people die in a population that size each year, perhaps 50,000 of them from respiratory diseases. To add to this Guangdong was experiencing an unusual “cold wave”, resulting in higher than normal incidence of pneumonia. For perspective there were only around 1500 SARS cases, and 57 deaths recorded through the entire epidemic in Guangdong. As public health events go, SARS might even have been viewed as trivial - if it wasn’t for that handful of unexplained super-spreader incidents.

But a few weeks later, AMMS and the over-eager press appeared to have been vindicated. On 23rd May, the HKU scientists and Shenzhen CDC announced they had sequenced a virus very close to SARS in samples taken from 6 civet cats and a raccoon dog being sold alive for food in a Shenzhen market. Miraculously these had the same 29-nucleotide insert matching the early Guangdong case AMMS had sequenced. It seemed the missing link to an animal host had already been confirmed.

The WHO announced this at a press conference, and it seems to have been nearly universally accepted by the general public that the case was closed. Yet even today, scientists can’t explain how it evolved and how it traveled to Guangdong. Few now believe civets were the source or a reservoir. No human or civet infections have been reported in 20 years. It is certainly related to bat coronaviruses but has never been found in a bat or proven capable of infecting one. While many details remain unknown or disputed, even most scientists accept SARS is natural. But on what evidence was an artificial origin ruled out?

As with SARS-CoV-2, There was never any investigation into the possibility of an artificial origin. US CDC Director Julie Gerberding’s comment that “we are keeping an open mind”, was echoed by Anthony Fauci during the Covid-19 pandemic.

Some of the haste to dismiss the possibility might be put down to terrorism fatigue. Prosecuting the terrorist acts of a few had already led to the invasion of Iraq and Afghanistan and the harassment of US scientists by the FBI. No-one wanted a confrontation with China, there was no military option that wouldn’t result in immense bloodshed. The Bush administration hoped China would become an ally in a global campaign to tame or effect regime change in “rogue states” - particularly North Korea. In any case, the US was relatively unscathed by SARS, there was no howling for vengeance from its few victims.

The cognitive dissonance is palpable in the biodefense and foreign relations communities. In early May, China and public health scholar Yanzhong Huang wrote a report on SARS for the Chemical and Biological Arms Control Institute (CBACI). The foreword by CBACI President Michael Moodie ruled out the possibility in one terse sentence. There are no citations or justification offered.

“One of the questions about SARS asked very early during the outbreak was: Was it deliberate? This time the answer was no. But the fact that the question is inevitably asked when an unusual outbreak of disease erupts anywhere around the globe reflects the unfortunate reality of today’s world.”

Huang skirts the issue - that SARS looks a lot like bioterrorism - by addressing it as a “weak proxy”, a useful learning exercise for the real thing.

“The SARS outbreak also yields some useful lessons for biosecurity by serving as a “weak proxy” for biological warfare or bioterrorism attacks…a global response is needed to address the bioterrorist threat because terrorists would likely introduce a pathogen in many locations simultaneously, making it more likely to spread…In that respect, a Hong Kong comedian was right when he commented that the worldwide SARS outbreak might be the first coordinated global exercise in the fight against biological warfare.”

Huang was invited to a Congressional roundtable to discuss SARS. He and the other speakers unanimously urged the US to engage more closely with China in the areas of public health and biotechnology. Some proposed the US should respect China’s “sensitivities” and refrain from too harshly criticizing the regime over its agreed deficiencies (lack of transparency, misinformation, bureaucratic dysfunction). No-one refers to a suspicion of bioterrorism.

But Huang again hints at the more general concerns about China’s interest in bioweapons.

“China is listed by the U.S. government as one of the countries of greatest concern regarding biological weapons proliferation. This led former U.S. President Bill Clinton to conclude: “The weakness of great nations can pose as big a challenge to America as their strengths.” While the rise of China as a belligerent superpower is not in the interest of the international community, the collapse of China into a “messy state” or “failed state” can be equally dangerous, given the sheer size and strategic importance of this country.”

Huang provides some insight into the factional wranglings among the senior leadership of the CCP and the PLA. Hu Jintao became CCP Secretary-General in November 2002, and President of China on March 15th, 2003, but he didn’t automatically assume command of the PLA. His predecessor Jiang Zemin retained the position of Chairman of the Central Military Commission until he voluntarily resigned in September, 2004.

So when, on 17th April, Hu Jintao ordered a new approach to SARS - demanding full transparency of the situation, and aggressive control measures - the PLA did not immediately comply. They awaited the command from Jiang Zemin.

“The military not only refused to divulge important statistics to the Ministry of Health on SARS cases, but also failed to extend its support to the nationwide campaign until April 28. Jiang’s order on April 28 to mobilize military health personnel is significant in that it suggests the lack of authority of Wen Jiabao and even Hu Jintao over the military. With the rise of the military as an independent force in Chinese politics, the traditional party-state dualism seems to be increasingly replaced by a triumvirate of state, military, and party institutions.”

Richard Fisher of the Jamestown Institute was a credible proponent of a bioweapon origin. He pointed out that, despite China’s signing of the Biological Warfare Convention, and official denial of an offensive bioweapons program, there was evidence suggesting otherwise.

“China does declare that it has research facilities devoted to “defensive” biological warfare. And a possible interest in biowarfare is, at the least, demonstrated by the large number of articles in PLA military medical journals on viruses like Equine Encephalitis, plague, tularemia, and cholera. In addition, Alibek [Soviet bioweapons expert who defected to the US] refers to Russian reports suggesting that Russian biowarfare specialists may be trying to sell their knowledge to China.”

Fisher urged caution, and to await the outcome of scientific investigations.

“Although it might be tempting to give China the benefit of the doubt, that could prove dangerous. China’s long record of failing to honor arms control commitments justifies a skeptical attitude toward its willingness to meet commitments in the area of biological warfare. The Chinese leadership’s paranoia, which led it to suppress reporting of and information about SARS starting last November, justly raises questions as to whether China may also be hiding a military-related disaster. Indeed, many Chinese harbored exactly this suspicion… As of late April, it remains impossible to conclude from the reported scientific research that the SARS virus is related to a man-made, or indeed, a military program. The key remaining question in this context involves the precise animal origin of this virus. If that animal source cannot be determined, then Kolesnikov’s suggestion that it is man-made deserves investigation.”

Over two decades later that animal source remains elusive, the evolutionary trail is incomplete and disputed, the scientific investigation - led by WIV and AMMS - is compromised by fraud. But this not how the public or the Washington commentariat perceives it. For most, the matter was settled in late April 2003.

Why there was such haste to declare SARS natural? When George Bush spoke to Hu Jintao on April 25th, he was grateful to Hu for having brought North Korea to the table for nuclear disarmament talks. That had been another looming confrontation for which there was little appetite. Bush offered Hu “any possible support and assistance” in dealing with SARS. The US understood the tension between Hu and Jiang Zemin’s faction which still controlled the PLA. Jiang was a close ally of General Chi Haotian - who officially retired in March 2003, but remains a powerful influence over the PLA to this day. Jiang and Chi were together responsible for the brutal military response at and after Tiananmen Square. Chi is reputed to be a proponent of biowarfare, an aggressive ethno-nationalist and expansionist. The day after the Bush-Hu call, articles started appearing in newspapers-of-record promoting (without evidence) a natural origin of SARS. Three days later Jiang appeared to back down from his stand-off with Hu over SARS - eventually resigning his military leadership quietly.

Coincidence?

My speculation is that a deal was made. The US would overlook the terrorism - assessing it as the plot of an extremist PLA faction, not the new civilian regime. They would increase their support for the civilian Chinese state under Hu. The hardliners were offered forbearance for past misdeeds in exchange for a smooth transfer of power.

All’s well that ends well. By early June, Hank Paulson, CEO of Goldman Sachs (later Treasury Secretary under Bush) was in Beijing touting for business, singing the praises of China’s leadership, encouraging the people in their heroic struggle against SARS (by then almost won). Sino-US relations seemed stronger than ever. The US and other Western nations committed to help China hunt for novel pathogens, to fund and train their scientists, and to help them construct new biosecurity labs - such as the Wuhan BSL-4. The search for the origin of SARS continued for many years led by the Wuhan Insitute of Virology and AMMS ,with the assistance of international collaborators: Institut Pasteur, CSIRO and EcoHealth Alliance. The terrorism potential of SARS was immediately recognized so, despite its disappearance from the world, research into it continued with that as justification.

The “hardline faction” in the CCP never truly relinquished power. Hu Jintao himself can hardly be considered moderate, having been promoted because of the brutal repression he oversaw in Tibet. The aged Chi Haotian still lurks in the background and seems to have been involved in some way in the recent purges of senior PLA officers. The authors of “Unrestricted Warfare” published a call for a national crisis-management system that would have powers to overrule government authorities, co-ordinate international efforts, and control the media. A blueprint for the recent WHO treaty?

Civil-Military Civets

The day of the politburo meeting, the PLA’s Academy of Military Medical Sciences and CAS Beijing Genomics Institute uploaded to GenBank the sequence of a virus they claimed was isolated from a SARS patient directly connected to one of the index cases in Guangdong. The sequence had a unique genetic feature - an additional 29-nucleotides. In a paper announcing the discovery, they speculated that this virus was close to an original variant that had been transmitted from an unknown animal host. They claimed the 29-nucleotide insert contained a shorter sequence that matched one from the human genome. They speculated that this had hindered replication in humans, and once deleted the virus was better adapted for human spread.

If true, this would represent an astonishing evolutionary lucky break -for the virus. It is similar to the way, SARS-CoV-2 purportedly gained a 12-nucleotide insertion creating a furin cleavage site - immediately before entering the human population. Insertions and deletions happen relatively infrequently in nature. For them to occur at such advantageous sites - within just one or two human transmissions - is remarkable.

They didn’t have to wait long to find a matching genetic signature in animals. Two HKU scientists Yi Guan and Bojian Zheng were invited to Guangdong to help local authorities in the search for an animal host. Working with Shenzhen CDC they sampled live animals that were being sold for food in markets. On May 23rd, 2003 they announced they had sequenced genomes of a virus very similar to SARS - but which had the extra 29 nucleotides. Positive samples were taken from 6 civets and a raccoon dog.

The civet news was announced by WHO and widely reported internationally. It quickly cemented in the minds of most non-experts that SARS came from civets, and that an artificial origin had already been ruled out. US politicians and commentators showed little inclination to question it. Within a week Goldman Sachs’ CEO (and later Treasury Secretary) Hank Paulson was in Beijing praising China’s leaders and touting for business. Participants in a Congressional roundtable recommended the administration offer China more assistance in bioscience and public health, and refrain from harsh criticism of their earlier secrecy and inaction. That advice was redundant. President George Bush had already offered any assistance needed and praised China’s handling of the crisis in a call to Hu Jintao. Bush was grateful for Beijing’s help in persuading North Korea to attend nuclear disarmament talks. It was an unconducive atmosphere for accusations of terrorism to emerge.

But for scientists, the case was far from closed. Another group from China Agricultural University in Beijing sampled far more widely - 76 farmed and wild civets, 54 other wild animal species, and 11 farmed species. Finding no trace of SARS, they challenged the HKU group’s claim. Their results were not so widely reported.

It’s important to stress that at no point was there an enquiry into the possibility of terrorism (or any sort of artificial origin). It’s unlikely precautions were taken to ensure that samples couldn’t have been deliberately contaminated with viral RNA, or sequence data fabricated. It’s simply not the way academic scientists are used to working. Unfortunately, there’s no practical way to verify sequence data, and no way for independent scientists to reproduce results. To do so might require being at the same location, sampling the same specimen, at the same time. When sampling the same bat colony a few weeks apart, scientists sometimes report entirely different results - perhaps finding nothing at all, where others claimed to have made important discoveries. But “absence of evidence is not evidence of absence”. Scientists are reluctant to cast doubt on a colleague’s work or integrity without solid evidence. On the other hand, tens of millions of people recently died of a SARS-like coronavirus, and our understanding of its origin is based on unverifiable data from Chinese state and military institutions. Is this trust-based system fit for the purpose of attributing potential acts of bioterrorism or biowarfare?

HKU’s Department of Microbiology was closely involved in the SARS investigation and was afterwards subsumed by the PRC. It was designated China’s State Key Laboratory for Emerging Infectious Disease. This came with extra funding from the PRC government, and collaborations with mainland institutions including WIV (designated the State Key Lab of Virology), and AMMS (State Key Lab of Pathogens and Biosecurity). During SARS-CoV-2, this HKU group collaborated on pangolin coronaviruses with AMMS.

Institut Pasteur assists the PLA - then loses all its samples

The civet claims were controversial even among scientists with a natural origin leaning. There was no evidence that civets were a reservoir species - that would require showing SARS was circulating in farms. It was instead possible that they were an intermediate host infected by an as yet unknown reservoir species, or even that humans had infected civets, rather than vice versa. The WHO managed to win agreement from Beijing that foreign teams could participate in an expanded origin search, but the scope of the investigation had already been restricted to natural causes.

Institut Pasteur was one foreign institution invited. Their scientists worked alongside the AMMS in Beijing. One joint paper looked at the molecular evolution of the virus in the Beijing outbreak, noting that the same series of mutations had occurred in Beijing as in Guangdong and Hong Kong. The evolution occurred independently (convergently) in isolation from the outbreak elsewhere. This allowed them to speculate the mutations were an artifact of the process of adaptation to humans.

This study was based on just 45 samples from 29 patients. Institut Pasteur had somehow accumulated thousands of samples which they had sent to their Paris lab. In 2004 sequencing so many genomes was impractical, so there are only around 200 SARS genome sequences in total. But with the new technology of Next Generation Sequencing (NGS) being introduced, it would soon become possible to analyze them all, to more completely understand the epidemiology and evolution of SARS.

In April 2014 Pasteur announced they had “lost” 2349 SARS samples stored in their Paris lab. In a bizarre incident, a freezer used to store the samples securely had broken down. The samples were then transferred to a temporary freezer in a less secure area, accessible to several different research groups. Vials of SARS first went missing a few at a time, before the remainder disappeared all at once - including the freezer. The case prompted public anxiety and a judicial enquiry but was never solved.

Recently, scientists from Institut Pasteur sequenced a polio isolate they had stored for over 60 years. To their surprise it matched a sequence WIV claims to have isolated from a child in 2014. Might this have come from the same freezer?

In a recent echo of this incident, hundreds of samples of dangerous bat viruses such as lyssavirus and hantavirus went missing from a Queensland government facility in 2021. Just as in the Pasteur incident, it occurred after a freezer broke down in a secure storage area and the samples were transferred elsewhere in the complex where control of access and documentation was less rigorous. The breach wasn’t reported for over two years. A small enquiry, led by a former Supreme Court judge, is ongoing.

Institut Pasteur also became deeply involved with WIV in this period. The Wuhan P4 lab was conceived as a joint Sino-French project. It was originally planned for Shanghai, but the site was thought too populous. The intention was that Institut Pasteur would have a permanent presence at the lab, for that purpose Institut Pasteur Shanghai was founded as a joint venture with WIV’s parent organization CAS.

More about Institut Pasteur and other French involvement here.

The SARS epidemic was effectively over by June 2003, but in December 2003 and January 2004 four new cases were reported in Guangzhou. Civets were again sampled and a nearly identical strain was claimed to have been found almost immediately. This led to the slaughter of thousands of civets, in markets and farms. A subsequent paper listing several Institut Pasteur authors, purported to strengthen the link to civets. Both the human and civet strains have the additional 29 nucleotides, and the authors propose this led to its relatively mild symptoms. Lurking among the long list of authors are several AMMS officers, all of whom are concealing their military affiliations.

After these events, SARS disappeared from the world (aside from labs) and hasn’t been reported since - in civets or humans (aside from lab leaks). This is unique in the history of infectious disease. The only precedent for the complete eradication of a human pathogen is smallpox, which required a 20-year intensive global campaign - armed with an effective vaccine.

But most international scientists still didn’t accept that civets were the culprit, and the origin search continued.

Batman arrives on the scene

Another collaboration was formed between Australia’s CSIRO, US-based EcoHealth Alliance and the Wuhan Institute of Virology (WIV). WIV’s Zhengli Shi is sometimes referred to as “batwoman”, but before SARS she studied viruses of marine crustaceans. Linfa Wang, a former Chinese national who led a team based at CSIRO’s BSL-4 lab in Geelong, was already a bat virus expert - as were his team. Was this group assembled because bats were already suspected? If someone had a hunch, it proved correct. It didn’t take long before this collaboration found and sequenced the first bat SARS related coronavirus (Rp3) which was sampled in Guanxi province. The HKU group announced their discovery of a similar virus (HKU3) in Hong Kong, at almost the same time.

While there is no doubt Rp3 and HKU3 are related to SARS and very similar through much of the genome, there is a catch. The important spike gene is different. In particular the Receptor Binding Domain (the part of the spike that binds to the host cell and so determines which species, organs and tissues can be infected) is shorter than that of SARS, and structurally different. As a result, Rp3, HKU3 and other bat viruses subsequently discovered in Southern China are unable to bind ACE2, the cellular receptor of SARS.

A few years later, a group led by well-known German virologist Christian Drosten discovered a virus in bats sampled in Bulgaria (BM48-31). This virus is quite different to SARS through most of the genome, yet surprisingly it had an RBD that was closer to SARS than any virus yet discovered in China. More recently, other viruses have been discovered in the UK, Russia, Uganda and Kenya that also have an RBD closer to SARS. SARS appears to be constructed of a Chinese lineage bat virus, with the RBD replaced with something like the RBD of an Afro-European lineage bat virus. How is this possible when tiny horseshoe bats are capable of only short migrations of perhaps a few kilometers? Although distantly related, the two viral lineages likely evolved in isolation from each other for centuries or longer.

Assuming somehow a rendezvous of the two lineages occurred, there are two ways genetic information might be exchanged between them: in a lab by editing the genomes to make a chimera, or in nature by an evolutionary process called recombination. The mechanism of coronavirus recombination wasn’t well-understood at the time, and there are still many unresolved questions. What is broadly agreed is that it can only occur when two viruses infect the same host, and the same host cell. During the replication process, the replication apparatus (RdRp) occasionally pauses. When it resumes it can switch from the RNA strand of one virus to that of another. The resulting virus is a hybrid of the two

But the devil is in the detail, and this is where controversies arise. At what locations in the genome do the crossovers (or breakpoints) from one virus to another occur? Do they occur randomly, or are they determined by structures or motifs (patterns) in the RNA? How frequently? How many times during the course of a replication might the strands be switched - one, two, or several? How similar do the viruses need to be to each other?

In late 2007, the WIV/CSIRO group ran an experiment in which they created chimeric spike proteins consisting of the spike of Rp3 with various lengths of the SARS RBD replacing the corresponding region of Rp3. The goal was to determine a minimal region to make a spike able to bind the human ACE2 receptor. The region they found to be optimal was that between amino acids 310 to 518. Make a mental note of these numbers, there may be a test!

Soon afterwards, a Baric-led UNC/Vanderbilt team went a step further, creating a chimeric live virus consisting of a consensus bat virus (based on HKU3) with the RBD replaced with that of human SARS. They determined this artificial virus was capable of infecting human cells and causing disease in mice. This group elected to use the region of SARS RBD bounded by amino acids 319 to 518. These bounds were chosen based on earlier experiments binding various fragments of SARS RBD to ACE2.

The hypothesis justifying these experiments is that there is the possibility two viruses might infect the same bat. One with a human infectious RBD could recombine with another non-human infectious and creates a novel virus that might be human infectious. This idea should have aroused more scientific debate because it conflicted with a widely accepted understanding of recombination.

• Why should crossovers happen precisely at the boundaries of the RBD as estimated by scientists? It was widely accepted that breakpoints occur at effectively random locations. Indeed, this is supported by recent observations of recombinant SARS-CoV-2 variants.

• Replacing a finite region such as the RBD requires two crossovers. But it was known from experiment that single crossovers are far more common. Again, this is supported by observations of SAR-CoV-2 recombinants.

• Why would an RBD that enables human respiratory transmission have evolved in a bat enteric virus? This question is even more pertinent to SARS-CoV-2 where that transmission is extraordinarily efficient.

There is also quite some diversity in the genomes of various horseshoe bat species. In 2008, it was shown that SARS RBD couldn’t bind the ACE2 of Rhinolophus pearsonii, the host of Rp3. That seemed to rule out that SARS could be formed by a recombination involving Rp3. WIV now claimed they had previously misidentified the host species of Rp3. It had actually been R. sinicus, they declared, whose ACE2 they had recently sequenced and shown could bind SARS. Problem solved, but this would cause further complications. R. sinicus has a range limited to China so how was the recombination with an Afro-European lineage virus possible? This gap in the evolutionary trail was later filled by AMMS Colonel Changchun Tu who claimed to have discovered a SARS-like virus in another species (R. ferrumequinum) with greater range.

CSIRO hosts WIV’s “gain of function” experiments, then loses all its documents

It is not widely known that in 2011 a scientist from the Wuhan Institute of Virology, interned at CSIRO’s BSL-4 lab in Geelong attempted to engineer a live chimeric virus based on Rp3, with the RBD of SARS. This work was never disclosed. I discovered it serendipitously in a response by CSIRO to one of my FOI requests.

After seven FOI applications to CSIRO, they haven’t been able to provide me a single document from their 14-year collaboration with WIV directly relevant to their work on the origin of SARS. Yet this was the primary focus of their collaboration and resulted in over a dozen papers. They have furnished me correspondence with WIV of a more general nature and some unrelated work e.g. a study on the immune system of fruit bats, book chapters, conference invitations etc. Among hundreds of uninteresting pages, the single interesting snippet (the email above) slipped. Disturbingly, SARS related material wasn’t denied to me on typical privacy/commercial-in-confidence/too-much-work grounds, but because CSIRO claims no such documents exist. Why might this be - and why was I requesting this information?

In 2013, the WIV/CSIRO team announced they had discovered three new bat viruses in a cave in Yunnan. Two of these (WIV1, Rs3367) had an RBD that was very similar to SARS and could bind human ACE2. A third, RsSHC014, had quite a different RBD, but was later shown (by Vineet Menachery and Ralph Baric) to still be capable of human ACE2 binding and causing disease in mice. What’s more, WIV claimed they had cultured WIV1 as live virus from a bat fecal sample. This had never been accomplished before. It was big news in the scientific world, heralded as definitive proof SARS came from bats. It even resulted in some mainstream media coverage for CSIRO (though according to their FOI staff, no-one sent a single email about it).

In light of SARS-CoV-2 I re-analyzed these viruses and found that when compared to each other they were almost identical through the genome, with only the RBD materially different - almost as if they were chimeras like the Baric experiment above. There were so few mutations in most of the genome, if there had been a natural recombination, it must have occurred very recently. But most surprisingly, the crossover points are at (almost) the precise locations WIV had previously determined were ideal for making chimeras - at amino acids 306 and 518 (c.f. 310 and 518).

Were scientists just extremely accurate at predicting nature? Was nature imitating science? Or was the claim that these viruses were found in nature fraudulent? They look as if they were made in a lab, and the email above shows that they were trying to make similar chimeras in the lab. Could CSIRO documentation help support or refute their claims?

An intelligent layperson might be tempted to think that perhaps there is something about the structure of the protein that makes these specific locations ideal for a recombination breakpoint. But recombination happens at the RNA level. The replication apparatus knows nothing about protein structure, it simply reads a sequence of nucleotides from the RNA strands and duplicates them.

Some experts argue that it’s a little more complicated. It’s true there are various unproven and sometimes competing theories involving RNA secondary structure, TRSs and other RNA motifs etc. But observational evidence doesn’t support this. The most compelling evidence comes from SARS-CoV-2, which has left us with tens of millions of sequences - a unique opportunity to study recombination. For comparison, there are only around 100 bat sarbecov genomes sequenced - most of which are published by WIV, AMMS and other Chinese state institutions. It is unwise to base general theories on these alone - or to make exceptions from principles that apply broadly to other viral families. For a more thorough discussion of recombination, please see my preprint here - or post a comment below.

There is another extraordinary feature of the WIV/CSIRO viruses. WIV1 and Rs3367 are almost identical through most of the genome (>99.9% in nucleotides), but WIV1 has an entire extra gene inserted - called ORFX. If genuinely natural, both the RBD recombination and ORFX are scientifically remarkable and have profound implications for our understanding of viral evolution.

Conversely, if scientists are wrongly led to believe that a virus can instantly acquire an extra gene, or switch RBDs in nature, this has profound implications for the misattribution of bioweapons. An extra gene could code a protein that e.g. suppresses the immune response, while an RBD switch can instantly confer human infectivity. These claims warrant intense scrutiny and debate - which they did not receive! Bizarrely, while these features are evident from the sequences, neither is discussed in the Nature paper describing their discovery.

In later work published only in Chinese, WIV claims to have discovered a virus Rs4084, that has two variants with different version of ORF8, but is otherwise identical through the genome. This implies an entire gene has been switched through recombination, precisely at its boundaries. This is another dangerous precedent enabling the misattribution of bioweapons - if it comes to be widely accepted.

My conjecture is that WIV’s objective wasn’t to design a new bioweapon agent, but to cover up the unnatural origin of SARS-1, and more chillingly to enable the misattribution of future bioweapons. WIV certainly wasn’t capable of engineering SARS-1 in 2002, and though more proficient in genetic engineering by 2019, I doubt it had the capability of engineering SARS-CoV-2 (which is, in my view, a more sophisticated work than just a bat virus with an FCS insertion). At least, it’s unlikely WIV could engineer SARS-CoV-2 alone - but perhaps in a military-civil fusion collaboration with AMMS.

I had expected that WIV’s long-term collaborators CSIRO would retain some documents and correspondence that could provide clues that could either support or refute their claims. It’s hugely disappointing that they either retain nothing, or are lying to the public about what they have. It isn’t necessary that they accept my theories, their obligation is to store government documents securely and comply with reasonable FOI applications.

In an interesting coincidence, at almost the same time WIV’s viral sequences were published and the Nature paper went to press in November 2013, CSIRO was the target of a data-security incident. This was investigated by Australia’s intelligence service, ASIO, and the Australian Federal Police, and was escalated at diplomatic levels. A CSIRO scientist, a Chinese national, had failed to show up for work one day, or ever again - eventually resurfacing in China. Police interviews with his colleagues and supervisors showed that he didn’t seem competent in his role. What data was stolen - or deleted - was never determined. I suggested to CSIRO executives this incident may be connected, but they were dismissive. Yet they are still unable to explain why they retain no documents.

In 2003, with optimism high that China might open up and reform its political system, there may have been few objections to partnering with WIV, even if wrongly presumed to be a public health investigation. Facilitating WIV’s gain of function research was stretching it, there was no justification for such experiments - the hypothesis had already been proved. Partnering with AMMS - who were known at the time to have offensive bioweapon ambitions - is less justifiable. Depressingly, CSIRO have proven unwilling to re-assess their past collaborations, or re-examine the work they produced. In not furnishing documents they have forsaken democratic standards of transparency and accountability, and a fundamental principle of science: that extraordinary claims can be independently scrutinized - if not entirely reproduced.

In May 2020 the then head of ADCP, Trevor Drew, was interviewed about CSIRO’s engagement with WIV. He blatantly lied that the work was of a general nature relating to bat immune systems, after prompting by the ABC interviewer that perhaps the work had been about the origin of Hendra (from 2:17).

CSIRO has faced criticism for other joint ventures with China e.g. with CETC - a Chinese state-owned defence manufacturer, a cybersecurity JV with Shanghai Jiao Tong University notorious for training hackers, CSHOR - a JV with Qingdao National Marine Laboratory set-up to map the ocean floor around Australia either for addressing climate change - or submarine warfare (depending on who you ask). CSIRO pretends to be a science organization acting in Australia’s interests but apparently has no concern for our national security or democratic values.

The CCP corrupts all and degrades our trust in institutions.

Even among “lab-leakers” who believe SARS-CoV-2 was artificial, I encounter resistance to the idea that SARS-1 was also artificial. Most are content to use SARS-1 as a natural origin baseline from which they can distinguish SARS-CoV-2. Compared to the latter it superficially appears more like a zoonosis might be expected to unfold. There are (purportedly) multiple introductions from wildlife, a known intermediate species which exists both in the wild and is farmed (civets), and a reservoir species in bats. There are problems with all of this - not least that those who established the scientific case for a natural origin of SARS-1 (particularly WIV and the Academy of Military Medical Sciences) are the same as those now under suspicion of involvement in SARS-CoV-2. Nonetheless few lab-leakers are motivated to look into it. Some of this reluctance is undoubtedly due to fear they will be labeled incorrigible conspiracy theorists

At the time SARS broke out in late 2002, the threat of bioterrorism wasn’t considered a conspiracy theory - it was very real and front of mind. It had been just over a year after the September 11th, 2001 attacks, and the anniversary raised fears of a repeat attack. 9/11 was followed - just a week later - by the anthrax letters. These were acts of bioterrorism which intentionally referenced 9/11 to heighten the psychological impact of what were otherwise low casualty incidents (just 5 deaths resulted from 22 infections). Although the FBI might argue otherwise, these attacks remain unsolved - but there is near universal agreement they are unlikely to have been the work of jihadists.

With the invasion of Iraq imminent, terror threat levels were being raised around the world. On Feb 9th, 2003, Hong Kong’s South China Morning Post (SCMP) published a piece “HK’s terror-risk elevated as war looms” noting the official assessment level had been raised from Low to Moderate. While politicians continued to reassure that the threat was low, police investigated leaflets distributed near Kowloon mosque, that were sympathetic to Bin Laden and proclaimed a “Terrorist New Era”.

Rumours of bioterrorism at a World Trade Center

Two days later, SCMP carried a story “Panic grips Guangdong as mystery pneumonia-like virus kills 6”. This mystery atypical pneumonia would later become known as SARS. Buried near the end, of the story with the suggestion that it might be “wild speculation” an incident is mentioned in which 200 people became sick and 30 died after being exposed at Guangzhou’s World Trade Center.

SCMP never used the word bioterrorism in their article, but a piece published in BMJ by two British expats living in Guangzhou did, describing the incident as a “rumour”.

“Another rumour was that a hundred people had been struck with the mystery illness at the World Trade Centre building in the center of Guangzhou, escalating fears of legionella or even bioterrorism. The center’s managers responded by disinfecting the whole building, and they subsequently vaporised white vinegar through its ventilation system”

But what is a rumour? In mainland China any reporting at all into the mystery disease was denounced as rumour-mongering. Early reports by local press to report on the disease were quickly taken down. Healthcare workers and officials were also kept in the dark, resulting in many needless nosocomial cases. In late January, provincial health authorities received a document labeled Top Secret from a central government health committee. For some days it sat unopened as no-one had the necessary clearance to read it. When eventually someone was found to read it, it contained information on the spread of atypical pneumonia in the province and instructions for responding to it. Hospitals were advised to be on the alert for cases, any regional cases were to be transferred to designated hospitals in Guangzhou. But in the Lunar New Year period during which many people travel, the public wasn’t to be informed.

With no official or media comment, information instead spread by word-of-mouth, text message, email - so while everything might be regarded as rumour, some was verifiably factual (such as the large number of cases among healthcare workers). These “rumours” weren’t all being circulated by superstitious peasants in rural backwaters. Guangzhou is one of China’s four Tier 1 metropolises. Wealthy professionals and expats alike were withdrawing their children from the foreign schools, causing some to close. Southern Weekly, a Guangzhou paper with a reputation for fearless coverage in the face of government censorship published an article citing data from Guangzhou Mobile, that appears to be saying the text messages contained similar or identical content, with over 40 million messages a day being sent. This suggests an orchestrated campaign to fuel fear, rather than spontaneous mass hysteria. One standard message was “Since the Spring Festival, there have been many fatal cases of influenza pneumonia in Guangzhou, and several patients have died in several hospitals”. Whether or not intended, the effect was to deter people from attending hospitals (the first place Chinese people go for medical treatment). In April the editor-in-chief of Southern Weekly was removed and replaced with an official from Guangdong’s propaganda department. In May, Southern Weekly was accused of having published “state secrets” related to SARS. Days later authorities claimed to have implemented a tracking system to catch “rumor mongers” sending mass text messages about SARS.

The WHO office in Beijing received a report from an expat in Guangzhou suggesting that 100 people had died in a single week of this mystery illness. This appeared to be confirmed by Guangzhou City Health Bureau who on February 11th issued a press release announcing 100 deaths of atypical pneumonia. Later the same day this was contradicted by China’s Ministry of Health. They announced that 305 cases of an atypical pneumonia had been recorded, resulting in just 5 deaths. More than 100 of these cases were in health care workers. The pathogen was still unknown, but wasn’t anthrax or avian influenza. Guangdong’s provincial health department added that it was under control, case numbers were falling, and the disease was not as serious as rumored.

It is important to understand that the mode of transmission of SARS was - in most cases - by larger respiratory droplets (released by coughing) or fomite (mouth-hand-mouth), and required the source to be symptomatic. This is unlike SARS-CoV-2, which is often transmitted by aerosol, even from asymptomatic cases. These attributes account for the vastly different scale of the epidemics. While SARS traveled to 31 countries, only ~8500 cases were ever documented. Many cases likely went unrecorded as they were asymptomatic, but even assuming tenfold higher case numbers doesn’t radically alter the picture. There have been perhaps a billion or more SARS-CoV-2 cases, and it continues to transmit in nearly every country. SARS was completely extinguished from the world within months. Nosocomial transmission was a problem at first, but with awareness and basic infection controls implemented, SARS wasn’t difficult to bring under control. This feat was repeated in countries around the world. Spread within the community was also limited, close contact was needed, many cases transmitted no further even when undetected.

But there are a handful of “super-spreader” incidents in which airborne transmission of SARS does occur. These are critically important to the epidemiology - particularly the spread to other countries. The Guangzhou WTC may have been the first of these (if we could be certain it happened). But even if it was only a rumour, that in itself is interesting. Was that rumour planted for a reason? Why the World Trade Center, was it a deliberate attempt to link it to September 11th? On its own alone, it may have just seemed a coincidence, or perhaps a symptom of mass hysteria. But the next major super-spreader incident would have a verifiable link to 9/11.

What happened outside Room 911?

On 21st February, Dr Liu Jianlun, a retired professor from Sun Yat-Sen Medical University in Guangzhou travelled to HK for the wedding of a nephew. At 5pm he checked into Room 911 of Kowloon’s Hotel Metropole. Although a few contemporary media articles mentioned the room number, none assign any more meaning to it than a curious co-incidence. But it is a very unlikely coincidence - the Hotel Metropole had 487 rooms.

During Liu’s overnight stay he managed to infect 20 other people on the 9th floor with the mystery disease. Five subsequently died, and some went on to seed outbreaks in Singapore, Vietnam, Canada and elsewhere in Hong Kong. In all, over 4000 cases have been traced back to his brief stay at the Hotel Metropole. But just as curiously, no-one else in the hotel was infected, guests on other floors or in the lobby, or even the staff who cleaned his room.

The WHO sent a team of Canadian environmental forensic specialists to investigate. They found traces of SARS genetic material in an air-conditioning inlet, and high concentrations on the carpet outside the door to Room 911 and adjacent rooms. They found no trace inside any of the rooms however, and ascertained using a smoke plume that there was a positive air pressure differential between the rooms and the hallway. Air flowed out of the rooms, not in. One clear conclusion was the spread had been via aerosol and had occurred in the hallway. But how could this have happened?

The best explanation they could concoct is that perhaps he had vomited in the hallway and staff had used a vacuum cleaner to clean it up, in the process aerosolizing it. But hotel staff hadn’t reported any such incident, the vacuum cleaner on the floor was found to have no trace of SARS, and no staff became ill. The incident remains officially unexplained, despite then HK Health Director Margaret Chan’s unlikely suggestion that “perhaps they all stood outside the elevator at the same time and somebody sneezed or coughed”.

One plausible explanation is that the incident was terrorism - but this was never considered or investigated. Although the 911 link may seem spurious, the recent bioterrorist incidents (anthrax) referenced 911, as did the Guangzhou World Trade Centre “rumour”. Moreover, it is easy and parsimonious to explain so many people getting sick at once - but only on one floor - if an artificially aerosolized viral isolate was used.

SARS may have been the wrong weapon for causing psychological terror - at least in the short term. If Sarin had been used instead, the floor might have been strewn with corpses and there would have been little doubt over the nature of the incident. But the only immediate impact was that the next day an old man took himself to a nearby hospital with symptoms of atypical pneumonia. It would be weeks before the pathogen was identified, and months before the full trail of devastation was traced back to Room 911. By then the perpetrators would have second thoughts about wanting the incident to be identified as terrorism. A natural origin narrative would instead be promoted.

The time lag also meant that several key witnesses weren’t interviewed - or not thoroughly, as they might in a criminal or terrorism investigation. Liu himself was only capable of giving a brief account before being put on a ventilator and taken to ICU. He told staff he was a retired professor, who had been working as a volunteer in a clinic attached to the university hospital. There he had come into contact with two patients with symptoms of atypical pneumonia. He had experienced mild flu-like symptoms himself a week earlier, but had fully recovered before traveling. He had taken a chest X-ray of himself and was convinced he hadn’t had atypical pneumonia but a regular seasonal flu. The day of traveling he had felt fine, had a long banquet lunch with his sister’s family before checking into the hotel.

But to someone relying on transcripts years later, many questions come to mind, which - frustratingly - may never be answered. It is never explained why Liu’s wife returned to Guangdong so quickly, leaving him to die alone in ICU. Why did three visitors purporting to be old colleagues there to pay their respects, ask for his test results, leave and never again check-up on his well-being? Why did his sister refuse to co-operate with contact tracers? Although there was a subsequent Legislative Council enquiry which took witness statements, this was primarily for the purpose of evaluating the performance of the health system. There was nothing that resembled a police investigation.

On March 15th, SCMP ran a story headlined “Terror scenarios help HK to prepare”. This piece acknowledged that bioterrorism was one scenario being prepared for “multinationals, financial houses, international schools and embassies” under a predicted surge in terror attacks if/when the Iraq invasion went ahead. This would be the last time the word bioterrorism appeared in any SCMP article for many years to come. Yet that very day the mystery pneumonia struck 24 passengers on a traditional terrorist target - an airline passenger flight.

SARS gets airborne on Flight CA112

SARS might be more notable for the number of flights that didn’t result in transmission, than those that did. The WHO retrospectively investigated 35 flights on which known SARS cases travelled and found that only 29 secondary infections resulted in total - further evidence if needed that SARS usually doesn’t transmit by aerosol. But of these 29 cases, 24 resulted from just one flight: China Airlines Flight 112 from Hong Kong to Beijing on March 15^th, 2003.

The flight from Hong Kong to Beijing is only 3 hours, not considered long enough to contract most respiratory infections (such as tuberculosis - which is considered a risk on long haul flights - albeit a very small one). The presumed index case, Mr LSK, a 72 year-old Beijing resident returning home, later died, as did 4 others who were infected on the flight. Passengers were infected many rows away, and across the aisle, while 6 of the 8 seated directly next to, in front and behind him - were not.

The passengers who contracted SARS on the flight included several Taiwanese businessmen in transit, one of whom went on to seed a new cluster there (the first Taiwanese SARS case was recorded a day earlier). Ten of the victims came from one Hong Kong tour group. They all returned home together on the same flight, interestingly, no-one else on that flight was infected. Mr LSK went on to infect family members and hospital staff, starting a new cluster in Beijing. An Inner Mongolian flight attendant was infected and on her return home seeded a cluster of 300 cases. Two Chinese officials were also on the flight though their seats aren’t identified on the manifest. They traveled on to Thailand where one of them developed severe symptoms and was hospitalized. Still sick, he checked himself out of hospital and on their return trip infected the first foreigner to die of SARS in China, a Finnish expat living in Beijing.

All five transmissions that occurred on flights other than CA112 resulted from direct contact with a source case - from passengers seated directly adjacent or contact with a flight attendant during meal service. On CA112, transmission can only have been via the airborne route. The pattern of infections has little correlation with the seat locations. It is another incident that defies simple explanation - other than terrorism. But again, if the goal was to induce terror, the dispersal of the victims and delay in symptom onset lessened the psychological impact. There was no immediate body count for media to report. While Flight CA112 led to hundreds of cases and many deaths, this was only possible to establish retrospectively after the pathogen had been identified and contact tracing completed. The next incident would be an order of magnitude larger, and this time would inflict serious psychological and economic damage to Hong Kong.

If there is symbolic meaning that can be read into this incident it was perhaps aimed at a Chinese audience, not the West. March 15th, 2003 was also the day Hu Jintao was elected President of China at the National People’s Congress. This was a foregone conclusion, he had been named General-Secretary of the Communist Party in November, 2002 (11/2). Hu didn’t immediately assume leadership of the Central Military Commission - and thereby control of the PLA. In a negotiated power-sharing arrangement, his predecessor Jiang Zemin retained that position until he voluntarily resigned in September, 2004. Chi Haotian, a close ally of Jiang, did step down as Defense Minister at the conclusion of his 10-year term but remained influential. Chi and Jiang implemented the hardline response to Tiananmen Square, while Chi has been credited with a speech calling for the use of bioweapons in a future invasion of the USA.

The scale of the SARS outbreak in Beijing was concealed by the PLA. Case numbers in military hospitals weren’t disclosed to civilian authorities, including the Ministry of Health. When WHO inspectors visited two military hospitals in Beijing, SARS patients were moved temporarily to a hotel, and returned later that evening. While the Health Minister and Mayor of Beijing were later sacked over the cover-up, no PLA officers faced consequences.

From Aum Shinrikyo to Amoy - a copy-cat apartment attack?

The Amoy Gardens housing estate comprises 19 high-rise towers each of 30-40 floors. The official story (which changed several times during the course of investigations) is that a 26 year-old Shenzhen man with kidney disease traveled regularly for dialysis at Hong Kong’s Prince of Wales Hospital, where he may have acquired the atypical pneumonia. He sometimes stayed overnight at his brother’s apartment in an Amoy Gardens tower. On the 21st March while visiting, he had diarrhea. When he flushed the toilet, virus-laden feces became aerosolized. Due to a faulty plumbing system these aerosols were carried into neighboring apartments. Ventilation systems further transmitted the plume.

Although this seems a plausible way that he may have transmitted to a handful of close neighbors, the total infected from this single event was over 320 people, scattered among 15 tower blocks. This requires not only that the disease could survive in feces, but fecal aerosols can transmit to the respiratory system, outdoors in a breeze, for distances of up to 100m. There is no known pathogen with such capability (thankfully). Authorities then suggested the infections in other tower blocks were secondary transmissions, acquired from contact in common areas of the estate. But the date of symptoms onset in all the towers was so similar, this explanation was also ruled out

Academics from China University Hong Kong thought the spread to other towers may have been by an animal vector - rats or cockroaches perhaps. Fur samples taken from rats were found to have traces of SARS, but rats themselves weren’t infected. Cockroaches were also ruled out. And again, it seems unlikely this explanation could account for the closeness of the dates the infections must have occurred, or the pattern of infections, some cases only occurred at high levels in different tower blocks. The Department of Health was criticized for keeping the official report with the locations of cases secret.

Adjacent to the estate was a high-rise construction site. One of the workers became a SARS case. Authorities discovered that the site had no toilets, workers were found to be just using the ground. There is a prevailing breeze towards the tower blocks. But it’s still impossible to believe hundreds of infections could result as far as 100m downwind.

A bioterrorism attack at Amoy Gardens may have taken inspiration from Aum Shinrikyo’s 1994 attack on the town of Matsumoto. In this less well-known incident, the cult used an improvised aerosolization device installed in the back of a converted refrigeration truck. The main components needed are a heater, pump and fan.

They parked in an empty carpark downwind and relied on a gentle prevailing breeze to waft a cloud of aerosolized Sarin into the windows and air-conditioning inlets of residents of a housing compound, killing 8 and injuring hundreds before driving away. The Matsumoto attack wasn’t immediately recognized as bioterrorism. It was blamed by police on a local resident who liked to mix his own fertilizers and pesticides (despite that it was impossible to produce Sarin from the chemicals he had). It was only after the devastating attacks on the Tokyo subway a year later that the true nature of the incident was established.

Aftermath and Enquiry

At a politburo meeting on 18th April, 2003 the Chinese government approach to SARS changed dramatically. No longer was the spread of SARS to be concealed and allowed (if not encouraged) to spread, it became a patriotic struggle to suppress the epidemic. Officials were chastised for having previously covered it up. A hand was extended to the rebellious province of Hong Kong, PPE and other medical supplies were sent. Scientists from HKU were invited to the mainland to help trace the cause of the outbreak. They very quickly reported sequencing a very close virus in samples swabbed from civet cats in a wildlife market. The PLA Academy of Military Medical Sciences had conveniently already sequenced a virus from a human patient sample with a similar genetic signature to the civets. Although it was far from the end of the scientific investigation into the origin, this seemed to prematurely cement in many minds that the cause was natural. I argue that the key evidence for this is fraudulent.

Hong Kong’s Legislative Council held an enquiry into the epidemic. HK at the time still clung to democratic traditions, so there were differing views presented, criticism of officials was tolerated, some transcripts were made available - but not all. A typical excuse (sadly also used in western countries) was to withhold documents on “privacy” grounds. Although he had long since died, Dr Liu’s room number 911 was redacted from official transcripts, along with his and other names.

There were debates between academics and the authorities over incidents like the Amoy Gardens, but the official report was withheld, even from interested experts. The WHO played some role behind the scenes and their investigators produced some intriguing revelations and raised eyebrows, but ultimately the reports they produced go out of their way to avoid conflict with official accounts. One WHO document claims terrorism had been “ruled out” by Margaret Chan - but it’s unclear on what basis since there are no references to the possibility of terrorism in any public document.

Margaret Chan was subsequently sponsored by the PRC government in her successful quest to become WHO Director-General. Her handling of SARS was criticized by elements of the media - notably Apple Daily (whose proprietor Jimmy Lai is presently in solitary confinement awaiting charges that could see him jailed for life). A particular criticism was that she pandered to mainland authorities and didn’t push them for crucial information on the situation in Guangdong. She had also been reluctant and slow to inform the public of the situation, justifying this as having to balance the impacts to business and tourism. She reportedly told a colleague that she had been privy to otherwise secret information from the mainland all along - as if that should allay their concerns.

As WHO Director-General, Chan would later deflect calls for an enquiry into the possible artificial origin of SARS (that will be the subject of a future article).

In 1999 two People’s Liberation Army Airforce colonels published a book describing a military strategy they called “Unrestricted Warfare” – or “warfare without bounds”. They recognized at the time that the US had overwhelming military superiority and were unassailable in conventional combat. They were looking for non-conventional methods that might have asymmetric payoffs for the underdog vs the hegemonic power. They saw that non-state actors had already exposed vulnerabilities, shown themselves capable of causing strategic setbacks and significant damage to societies and economies. They accomplished this with limited resources, sometimes even without violence. These non-state actors included “conventional” terrorists like Al-Qaeda, but also hackers, doomsday cults, financial speculators and drug cartels.

“The principal actors starting conflicts are no longer only sovereign states, but Japan's Shinrikyo, the Italian Mafia, Islamist terrorist groups, the Columbian drug cartel, underworld figures, financiers who control large liquid funds, psychologically unbalanced individuals fixated on a goal… can all instigate a military or non-military war. The weapons might be airplanes, cannons, poison gas, bombs, biochemical agents, computer viruses, web browsers, or financial derivatives…these attacks can achieve similar goals to military actions in forcing nations to yield to their interests and demands. They can have more destructive force than military warfare. The threats posed are diverse, and different from the past.”

In Al-Qaeda’s 1998 bombing of US embassies in Kenya and Tanzania the authors were impressed that the US had been dealt a strategic defeat, with tactical means. The safety of Americans was no longer guaranteed in much of the world – and this was accomplished with two truckloads of explosives.

“Bin Laden used a tactical level method - only two truckloads of explosives threatened U.S. national interests on the strategic level, whereas the Americans can only achieve the strategic objective of protecting their own safety by carrying out tactical level retaliation against him.”

At the time of the book’s publication, Al-Qaeda were yet to commit their most infamous atrocity - the attacks of September 11^th 2001. These would have a dramatic psychological impact on a different scale, undermining Americans’ sense of security even within the US. Again, this was accomplished without need for sophisticated weaponry – plane tickets and box cutters were sufficient.

Some have suggested Unrestricted Warfare foretells the 9/11 attacks. Osama bin Laden is mentioned frequently, and it refers to the notion that planes may be used as weapons. It doesn’t say how planes might be used as weapons, there is also a conventional hijacking model. But it’s possible it may have provided inspiration to those fanatical enough to sacrifice their own lives. Though the authors frequently describe the subjects of their study as “lunatics” or “fanatics” – it is with a certain admiration for their nefarious achievements and innovations.

They admire bin Laden’s evasion of accountability and the ease with which al-Qaeda was able to operate and finance itself through drug trafficking, arms dealing, forgery, counterfeiting, and donations from Islamists. These activities were coordinated through a network of semi-legitimate shelf-companies which operated unimpeded for many years. The Bin Laden family construction company was even contracted by the US Army to build its barracks in Saudi Arabia. In free market economies the unconstrained pursuit of private profits and individual wealth creates opportunities to undermine society - through elite capture, institutional corruption, opportunistic acquisition of technology, enterprises, land and resources.

“Prior to the major bombings at the American embassies in Nairobi and Dares Salaam which shocked the world, Osama bin Laden was not on the list of known terrorist organizations. Though he had many previous murders attributed to him, he was a "nameless hero" in the Islamic world and never boasted of them. Even after the Americans launched cruise missiles at him and issued an arrest warrant, he repeatedly denied that he was personally involved. "Concealing oneself and shielding" while complaining of an undeserved reputation are characteristic of the new bin Laden type terrorist organizations. Having learned to exploit loopholes in free market economies, they set up legitimate-looking shelf companies and banks, while engaging in large-scale drug trafficking, arms reselling, forgery and counterfeiting to supplement donations from their religious followers.”

The authors consider a wide variety of unconventional “attacks” that might be used against the west: computer hacking, smuggling and counterfeiting, espionage and IP theft, market manipulation, “lawfare”, drug trafficking, the manipulation of public opinion. Today China engages in all these activities, though they are rarely recognized as “warfare”. To an extent they have become normalized – often ignored by the media, and rarely prosecuted by overwhelmed security services. Some even see these as a legitimate form of competition for the underdog seeking to accelerate its own economic development.

“Means and methods include psychological warfare (spreading rumors to intimidate the enemy and break down his will); smuggling warfare (throwing markets into confusion and attacking economic order); media warfare (manipulating what people see and hear to lead public opinion); drug warfare (obtaining illicit profits while spreading disaster in other countries); network warfare (venturing out in secret, concealing one's identity before launching attacks); technological warfare (creating monopolies by setting standards independently); fabrication warfare (presenting a false appearance of strength); resources warfare (seizing wealth by plundering resource deposits); economic aid warfare (bestowing favors, while contriving to assert control); cultural warfare (leading cultural trends to assimilate those with different views); and international law warfare (seizing the earliest opportunity to set regulations)”

Another terrorist group acknowledged by the authors of “Unrestricted Warfare” are the Japanese doomsday cult Aum Shinrikyo, who the authors appreciate for the innovative methods and weapons used in their attacks.

“If terrorists confined their operations simply to traditional approach of bombings, kidnappings, assassinations, and hijackings, this would represent less than the maximum degree of terror. What really strikes terror into people's hearts is the melding of terrorists with new technologies that may evolve into superweapons. We already have a hint of what the future may hold. When Aum Shinrikyo discharged Sarin gas in a Tokyo subway, the casualties from the poison accounted for just a small portion of the terror. This event put people on notice that modern biochemical technology had forged a lethal weapon for terrorists whose ambition was the mass destruction of humanity.”

In the early 1990’s Aum Shinrikyo made several unsuccessful attempts at bioterrorism. In 1990 they tried to release botulinum toxin sprayed from a car driving around the government district in Tokyo. In 1993 they made a similar attempt at the time of the wedding of the crown prince, but again there were no casualties. A few months later they released anthrax spores from their Tokyo office, but used a mild vaccine strain. Nearby residents reported a foul odor, and some brown steam emitted from the building, but no fatalities occurred, and the incident wasn’t thoroughly investigated. They cultured and experimented with a variety of biological agents. A group of cult members, which included doctors, travelled to Central Africa, hoping to obtain samples of Ebola.

Aum Shinrikyo’s first fatal attack occurred in 1994. A converted refrigerator truck was parked in a stand of trees contained an improvised aerosolizing device consisting of a heater, pump and fan controlled by computer. By night, a cloud of sarin, an organic nerve agent was released, wafting on a gentle breeze towards a cluster of residential buildings. The inhabitants included three judges sitting on a case in which the cult was the defendant. The gas entered through open windows and air-conditioning inlets. Before long eight people were dead, with hundreds more needing hospitalization. This attack may have provided the inspiration for an unrecognized bioterrorist attack on Hong Kong during the SARS epidemic (subject of a future post).

The ultimate strategic objective of the CCP was perhaps articulated in a speech given by a party and military elder Chi Haotian to senior party cadres prior to his retirement in 2003. Chi was PLA chief of staff at the time of the Tiananmen massacre, a 3-star General and former Defense Minister. Chi says that the statement “development is our top priority” doesn’t only mean domestic economic development, it implies territorial expansion.

“…many comrades tend to understand ‘development’ in its narrow sense, assuming it to be limited to domestic development. The fact is, ‘development’ refers to the great revitalization of the Chinese nation, which, of course, is not limited to the land we have now but also includes the whole world.”

This isn’t mere symbolism. Chi was forthrightly discussing the colonization of the US as a Lebensraum for people of Chinese ethnicity. And how to accomplish this, in the face of US military dominance?

Biological weapons.

“Conventional weapons such as fighters, cannons, missiles and battleships won’t do; neither will highly destructive weapons such as nuclear weapons. We are not as foolish as to want to perish together with America by using nuclear weapons…only by using non-destructive weapons that can kill many people will we be able to reserve America for ourselves. There has been rapid development of modern biological technology, and new bioweapons have been invented one after another… we have not been idle, in the past years we have seized the opportunity to master weapons of this kind. We can achieve our purpose of “cleaning up” America in an instant…Biological weapons are unprecedented in their ruthlessness, but if Americans do not die then Chinese have to die. If the Chinese people are confined to our present land, a total societal collapse is bound to take place…our land has reached the limit of its capacity…If our biological weapons succeed in a surprise attack, our people will be able to minimize losses in a fight against the United States.”

Of course some will likely dismiss this as paranoid delusion, even though events we witness match what is written and spoken by senior CCP leaders behind closed doors.

While China projects an image of a rapidly developing and technologically advancing society, there is a darkness at its heart. The political system hasn’t developed as the economy has, perhaps even the opposite. Its leadership are fearful of, and fiercely resistant to change. In the face of people’s rising incomes, aspirations, and awareness of the outside world, the regime becomes ever more paranoid and domineering, tightening its surveillance and control over every aspect of their everyday lives. No-one is free, even senior CCP officials and military officers live in fear of a purge, or “corruption inquiry”.

Our inability to attribute or even debate the possibility of biological attacks is a serious vulnerability.

The documentary comes amid tantalizing (although still unsubstantiated) rumors from US, German and Italian IC sources. The media coverage triggered further action. The French Academy of Medicine declared a lab accident a realistic possibility, and a group of scientists and journalists published an open letter in Le Monde, calling for a parliamentary commission into the possibility.

The conversion wasn’t really sudden or dramatic as it seems. Some French scientists have long been open to an artificial origin - but nuance matters. An artificial pathogen resulting from some misguided, but perhaps morally justifiable motive is acceptable, but that it was deliberately designed to be a bioweapon - is not.

Arguments against a bioweapon are various: it isn’t well-targeted, would attack civilians/military alike, it is difficult to control, there’s no effective vaccine, it isn’t lethal enough for battlefield use. But this isn’t scientific evidence. These are presumptions about the objectives and willingness of a regime to engage in biowarfare (or bioterrorism), and their tolerance of collateral damage to their own people and economy. Perhaps intelligence agencies, and dissidents/defectors who lived under the CCP are better placed to assess the scenarios than are western scientists.

Institut Pasteur’s Marc Eloit is the senior author of the Banal sequences - which include the closest known bat virus to SARS-CoV-2. Eloit has always been open to the possibility of a lab origin. The Banal sequences don’t include a furin cleavage site (FCS) so they leave open the possibility one was artificial inserted. But if they are genuine (which I question) they support that several other anomalous genomic features of SARS-CoV-2 are natural. These include the receptor binding domain (RBD) - which is key to its affinity for humans, the N-terminal Domain (NTD) - which may well explain its multi-systemic tropism (including respiratory transmission and neurotropism) and ORF8, which strongly influences the immune response.

Can all this respiratory transmissibility and virulence have evolved in an enteric bat virus? That is the inherent claim of these sequences, and not one we should accept without question. Sequences (and also the files they are assembled from) are plain text files, easy for someone with expertise to fabricate. The system is based around trust in the submitter. While Institut Pasteur is a storied institution that has produced many Nobel laureates, it has also been enmeshed in collaborations with Chinese state and military scientists.

From Barefoot Doctor to B-52s

Immediately after the infamous teleconference involving Fauci, the “Proximal Origins” authors, and European scientists, Jeremy Farrar contacted a backchannel in China to discuss their concerns over an artificial origin. That was China’s former Minister of Health, Chen Zhu (at the time still Vice Chair of the National People’s Congress).

Chen is a Francophile who did his PhD and postdoc study in France. Later, as Vice President of China’s Academy of Science (CAS), he was the main driver of the project with France to design and construct the Wuhan P4 lab. Integral to this was the creation of Institut Pasteur Shanghai (IPS), a joint venture with CAS, which was intended to provide an ongoing presence of international scientists at the lab, which had been initially planned for Shanghai.

Chen’s French counterpart in overseeing the lab construction, the founding of IPS and other Sino-French collaborations was biotechnology businessman and philanthropist Alain Mérieux. Mérieux was also a long-time Sinophile and the two became great friends.

Chen and Mérieux had more recently been organizing a new collaboration on bio-surveillance at the request of Xi Jinping. This would have seen the Indochinese outposts of Institut Pasteur and Mérieux Foundation help China in the search for novel zoonotic pathogens on the other side of the Yunnan border in Laos, Cambodia and Vietnam. This would have expanded into new territory a long running project which had involved several “State Key Labs” including WIV and the PLA’s Academy of Military Medical Sciences (AMMS). But for unknown reasons this agreement wasn’t signed as anticipated.

Farrar’s conversation with Chen seems to have triggered an immediate response. The next day Tommy Lam, a former postdoc of Edward Holmes, called to tell him about the similarities of the RBD of pangolin coronaviruses to that of SARS-CoV-2. Holmes was apparently swayed by this new evidence and co-authored a paper with Lam and several members of the AMMS.

The same day, Anthony Fauci was contacted about a USD$118 million offer to fund Harvard Medical School and Guangzhou Respiratory Disease Research Center which would include a joint study the origin of the new coronavirus. This appears to have been an effort to circumvent an independent international inquiry being proposed by others. Only the first tranche of $12 million was ever received.

On February 14th the Chinese Ambassador to France Lu Shaye visited Institut Pasteur in Paris with a delegation of scientists. Ongoing and proposed collaborative projects were discussed. Institut Pasteur Shanghai was central to these collaborations.

In a twist of fate, also on February 14th, Pyotr Pavlensky, a Russian émigré known for provocative performance art released images “sexted” by the Republican candidate for Mayor of Paris two years earlier, to a now ex-girlfriend. Barely a scandal by French standards, but it was decided a new mayoral candidate was needed.

Two days later the replacement candidate was announced: Agnès Buzyn - at the time France’s Minister of Health, amid a growing health crisis. Inevitably she lost the mayoral election (it wasn’t close, she came 3rd), but had resigned as Health Minister in order to run.

Intriguingly, the recent documentary revealed she had feared an artificial origin almost from the outset, and had sent strong warnings to both Prime Minister Édouard Philippe, and President Macron.

Buzyn is no conspiracy theorist, and her concerns should not have been readily dismissed. She is a qualified medical doctor, PhD immunologist, researcher and professor. Her husband, Yves Levy, is CEO of INSERM (the French equivalent of NIH). Levy had expressed concerns about biosecurity, and potential for nefarious use of the Wuhan P4 lab long before it opened. So had French intelligence agencies.

Ian Lipkin is also a friend and colleague of Chen Zhu since the SARS-1 period. Lipkin was also involved in setting up IPS in 2004. The US Select Subcommittee interview with Lipkin revealed he and Chen were engaged in ongoing email correspondence over the origin. Lipkin appears to downplay US suspicions of a natural origin to Chen, but proposes international involvement in an origin search.

Chen’s response is to insist that WIV would have to be involved in origin collaboration, but that it might be too controversial at the current time.

France’s China boosters were unrepentant about their involvement in the P4. Former Institut Pasteur/INSERM/Mérieux director, and WIV advisory board member, Christian Bréchot, was defiant - appalled at the "rumor the virus had been manufactured" and railing against "anti-Chinese sentiment".

In May 2020, Alain Mérieux announced he would strengthen co-operation between his organizations and WIV/CAS. Institut Pasteur Shanghai announced they had recently recruited more scientists to expand the research collaboration between France and China.

What were these projects, and which scientists were involved in them?

Once scientist who seems a likely candidate is Cui Jie (another former postdoc student of Edward Holmes). While based at WIV, in July 2018 Cui uploaded ~160 partial sequences to GenBank consisting of the RdRp, ORF8 and Spike genes of ~55 unpublished viruses. But he didn’t make them public. They only came to light in 2022, after an automatic embargo expired after 4 years. They were briefly visible to all, then hidden again (however they can still be downloaded with the right accession).

One of these viruses was Ra4991 - now known as RaTG13 (for a while the closest known relative of SARS-CoV-2). But for Ra4991/RaTG13 the all-important Spike gene was missing. In June 2019, a graduate student supervised by Cui submitted a master’s thesis which described the sequencing of Ra4991/RaTG13. The thesis provided statistical comparisons to SARS and other viruses. It also included a sequence alignment of the RBDs of some 50 viruses. Once again, Ra4991/RaTG13 was conspicuously absent.

But the thesis states that Ra4991 had been fully sequenced, and it appears in a table comparing its similarity to SARS in each gene. Why was its spike sequence kept hidden?

There’s another intriguing feature to this table. Another virus, Rs8561, has almost the same nucleotide identity - in each gene - to SARS, as Ra4991 does. Rs8561 was another of the sequences Cui has kept hidden on GenBank. It turns out Rs8561 is very similar to another bat virus ZC45, even though Rs8561 is from Guangdong, and ZC45 from Zhoushan, ~1500km apart. Rs8561 and ZC45, are in turn very different to Ra4991, so is it just an uncanny co-incidence?

There are many uncanny co-incidences in this saga. Another is that ZC45 was published (by the PLA’s Nanjing Command) mere hours after the DEFUSE collaborators submitted their proposal to DARPA. DEFUSE wanted to find viruses ~20% distant to SARS, and ZC45 was the first published virus that met that criteria (it was also the first published virus related to SARS-CoV-2). Later the PLA published a paper showing it could infect immune suppressed mice - another box checked. WIV (a DEFUSE partner) in fact had 4 viruses very similar to ZC45 which would have been ideal, but they kept them secret - even when they later published papers discussing ZC45.

It isn’t clear what was intended here, but I speculate DEFUSE (had it gone ahead) was a honey-trap to misattribute the origin of a planned outbreak to US scientists. What is clear, is that Cui’s ZC45-like sequences aren’t natural. Science can tell us that - if scientists would look at sequences and trust established principles of molecular evolution, rather than the protestations of their Chinese colleagues.

Sometime later in 2019, Cui joined Institut Pasteur Shanghai. It’s likely he remained in Wuhan, while also joining Pasteur’s network. On some papers he uses both WIV and IPS affiliations, later he omits the WIV.

Banalities of Evil

In 2020, Institut Pasteur had only recently ended a project “BatMap” to search for novel bat viruses in Laos. Funded by the US Defense Department, the project began in 2017, had exceeded budget and timelines more than once, and was eventually terminated, but had meanwhile accumulated over 500 samples from bats. These samples are still in Pasteur’s possession, but none have been sequenced. Instead of sequencing these first, Pasteur decided to launch a new field trip to the same caves.

This seems a strange decision during a period of rolling lockdowns and travel restrictions. Perhaps the reason was the planned involvement of IPS. The US DoD funders may not have approved sharing the samples with an entity so close to WIV. But why didn’t they analyze these samples without involving Chinese state scientists?

Perhaps they belatedly considered that. Ultimately no IPS authors were listed on the paper announcing the Banal discovery. In July 2021, two months before their publication, Pasteur Network underwent a reorganization, and IPS was quietly excised from the network.

Nonetheless, collaboration between IP and IPS/CAS/WIV didn’t immediately cease. In another uncanny co-incidence, sequences were uploaded the evening before the Banals by another WIV/IP group, including the former head of virology at IP Laos. Despite being entirely unrelated viruses, there is unexpected homology to SARS in at least one sequence.

The fortuitousness of the Banal discovery is incredible - literally. Before 2020, besides the ZC45 group, only one SARS-CoV-2 like virus had been found (RaTG13), and that is dubious. But Pasteur claimed to have found 5 SARS-CoV-2 like viruses in the first cave they went to (but none at the other 3 sites). Banal-52 is the best known of the 5, as it can explain the evolution of SARS-CoV-2 without relying on a hypothetical recombination. Two others provide support for the widely disparaged pangolin covs, and two have uncanny similarity to RmYN02.

But they raise more questions than they answer. They suggest an evolution where there is no pressure to adapt, even as they switch between multiple bat species, pangolins and humans. They show evidence of frequent recombination at uncannily precise genomic locations, much as earlier dubious WIV “discoveries” claimed to. They have remarkably similar RBDs in bat/pangolin/human.

Some evolutionary biologists have argued to me, that nature found an optimal sequence for all. But in human SARS-CoV-2 variants the RBD is the most variable region of the genome, and even after >20 mutations is still remarkably good at binding human ACE2. The RBD needs to keep evolving to evade immune recognition. That pressure means it can’t ever settle on an “optimum”. It’s a constant game of cat-and-mouse, pathogen-and-host. If the Banals really are natural, they challenge long-established scientific understanding of molecular evolution - they challenge Charles Darwin. We shouldn’t rule it out, but Pasteur should substantiate their case with something more than plain text files of murky provenance.

Unfortunately the Banal sequences didn’t attract the scrutiny earlier sequences did, somewhat due to Pasteur’s high reputation and the unwarranted perception of their independence from China. But also because they don’t include an FCS, they don’t entirely preclude an artificial origin, and some “lab-leakers” welcomed them as more evidence in favor of this. The suggestion was made that because the new closest virus came from Laos, not China - that pointed the finger more strongly at the US (or at least the various members of the DEFUSE consortium).

Validating the Banals is crucial. If genuine we can rule out that SARS-CoV-2 might be a heavily engineered bioweapon, but should be alarmed at the potential threats from nature (SARS-CoV-2 has been shown able to transmit between humans even without an FCS ,and SARS-1 was deadly enough). For most scientists, diplomats, politicians and businesses, this is a more palatable scenario. An unfortunate accident, the remedy is relatively painless: better biosecurity, more oversight, a mild rebuke for China, but we all share some responsibility.

But if they aren’t genuine, the ramifications are deadly serious, because:

• They obfuscate unnatural mechanisms of pathogenicity and tropism that should (have) inform(ed) the safe design of vaccines and therapeutics.

• They give credence to a hoax theory of viral “evolution by horizontal gene transfer” that can be used to misattribute future bioterrorist attacks.

• They allow the culprits of a massive bioterrorist attack to go unpunished. Bioweapon development and proliferation is extremely difficult to detect. The best deterrent is unified international condemnation.

So it is important that France should participate in the investigation. But is France genuinely interested in finding out? Is there an appetite to investigate their own institutions, scientists, business leaders, politicians? French scientists I’ve been in contact with seem more interested in the US engagement with WIV, than their own. The US has taken steps to investigate itself, and these will continue. Daszak, Baric and Fauci have appeared before Congressional hearings and thousands of pages of documents have been released by FOIA. But other countries whose institutions partnered which China haven’t opened their own books. This can cause a streetlamp effect.

As Europe swings between the orbits of US and China, trade, investment, and political personalities dominate discourse. Perhaps shared values rooted in the Enlightenment should be given more prominence? China's totalitarian regime is anathema to human rights and freedoms, and open science.

Institut Pasteur eventually announced the separation from CAS had occurred in December 2022, but “discussions were ongoing” over a future partnership. Pasteur continued to be involved in the search for bat coronaviruses in Indochina, particularly Vietnam.

I will analyze these in a future paper.

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There have many curious features that our current understanding of evolution struggles to explain. Do the laws of science need revising, or could this be the result of fraud?

Please view the full story at my new WordPress hosted site.

https://covorigin.org/2023/06/30/the-plangolin-capers/

Several theories have been proposed to explain its precise composition:

1. An unconnected sequence from a bat virus - HKU9

2. A sequence from a 2017 Moderna patent

3. Human α-ENaC

4. An FCS identical to a Feline Peritonitis strain

5. A patent for a SARS vaccine

There is interesting background, and some merit to all of these, but they have in common that they seek an external source of the exact nucleotide sequence for the insert. But it isn't necessary to find an exact match in literature or a database, however appealing its simplicity. It's likely that the FCS came about through experimentation and an exact sequence or the rationale for it was never previously documented publicly.

Of most significance to me is the last paper that was submitted for publication by a team including US, Chinese, civilian and military researchers immediately prior to the pandemic: “Molecular Mechanism for Antibody-Dependent Enhancement of Coronavirus Entry”. Experiments in this paper include introducing mutations to the furin cleavage site of MERS. While the experiments described in the paper are "loss of function" in that they disable, rather than add an FCS, they demonstrate where a focus of the team's research was, as do the references listed in the article. The connection to MERS complements the other unexpected homology I've recently discovered (published on this site as "Uncanny Inserts in the N-Terminal Domain").

But most intriguing of all is the back-story. Most public and media attention has been on the collaborations between Wuhan Institute of Virology and EcoHealth Alliance, but here is another nexus of US/Chinese collaboration that deserves more attention.

A Marriage of Convenience

The "Molecular Mechanism" paper brings together researchers from:

• University of Minnesota (UMN) (senior author Fang Li)

• The PLA’s Academy of Military Medical Sciences' a.k.a. Beijing Institute of Microbiology and Epidemiology or State Key Lab of Pathogen and Biosecurity (AMMS) (senior author Yusen Zhou)

• New York Blood Center (NYBC) (senior author Lanying Du)

• Wuhan Institute of Virology (WIV) (senior author Zhengli Shi).

Why is New York Blood Center 's Lindsay F Kimball Research Institute (NYBC) involved in a research project with the PLA's Academy of Military Medical Sciences (AMMS)? The proximal reason is that NYBC's Lanying Du was married to now deceased AMMS Professor and PLA General Yusen Zhou, and they had also been involved in many research collaborations over the years. But there is a longer history to this partnership.

Between 2005-07 Lanying Du was based at Hong Kong University’s Department of Microbiology where she completed her PhD thesis on the function of the SARS spike protein. But her relationship with Yusen Zhou began earlier, likely in Beijing, as the dedication on her PhD thesis suggests:

Her supervisor at HKU was Bo-Jian Zheng who, with Guan Yi, had led the effort to prove that civet cats were the proximal cause of SARS via a zoonotic spillover in a Guangdong market (there have been doubts over that theory almost from the start). Zheng and Yi worked closely with mainland institutions on the project, and they began to move into the orbit of the PRC state. In 2005 their HKU Microbiology lab was named the State Key Laboratory for Emerging Infectious Diseases, the first lab to be designated such outside mainland China. They began to receive direct funding of USD$5m/year from the PRC government, allowing a major expansion. In 2006, Bo-Jian Zheng became a guest professor at AMMS.

Lanying Du appears on at least one paper with an AMMS affiliation of her own, it's not clear what her military background is prior to this.

Lanying Du and Yusen Zhou collaborated frequently with Shibo Jiang, who was then based at the New York Blood Center. Jiang received funding from China's "973" program which sends Chinese scientists out into the world, to gain knowledge to advance China's strategic technological ambitions. Jiang occasionally also used a Fudan University affiliation.

In 2007 Lanying Du moved to NYBC, while continuing to author papers with her husband and others with AMMS affiliations. Another colleague Yuxian He states his affiliations as both AMMS and NYBC. Chinese military connections appear no barrier to employment at NYBC.

In 2013 Lanying Du and Shibo Jiang were involved in a paper in which a 12 nucleotide FCS (encoding RIRR) was inserted into a DNA sequence. The protein isn't viral, and the other authors are from a peripheral field. Perhaps this is what makes it interesting. Their role is largely as observers (Du is listed as editor) and suggests their interest in the genetic engineering techniques, rather than the specific clinical applications.

Fang Li’s undergraduate education was at Peking University and after graduating in 1996, he has studied and worked only in the US. Unlike Jiang he has never sported a Chinese institutional affiliation, or received funding from the 973 program. After post-doc at Harvard, he has been solely at University of Minnesota.

The first collaboration between Fang Li, Lanying Du, Shibo Jiang and Yusen Zhou is in 2014 when they produced 3 papers related to MERS. Ralph Baric from UNC is involved in one of these identifying DPP4 as MERS receptor. In another Chien-Te K. Tseng from UTMB's Center for Biodefense and Emerging Disease works alongside 6 AMMS researchers including Yusen Zhou.

In 2015 a team which included Zhengli Shi, but without Yusen Zhou, published a paper in which they introduced two mutations into the MERS related bat virus HKU4. They conclude these would be sufficient to allow it to transmit to humans. One of these mutations (S746R) creates an FCS in HKU4 in the same S1/S2 position. It is similar to MERS in that it is non-canonical i.e. it contains the minimum R-X-X-R motif an FCS needs (where X is any amino acid), but not the more optimal R-X-R-R which has an additional R in the third position. SARS-CoV-2's FCS (R-R-A-R) is also non-canonical. Though it contains 3 Rs, it has one in the second, not third position.

Fang Li Emails

We get a glimpse of the working relationships from some of Fang Li's emails obtained under FOIA by US Right To Know. It's difficult to say if these exchanges are directly relevant to the origin of SARS-CoV-2, as much has been redacted, but they suggest a pathway that intellectual property and possibly viral samples and isolates may have been transmitted from US institutions to the AMMS.

In one exchange Fang Li has apparently recently introduced Lanying Du to Matthew Aliota, also at UMN. A few days after making contact she asks him for a reverse genetic system that would allow her to construct a synthetic Zika virus clone. I don't wish to suggest this is a case of espionage, but it illustrates the ready availability of US intellectual property to someone who has strong PLA connections.

Ralph Baric and Fang Li in 2017 collaborated on (among other things) making a synthetic clone and chimera based on a Ugandan SARS-like coronavirus (PDF2386). Interestingly, SARS-CoV-2 has a mutation in the Envelope gene that was seen previously in African SL-CoVs, but never before in Chinese SL-CoVs (with the notable exception of ZC45/ZXC21). But again, much that might be interesting has been redacted.

Baric and Fang Li appear to enjoy working together.

Here an unidentified graduate student of Fang Li’s assists Zhengli Shi with predicting the 3D structure of the RBD of HKU2. The reference to NL63 is interesting.

It was Fang Li’s team who previously determined the 3D structure of NL63 binding to ACE2. Curiously SARS-CoV-2 has an NTD site which looks very similar to a region of the NL63 Receptor Binding Motif. I explore this in more detail in "Uncanny inserts in the N-Terminal Domain".

A NIAID grant to Lanying Du for her most recent coronavirus project suggests NIH are aware, and allow that research may be conducted on-site at the AMMS microbiology lab in Beijing. WIV is however not mentioned.

Interestingly, the abstract from this grant application states:

"Second, we will construct chimeric RBDs containing the core subdomain from one coronavirus RBD as the structural scaffold and the RBM from another coronavirus RBD as the immunogenic sites".

This sounds very similar to the structural engineering I describe in "Uncanny inserts in the N-Terminal Domain". The core structural scaffold in this case is largely residues from MERS, while the immunogenic sites come from NL63, SARS and ZC45. And although the structure is located in the NTD, rather than the RBD it likely has similar function.

The Mysterious Death of Yusen Zhou

Yusen Zhou died in May 2020, aged 54, reportedly of a heart attack. Journalist Sharri Markson reported via an IC source that:

Unfortunately nearly two years after Markson's story, none of this information has been released. After his death Lanying Du continues to work at NYBC and gain new NIAIAD funded contracts.

Peter Hotez' Denial

Peter Hotez was the Principal Investigator on a long running program "RBD recombinant protein-based SARS vaccine for biodefense". Funding commenced in 2012, and was still being extended in 2020. Hotez often subcontracted Lanying Du, Shibo Jiang and also Yusen Zhou - despite the project being related to biodefense, and Zhou belonging to a foreign military.

I managed to "interview" Hotez briefly on Twitter before he blocked me.

On Lanying Du he said:

It's not clear if she's a US citizen, and/or whether she is permanently based in the US, or even whether she might be a PLA officer like her deceased husband. Asked about Yusen Zhou's death:

That would seem a blatant lie considering Zhou is named on his project, involved in 5 publications, and is the husband of someone he admits to have known for many years and written several papers with.

I pointed out to him that AMMS had been suspected by US State Department of being involved in clandestine bioweapons development in breach of international conventions, isn't that a concern for him in his role? His flabbergasting response: "no clue what China does".

I asked him if he thought he should be across potential bioweapons development and dual-use potential if he's leading biodefense projects?

Hotez is now promoting his new book about the "Rise of Anti-Science". If there's been a loss of confidence in science, perhaps he should reflect on his contribution to that.

The FCS: MERS Homology

I will look at the molecular biology of the FCS in much more detail in the next article. That will cover advanced topics like flanking residues, restriction sites, glycosylation sites, codon choice, the structural biology behind the "Molecular Mechanisms" paper. Also I will debunk a few sequences that purport to show path of natural evolution of the FCS.

For now I just want to point out three key features that make it similar to MERS, and unlike most other known cleavage sites.

1. The presence of Proline in same relative position.

2. The absence of an Arginine (R) at P2, making it non-canonical.

3. A similar pattern of potential O-glycosylation sites (S or T) close to the Proline residue (proximity to Proline enhances glycosylation potential).

And there is nothing even close among SARS-like viruses.

For more interesting connections between SARS-CoV-2 and MERS please see my article "Mysterious Inserts in the N-Terminal Domain".

The Pradhan et al controversy marked the end of any semblance of reasonable discussion about pandemic origins and seems to have been the trigger for the infamous Fauci/Farrar teleconference. After this a lab origin became a “conspiracy theory” and a concerted effort was made to suppress discussion of the idea. Pradhan et al admitted their pre-print was written hastily, and perhaps didn’t get everything right. But they, quite sensibly, wanted to alert the world urgently to sequence anomalies they thought important for understanding pathogenesis and the possibility of an artificial origin.

They were criticized mostly because the regions of identity they found are small, and the corresponding regions in HIV are variable. HIV’s variable loops mutate even during the course of an infection within one individual (which is potentially decades long). So there are many possible HIV sequences these could match, and there wasn’t a single genome or region that was the source of their matches, but rather different regions in different genomes. Their hypothesis was perhaps over-reach, but it always came with caveats and disclosure.

But there are some things about which they were correct, that were lost in the shameful censorship and mockery that followed:

1. These are all inserts compared to sequences known at the time. The only viruses having any similarity to those regions were the PLA published sequences ZC45 and ZXC21. However, since that time new sequences (starting with RaTG13) have been published that tend to obscure this fact, and, I suspect, intentionally.

2. The regions do have homology with HIV-1’s variable loop regions, not only in the linear sequence, but structural and post-translational (e.g. N-glycosylation sites). This could also have suggested a natural explanation – convergent evolution. Sadly even this discussion was suppressed.

3. Even if sequence identity to HIV-1 was coincidental it might have pointed to important viral functions (e.g. co-receptor binding, trafficking by immune system cells via DC-SIGN/L-SIGN, mechanisms of immune evasion via evolving patterns of glycosylation) and aided the development of safe vaccines and therapeutics.

Regardless of their origin, these sites have always been of interest to researchers. They have indeed proved to be evolutionary hotspots in the formation of new immune evasive variants, and there is evidence to suggest a possible role in co-receptor and/or sialic acid binding. Somewhat serendipitously I’ve found some surprising, but perhaps more plausible, explanations for their origin – in conserved regions of various distantly related human coronaviruses.

Assessing the probability of a sequence occuring “at random”

Prior to SARS-CoV-2 there were 6 known human coronaviruses (229E, OC43, NL63, HKU1, MERS, SARS). Each has a spike of ~1250 aas for a total of 8750 amino acids. This is small dataset, so finding a small sequence of common amino acids is within it is more significant than finding it within a variable HIV region (many thousands of sequences), let alone finding it in an unrestricted blast search of Genbank (which contains >10 trillion bases). It isn’t unexpected to find a simple 5 amino acid match between SARS-CoV-2 and another hCoV at random (we’d expect to find about one every 366 positions), in each case there are circumstances that make it far more unlikely, but calculating probabilities somewhat more difficult. Further complicating any discussion on probability is that evolution isn’t random, and also that all of these inserts occur at positions that are functionally important. So any numbers mentioned are just to give a rough idea.

NTD Loop 1: A mash-up of Adenovirus D and MERS?

I featured this region in the article on SARS-1, because it seems almost identical to the first few residues of the NTD of certain types (e.g. 37, 19) of an Adenovirus D protein found to be associated with sialic acid binding causing broad tissue tropism resulting in diverse clinical symptoms including conjunctivitis, corneal infection and pharyngitis.

Interestingly the significance of this protein was featured in a paper published just a few months before the first SARS case in 2002.

In SARS-1 the homology to Adenovirus 37 is striking, and improbable. It’s simple to calculate there are 25.6 billion possible combinations of 8 amino acids. A 7 out of 8 match is more frequent but still around 1 in 200 million. And that’s without the additional stipulation of a conserved N-glycosylation site in the final residues.

In SARS-CoV-2 some residues from the Adenovirus sequence remain, but there is also interesting homology to MERS, a region identified as forming part of its sialic acid binding pocket. The homology was first identified in early 2020 by a University of Warwick team):

A paper from June 2019 paper (Tortorici et al). found a conserved sequence in coronaviruses that have been previously confirmed to bind sialic acids: OC43, BCoV, PHEV and HKU1. The sequence is different in MERS, but two aromatic amino acids – Tryptophan

adjacent to a Phenylalanine (F) – occupy similar structural positions, despite being separate in the linear sequence. At the base of this loop in SARS-CoV-2 an adjacent W-F pair is formed, that is not present in MERS.

A curious pattern in ZC45

This Tryptophan residue is one of a couple shared uniquely with ZC45/ZXC21 at this site. These sequences are of interest for their provenance (being published by a largely PLA team from Nanjing Command in 2018). Notice also in ZC45 at this site the unusual number of doublets YY-SL-TT–NN–AA and the pattern of nucleotides, with the wobble base varying in each member of a pair.

Although the homology between ZC45 and SARS-CoV-2 isn’t exceptionally strong at this particular site, its significance is best understood in context of the other sites in the NTD, and some uniquely share mutations elsewhere in the genome (such as E and S2). Viewed in totality these suggest ZC45 maybe also an engineered virus (or fabricated sequence). This has important implications regarding the intentions of the engineers, suggesting a premeditated release of the virus, with ZC45/ZXC21 intended to provide evidence that such mutations had a precedent in nature.

NTD Loop 3: An ACE-2 binding region from NL63

*Numbering reflects position within the gene sequence, not the article.

This sequence is another extended exterior loop and also is an insert compared to related bat viruses. This sequence contains a 5 amino acid sequence PGDSS which is identical to one from unrelated human coronavirus NL63 – which as with SARS and SARS-CoV-2 uses ACE2 as its main receptor.

Once again there is also homology with ZC45/ZXC21, particularly in flanking residues, that is not seen in SARS or other bat SARS-like viruses known at the time.

But it isn’t just the 5 aas of sequence identity, 13 out of 14 residues in this region match, but in a different position, (including one conservative substitution (R→K). In a loop region which is intrinsically disordered, and contains many flexible residues (such as Serine (S) and Glycine (G)) the order in which they occur is likely less important.

Most important is the location of this sequence in NL63. According to a 2009 paper (Wu et. al.), which includes Fang Li as senior author, NL63’s RBM is composed of three loops separate in the sequence but adjacent in 3D structure. The SARS-CoV-2 NTD site matches the central loop of these (highlighted below). It’s also interesting that in SARS-CoV-2, three NTD loops that are separate in the sequence, come together in a similar way in the 3D structure.