In a preliminary abstract published on September 17 in Frontiers in Public Health, Indian researchers Monali C. Rahalkar (pictured left) and Rahul A. Bahulikar say that RaTG13 (RaBtCoV/4991) was collected from the Tongguan mineshaft in Mojiang, Yunnan, in 2013.

“Surprisingly, the same mineshaft was also associated with a severe pneumonia-like illness in miners in 2012 killing three of the six miners,” Rahalkar and Bahulikar write.

“A Master’s thesis (in the Chinese language) was found on the cnki.net website which described in detail the severe illness in miners. The thesis concluded that a SARS-like CoV originating from Chinese horseshoe bats (Rhinolophus) was the predicted causative agent.”

The thesis was written by the Chinese doctor, Li Xu, who treated the miners and sent their tissue samples to the WIV for testing, and was published in May 2013.

Rahalkar and Bahulikar explain that the cases were remotely monitored by a prominent pulmonologist in China.

“The retrospective analysis of the pneumonia cases shows striking similarities with Covid-19. Bilateral pneumonia, vascular complications like pulmonary thromboembolism, and secondary infections are the main similarities,” Rahalkar and Bahulikar write.

‘The treatment regimes were similar to the currently given treatment for Covid-19. We propose that the Mojiang mineshaft and the miners’ illness cases could provide important clues to the investigation of the origin of SARS-CoV-2.”

In their full, peer-reviewed article, published in Frontiers in Public Health on October 20, Rahalkar and Bahulikar write that the striking similarities between the Mojiang pneumonia cases and Covid-19 are noteworthy, “as is the fact that RaTG13/CoV4991, the next genomic relative of SARS-CoV-2 was found in the same mineshaft”.

The two researchers write: “Although we cannot say that RaTG13 or SARS-CoV-2 infected the miners, there is a high chance that it could be a virus quite similar in genetic composition to these two.

“The coincidence between the 2012 illness in Mojiang miners, the subsequent samplings, and finding the nearest SARS-CoV-2 relative from this single mine warrants further inquiry, and the data along with the full history of this incident would be invaluable in the context of the current pandemic.”

Rahalkar and Bahulikar go into detail about Li Xu’s Master’s thesis, in which he concluded that “the pneumonia cases were due to viral pneumonia, primarily from SARS-like coronaviruses originating from horseshoe bats”.

They write: “According to the Master’s thesis, in April 2012, six miners were given a job of clearing bat waste and bat faeces from a copper mineshaft in Tongguan, Mojiang, Yunnan. After working for ~14 days in the case of four miners, and 4–5 days in the case of the last two miners, they started facing breathing problems, cough, and fever which required immediate admission to the Kunming hospital in late April and early May.

“Three of the miners died in the course of ~100 days and three survived. The thesis featured medical reports, radiological images such as CT scans, and detailed information regarding the diagnosis and treatment of the miners.”

Radiography showed interstitial pneumonia, ground-glass opacities, and severe acute respiratory distress syndrome (ARDS) in some of the patients and some showed clotting complications such as pulmonary thromboembolism or thrombosis and elevated D-dimer values.

Dr Zhong Nanshan, an expert in respiratory diseases and a national advisor about the SARS and Covid-19 epidemics, provided remote consultation for the two patients who had the most serious illness.

Nanshan’s conclusion that the Mojiang miners’ pneumonia appeared to be primarily viral and that it was most probably due to bat-related coronaviruses, is noteworthy, Rahalkar and Bahulikar say.

“Based on the detailed evidence presented in the Master’s thesis and the PhD thesis and the discussion presented here, we do not think that fungus was the primary reason for the illness,” they add.

“We think that if it was a fungal disease, only antifungals could have cured the illness. Vascular complications such as elevated D-dimer and thromboembolism are not common in fungal disease and have been observed in the miners’ illness and COVID-19. Elevated SAA (serum amyloid A) and declined lymphocytes are indicative of the fact that it was primary viral pneumonia.”

The two researchers add that, according to a translation of a PhD thesis by Canping Huang, supervised by George Gao, the “blood test results of four cases showed that: four people carried SARS virus IgG antibodies, of which two were discharged with higher antibody levels … and two which were hospitalised had lower antibody levels …”.

Rahalkar and Bahulikar pose numerous questions: “We are curious to know what kind of samples the WIV received from the Mojiang miners, along with other questions, such as whether the samples are still stored in WIV, and whether they are available for study by other researchers.

“It would also be of particular value to know whether any viruses were isolated and if there is any DNA/RNA available from these samples. It would also be useful to know if PCR was performed on the miners’ samples and available sequences.”

Other questions include “Why were the severe pneumonia cases in 2012 not mentioned in any of the WIV publications before 2020?’ and ‘Were any SARS-like CoV isolated from the bat faecal samples collected in 2012–13?”.

Rahalkar and Bahulikar also ask why the Mojiang miners pneumonia cases in 2012 were not reported to any public health agency such as the WHO and why programmes like PREDICT didn’t mention the lethal pneumonia cases as a mini-outbreak.

“Why was the Mojiang mine being visited by researchers until October 2014?,” the researchers ask. “Questions also remain as to why Dr Shi attributed the outbreak in Mojiang to a fungus in the interview with Scientific American. Was the mine open for researchers and were any samples brought after 2014?

“Did any of the researchers who visited the Mojiang mineshaft get infected by any coronavirus between 2012 and 2019? Are there any whole genome sequences available for SARS-like CoV originating from this mine?”

Rahalkar has issued a detailed critique of an addendum that has been added to the article published by Zhou Peng, Shi Zhengli et al. in Nature on February 3, 2020, entitled ‘A pneumonia outbreak associated with a new coronavirus of probable bat origin’.

The addendum was published in Nature on November 17 and provides further information about the bat SARS-related coronavirus (SARSr-CoV) strain RaTG13 referred to in the original article.

In the original paper, the researchers said they obtained full-length genome sequences from five patients at an early stage of the outbreak in Wuhan.

“The sequences are almost identical and share 79.6% sequence identity to SARS-CoV,” Zhengli et al. said.

The researchers said that a short region of RdRp from BatCoV RaTG13 showed high sequence identity to 2019-nCoV.

“Simplot analysis showed that 2019-nCoV was highly similar throughout the genome to RaTG13, with an overall genome sequence identity of 96.2 percent,” they said. The SARS-CoV-2 genome and its spike glycoprotein show 96.11% and 92.86% identities to the Rhinolophus affinis bat coronavirus, respectively.

In her critique of the addendum, Rahalkar states: “For the first time the WIV authors admit that the Mojiang mineshaft miners had severe respiratory disease. Further they also tell us that they collected the sample which they renamed RaTG13 from the same mineshaft.

“This is the first written evidence that WIV agrees that they collected a virus or a sample, which is until now the closest neighbour of SARS-CoV-2, from a mineshaft. And that the same mineshaft was the reason why the miners, or people working cleaning the mine, got ill.”

Rahalkar asks why the information presented in the addendum is coming nine and a half months after the original article was published.

“Looking at the gravity of the pandemic situation and the relevance of the information in deciphering the origin of the SARS-CoV-2, this delay is pathetic,” she states.

“None of the information in the addendum was unknown to the authors, except one test which they claimed to have done after the outbreak, meaning that this information was almost eight years or five years old, except for one assay which they claim to have done recently (we don’t know how recently).

“None of the information was given earlier despite repeated queries and comments about the original Nature article by the international community.”

The authors of the addendum state that, between July 1 and October 1, 2012, they received 13 serum samples collected from four patients (one of whom was deceased) who showed severe respiratory disease.

“These patients had visited a mine cave in Tongguan town, Mojiang County, Yunnan Province, China, to clean bat faeces in order to mine copper before being admitted to the First Affiliated Hospital of Kunming Medical University on 26–27 April 2012,” the authors state. “The samples we received were collected by the hospital staff in June, July, August, and September 2012.”

To investigate the cause of the respiratory disease, the samples were tested using PCR methods.

The samples all tested negative for the presence of the Ebola and Nipah viruses and bat SARSr-CoV Rp3 and the presence of antibodies against the nucleocapsid proteins of these viruses.

“Recently, we retested the samples with our validated enzyme-linked immunosorbent assay (ELISA) against the SARS coronavirus 2 (SARS-CoV-2) nucleocapsid protein – which has greater than 90% amino acid sequence identity with bat SARSr-CoV Rp3 – and confirmed that these patients were not infected by SARS-CoV-2,” Shi Zhengli et al. add.

Animals including bats, rats, and musk shrews were tested in or around the Mojiang cave.

“Between 2012 and 2015, our group sampled bats once or twice a year in this cave and collected a total of 1,322 samples. From these samples, we detected 293 highly diverse coronaviruses, of which 284 were designated alphacoronaviruses and 9 were designated betacoronaviruses on the basis of partial RdRp sequences,” Shi Zhengli et al. write.

“All of the nine betacoronaviruses are SARSr-CoVs, one of which (sample ID4991; renamed RaTG13 in our article to reflect the bat species, the location and the sampling year) was described in a 2016 publication.

“The partial RdRp sequence (370 bp) of ID4991 was deposited in GenBank in 2016 under accession number KP876546. All of the identified bat SARSr-CoVs are distantly related to SARS-CoV based on partial RdRp sequences. In 2018, as the next-generation sequencing technology and capability in our laboratory had improved, we performed further sequencing of these bat viruses and obtained almost the full-length genome sequence (without the 5′ and 3′ ends) of RaTG13.

“In 2020, we compared the sequence of SARS-CoV-2 with our unpublished bat coronavirus sequences and found that it shared a 96.2% identity with RaTG13.”

Rahalkar challenges the statement in the addendum about patient samples testing negative for SARS antibodies. Referring to the PhD thesis by Canping Huang, she says he clearly wrote that the four miners tested positive for SARS IgG antibodies.

She also points out that there is no reference in the addendum to the fact that six miners fell ill and three of them died. “The addendum fails to give any account of the death of the other two miners,” Rahalkar writes.

There is no reference to Canping Huang’s thesis or the Master’s thesis by Li Xu, she says. “There are CT scans in the Master’s thesis identical to those of Covid-19 patients.”

There is a serious lack of clarity about the WIV researchers’ testing methodologies and dates, Rahalkar says.

“After eight years, does anyone expect to get positive results? How did they store these samples? Would those samples stay fine? And why did they store them so long, since they were negative in 2012?”

Rahalkar also has questions about the samples taken in the mine. “If they had got negative tests for SARS-like CoV in the patients, why did they keep on sampling for three years to hunt for SARS-like CoVs or other viruses?”

Most importantly, Rahalkar says, WIV researchers state in the paper by Ge Xing-Yi in 2016 that they only discovered one SARS-like CoV, when they had in fact found eight more. No details about these eight SARS-like CoVs are given in the addendum, Rahalkar says. No IDs or sequences are provided.

“They say that in 2018 they sequenced these viruses (plural), which means they also could have the whole genome of the other viruses. They released only the RaTG13 sequence.”

@TheSeeker268 says that, in July 2012, a few months after the pneumonia outbreak among the miners in Mojiang, there was a disease-control operation in the area that lasted for six months.

“Oddly enough, the atypical pneumonia cases among the miners didn’t make it to the official CDC statistics for 2012, which definitely suggests a cover-up to me,” @TheSeeker268 tweeted.

@TheSeeker268 also tweeted about the case of a Thai tourist who was visiting Yunnan in 2013 and died of multiple organ failure caused by “unexplained pneumonia”.

Around the same time, China’s Ministry of Science & Technology initiated a project (2013FY113500) to identify and investigate viral pathogens and their relation with major infectious diseases, @TheSeeker268 also tweeted.

The project was initiated in May 2013, just two months before Shi Zhengli sampled RaBtCoV/4991, @TheSeeker268 noted. The first project meeting took place on May 31 in Wuhan.

“To add to this mystery, the viral database for Project 2013FY113500 has been taken down,” @TheSeeker268 also notes.

In a paper entitled ‘Proposed SARS-CoV-2 Spillover During 2019 Review of Samples from a Mineshaft in Mojiang, Yunnan Province, China’, which was published on Zenodo on September 14, a researcher who prefers to remain anonymous, but who credits the members of DRASTIC, reports on activity at the WIV in late 2019, when samples from the Mojiang mineshaft were being reviewed.

‘Anon’ poses the question ‘Did a Review of Samples Collected from a Mineshaft Cause the Covid-19 Pandemic?’ and proposes that spillover occurred during the review of samples of the RaBtCoV/4991 virus, which, ‘Anon” notes, is only 1% different to SARS-CoV-2 in its RdRp.

There is evidence in documents from China’s Ministry of Science and Technology that WIV staff were handling samples and specimens containing BtCoV/4991 (RaTG13) and related viruses around the time of the SARS-CoV-2 outbreak, ‘Anon’ says.

“Several Wuhan laboratories conducted research into SARS or SARS-related coronaviruses in the years prior to the pandemic,” ‘Anon’ notes. “These include facilities at Huazhong University, the Wuhan Centre for Disease Control, the Wuhan Institute of Virology, and Wuhan University (WU).

“This research focuses on a programme connecting these institutions and presents information supporting a potential spillover event due to mishandling of a sample or specimen stored at the WIV in late 2019.

“This is proposed to have taken place during a well-documented review of samples and specimens collected under the multiyear programme that identified the closest known virus to SARS-CoV-2.”

‘Anon’ says that the WIV filed its only patent for a device to protect against accidental virus transmission in a biosafety laboratory on November 15, 2019. This, ‘Anon’ says, shows that accidental transmission was a concern at the time of the SARS-CoV-2 outbreak.

The WIV is not the only research institute with safety issues, ‘Anon’ points out. Researchers at WU also worked on the programme that identified RaTG13 and the university operates its own Animal Biological Safety Level 3 (ABSL-3) facility.

WU facilities were being inspected in late 2019, ‘Anon’ says. This was to check that problems identified earlier had been rectified.

“These problems included: hazardous waste being exposed; no separation of the experiment area; students not wearing lab coats; no eyewash; a crowded experiment area clutter,” ‘Anon’ writes.

“The facts that WU staff worked on the same programme that identified RaTG13, and WU had such a poor track record of lab safety adds to the plausibility of a WIV staff member on the programme mishandling a sample or specimen.”

WIV and WU staff often work together, and move between the institutions.

‘Anon’ notes that much initial focus was on the wild animal trade at the Huanan seafood market in Wuhan, where the first reported cases of infection by SARS-CoV-2 were publicly confirmed.

“However, the earliest publicly reported case using unclassified data had no exposure to the Huanan seafood market and developed symptoms on 1 December 2019, nine days before the first patient connected to the market developed symptoms,” ‘Anon’ writes.

“The virus strains sampled in the market were shown to be already adapted to human transmission, indicating that the virus had jumped species earlier.”

‘Anon’ notes that the theory that the pangolin is the animal source of SARS-CoV-2 relies on data made public by “the State Key Laboratory of Pathogen and Biosecurity, under the Beijing Institute of Microbiology and Epidemiology, under the People’s Liberation Army’s Academy of Military Sciences”, on 22 January 2020.

“This lab was the single source of pangolin data used in multiple research papers, without this single source being disclosed,” ‘Anon’ writes.

“While the data from this lab was reportedly from smuggled pangolins, no evidence has been found of coronaviruses in Sunda pangolins entering the wildlife trade via Malaysia.

“Additionally, as the pangolin ACE2 receptor has a low binding affinity for the SARS-CoV-2 receptor- binding domain (RBD), it appears unlikely to be the intermediary host.”

According to ‘Anon’, there is evidence suggesting that SARS-CoV-2 was circulating in Wuhan months before the outbreak was reported publicly. This includes reports that athletes competing in the Wuhan Military Games in October 2019 fell ill after arriving in the city. Six of the athletes are reported to have later tested positive for SARS-CoV-2 antibodies.

‘Anon’ suggests that a change in guidelines about influenza in November 2019 may have increased the chance of misdiagnosis of Covid-19 cases as influenza and this could partly explain how SARS-CoV-2 may have spread undetected before December 2019. From November 2019, virus specimen isolation was no longer recommended in the case of patients with respiratory disease who tested negative for influenza.

“The Covid-19 outbreak was made public by the isolation of virus specimens from patients testing negative for influenza, against the recommendation of the 2019 influenza guidance. The results of this specimen isolation were shared with Dr Li Wenliang, who shared the results with others who shared them with the world.”

‘Anon’ notes that, under the 2013FY113500 programme (‘Investigation of viral pathogens of major natural hosts and vector insects in China’), researchers at the WIV investigated the main natural virus hosts and vectors in China, taking samples from bats, birds, mosquitoes, rodents, and ticks.

“The WIV had collected over 15,000 such samples from bats, over 1,400 live viruses and over 60,000 strains,” ‘Anon writes. “Data from over 20,000 samples and specimens collected on such trips were stored on an WIV database, and the samples themselves were stored at -80°C.

“Research into ACE2 receptors and spike proteins of SARS-related coronaviruses and vaccines was funded under the programme. SARS vaccine research had been carried out at Wuhan University and other institutions.”

‘Anon’ notes that the WIV collected samples containing RaBtCoV/4991 under the 2013FY113500 programme. “The partial BtCoV/4991 sequence published in 2016 is a 98.9% match to SARS-CoV-2. The complete RaTG13 genome published by the WIV after the Covid-19 outbreak is a 96.1% match to SARS-CoV-2.”

It has been reported in a comment in a PhD thesis that four of the six miners who were tested after becoming ill were shown to have SARS antibodies.

“These cases were not reported in China’s unknown pneumonia statistics, despite the PhD thesis being supervised by now head of China’s CDC George Gao, and samples being sent to SARS expert Zhong Nanshan’s laboratory,” ‘Anon’ writes.

“The 2005 international health regulations state that the WHO should be notified of cases matching the clinical definition of SARS.”

‘Anon’ highlights the inconsistencies in statements made about RaBtCoV/4991 (RaTG13).

“The sequence of events described by Shi Zhengli and colleagues in a 2020 paper implied that RaTG13 was sequenced after the WIV found that SARS-CoV-2 matched the short BtCoV/4991 RdRp.”

This, ‘Anon’ notes, was corroborated by Peter Daszak, who said that the Wuhan team had worked on the sample in 2013, but did no more on it until the Covid-19 outbreak because it had not been a close match to SARS. Daszak said the sample was just put in the freezer.

“This is contradicted by the 2017–18 dates present in the filenames of the RaTG13 amplicon and swab sequences,” ‘Anon’ writes. “Shi Zhengli later issued a statement saying that the WIV fully sequenced RaTG13 in 2018.

“RaTG13 was initially uploaded accompanied by a statement saying that it had been extracted from bronchoalveolar lavage fluid, which is inconsistent with it being a bat faecal swab sample.”

It is stated in Li Xu’s thesis that the Kunming Institute of Zoology confirmed that a Rhinolophus sinicus bat was the source of the mine workers’ virus, ‘Anon’ points out. “It was clear to the zoology institute that the virus came from a Rhinolophus bat, known as a reservoir of SARS-like viruses, even before the WIV sampled the only SARS-like virus they reported finding in the mineshaft.”

The hypothesis presented by Jonathan Latham and Allison Wilson that RaTG13 (RaBtCoV/4991) caused the death of the Yunnan miners has been disputed by a group of Chinese scientists.

In presenting their hypothesis, Latham and Wilson rely heavily on a translation of Li Xu’s thesis.

Latham and Wilson suggest that RaTG13, or a very similar virus, evolved into SARS-CoV-2 inside the bodies of the miners and that researchers at Zhengli’s lab used medical samples taken from the miners and sent to them from Kunming University Hospital.

“It was this human-adapted virus, now known as SARS-CoV-2­, that escaped from the WIV in 2019,” Latham and Wilson assert. “We refer to this Covid-19 origin hypothesis as the Mojiang Miners Passage (MMP) hypothesis.”

Passaging is a standard virological technique for adapting viruses to new species, tissues, or cell types.

“It is normally done by deliberately infecting a new host species or a new host cell type with a high dose of virus,” Latham and Wilson explain. “This initial viral infection would ordinarily die out because the host’s immune system vanquishes the ill-adapted virus. But, in passaging, before it does die out, a sample is extracted and transferred to a new identical tissue, where viral infection restarts.”

Li-Meng Yan said during a video conversation in March with the founder of Lude Media, Wang DingGang, that there had been no successful biopsy or autopsy examinations in the case of the six miners, which, Yan says, means that the whole virus that infected them could not be isolated and sequencing could not be done to identify it.

Yan’s colleague Shu Kang says it’s not possible for the 4991 bat coronavirus to be SARS-CoV-2.

“If it was exactly the same virus it would have caused a pandemic, or even an epidemic. There’s no way they could limit the infection to very local small cluster,” Kang said during the video conversation.

“Even if they say that 4991 evolved into SARS-CoV-2 slowly in the human population it’s also not possible because you would have then detected such viruses in the population previously. However, we all know that, before late 2019, there were no cases.”

Jie Guan said in the same video conversation that there was insufficient evidence that four of the miners tested positive for SARS antibodies. He also said that, in the case of RaBtCoV/4991, there was only 440-bp sequencing, which, Guan says, is sequencing only the equivalent of 1.5% of the coronavirus genome. (Bp is a reference to the number of base pairs sequenced from a DNA fragment.)

Guan says that, in Zhengli’s original paper about RaTG13, she doesn’t mention the source of RaBtCoV/4991 and doesn’t even cite her previous paper about RaBtCoV/4991.

“Suddenly, after all the questioning, she claimed that RaTG13 is basically the same sample as CoV/4991 … This doesn’t make any sense.”

Zhengli is trying to link RaTG13 with the case of the six miners in 2012, Guan says, but there is a lack of evidence, and there are flaws in her logic.

Retired US Army Reserve colonel Lawrence Sellin, who worked at the US Army Medical Research Institute of Infectious Diseases and conducted research in the pharmaceutical industry, writes, in an opinion piece for the WION (World is One News) television channel in India, that there are several weak links in the Latham–Wilson theory that SARS-CoV-2 evolved within one of the miners.

“First of all, such an extensive genetic evolution needed to go from its closest bat coronavirus relative, RaTG13, to SARS-CoV-2, about 1,200 nucleotides, has never been described to occur in a single patient,” Sellin writes.

“Furthermore, the structure of RaTG13’s receptor binding domain, which binds to the human cell, is sufficiently different from that of SARS-CoV-2, making an initial human infection by RaTG13 to begin a human adaptation process highly unlikely.”

Sellin says that, even if bat-to-human transmission had occurred in the miners and high adaptation for human infection was achieved, there is no record of any human-to-human transmission, despite no extraordinary precautions being implemented during the hospitalisation.

The simplest explanation for the Mojiang miners’ illness in April 2012, Sellin says, is histoplasmosis, a respiratory infection caused by the inhalation of fungal spores found in bat and bird droppings.

US-China collaboration

The United States directly, and through collaboration with the EcoHealth Alliance, has funded Shi Zhengli’s research since at least 2014 and the EcoHealth Alliance has received further SARS-related funding from the US National Institutes of Health (NIH) dating back to 2008.

Zhengli (pictured left) has been referred to as the ‘bat woman’ because of her extensive work in the field of bat virology. She has publicly denied that SARS-CoV-2 originated in her laboratory. In a WeChat post on February 2 she wrote: “… I promise with my life that the virus has nothing to do with the lab.”

The NIH funded the EcoHealth Alliance to surveil and understand the risks of the transmission to humans of SARS-related coronaviruses. That funding has now been withdrawn.

The director of the NIH’s National Institute of Allergy and Infectious Diseases (NIAID), Anthony Fauci, said the NIH cut off funding for the collaboration between the EcoHealth Alliance, which is based in New York, and researchers in Wuhan after president Donald Trump told it to.

The EcoHealth Alliance is also sponsored by the United States Agency for International Development (USAID), and NIAID. Its president is a British zoologist and an expert on disease ecology and zoonosis in particular who is on the board of the WHO.

While researchers from the EcoHealth Alliance, working with scientists from the WIV, identified a sequence of SARS-related coronaviruses found in bats that was 96.11% similar to SARS-CoV-2 in July 2013, the sequence was not published on the NIH website until March 2020.

Andre Watson, who is the founder and CEO of the regenerative medicine and pandemic defence biotechnology company Ligandal, which is based in San Francisco, says that a number of other coronaviruses have more than 60% sequence similarity to SARS-CoV-2 and they include viruses that cause neurological, vascular, gastric, and respiratory symptoms. Some of them have been studied for decades, “since the 1970s and earlier”, Watson says.

SARS from 2003 was only 80% similar to SARS-CoV-2 and MERS from 2012 was only 64.3% similar to SARS-CoV-2.

In 2017, the EcoHealth Alliance collaborated with the WIV and the Duke-NUS Medical School in Singapore on research that was funded by the NIH, NIAID, the USAID Emerging Pandemic Threats programme (under the umbrella of the PREDICT project), and by funding sources in China.

The scientists published a paper about research done in bat caves. Researchers drew blood from the bats, or took nasal swabs or fecal samples. They identified 11 new viruses that they called SARS R (SARS-related viruses) in bats, Watson notes. Of these 11 viruses, three of them had spike proteins that had a high affinity for human ACE2.

The authors said: “In this study, we confirmed the use of human ACE2 as receptor of two novel SARSr-CoVs by using chimeric viruses with the WIV1 backbone replaced with the S gene of the newly identified SARSr-CoVs.”

Watson (pictured left) says this means that the researchers admit to doing recombination work with higher-binding ACE2 spike proteins on various SARS-CoV-2-related viral scaffolds.

“Furthermore, overlapping authors published a study in 2015 in which they admitted to discovering ‘SARSr-CoVs’ that had immunological cross-reactivity with SARS-CoV-1 antibodies,” he said.

The 2015 paper is the one Jonathan Latham and Allison Wilson refer to in their June 2 article. The paper’s authors include Zhengli and Baric.

Watson said: “They have still not published the sequences of viruses taken from those infected with the virus.

“The authors directly admit to doing genetic engineering of the viruses, which means that they were taking bits and pieces of one type of virus and mixing it with bits and pieces of other clades and strains of virus.”

Extract from the 2017 paper:

Vineet Menachery, Zhengli, Baric et al. said in their article that both wild-type and chimeric viruses were derived from either the epidemic SARS-CoV Urbani strain or the corresponding mouse-adapted (SARS-CoV MA15) infectious clone.

“Plasmids containing spike sequences for SHC014 were extracted by restriction digest and ligated into the E and F plasmid of the MA15 infectious clone,” they wrote.

Menachery et al. go on to explain that plasmids containing wild-type, chimeric SARS-CoV and SHC014-CoV genome fragments were amplified, excised, ligated, and purified.

“In vitro transcription reactions were then preformed to synthesise full-length genomic RNA, which was transfected into Vero E6 cells … The medium from transfected cells was harvested and served as seed stocks for subsequent experiments.”

Synthetic construction of chimeric mutant and full-length SHC014-CoV was approved by the University of North Carolina Institutional Biosafety Committee and the NIH’s Dual Use Research of Concern Committee, the authors said.

The EcoHealth Alliance researchers and their Chinese colleagues took an RNA strand from each of the viruses they identified and converted it to DNA, Watson says. They then put the DNA into a plasmid, where it could replicate.

“When you want to do genetic engineering, you don’t do it on RNA, you do it on DNA,” Watson explained. “A plasmid is stable. You can put it in the fridge or the freezer and put it in some cells and they’ll produce RNA.”

The researchers took spike proteins and combined them with envelope and nucleic acid proteins.

“Basically you’re holding the core of the virus stable, and you’re swapping out the pieces on the outside to get one that binds more strongly to human cells,” Watson said.

“They did not publish any of those sequences, but they admitted that they did that work.

“The nature of studying these viruses in cells is that there are going to be mutation events; evolutions are going to happen – especially if you are optimising the virus for infectivity of ACE2-expressing cells with human ACE2.”

The researchers also admitted to infecting humanised mice that had the human ACE2 receptor, Watson says. “It’s clear that they were doing gain-of-function studies.”

Watson says it is known that SARS-related viruses were infecting people in November 2017, or earlier, in rural China, and that these viruses were subsequently transferred to the WIV.

“The funding trail certainly suggests that the USA has collaborated with China, the WHO, and others and had these projects funded since 2011 or earlier,” he said. “This was a joint, multinational effort.”

Watson added: “In rural China people living near bat caves were catching these ‘SARS-related viruses’ and were getting acute respiratory distress.

“The researchers admitted that they drew the blood of these people, collected the viruses, and studied whether or not those viruses were cross-reactive immunity wise with SARS-Cov-1. They were, but they weren’t SARS-Cov-1.

“Those sequences were never published. So, to this day, they did not show us what the sequences were that were part of that outbreak in 2017.”

The paper trails dating back to November 2017 or earlier show that humans were testing positive for a new SARS-related coronavirus, Watson says.

“The WHO, the United States, and China knew that this had occurred in November 2017, or earlier.

“Circulating bat coronaviruses evolved from SARS-CoV-1 (the 2003 outbreak) were known to have potential for human transmission in 2015, or earlier.”

Watson suspects that, in 2019, a SARS virus escaped from the Wuhan laboratory.

“There’s clear evidence that the first infections were not from people coming from the wet market in Wuhan, but that the virus was brought to the wet market.

“It’s awfully suspicious that Wuhan would be home to the only known biosafety level-4 research facility in China, and they worked on these viruses there.”

In the EcoHealth Alliance grant application for 2017, Daszak said the aim of the project was “to understand what factors increase the risk of the next CoV emerging in people by studying CoV diversity in a critical zoonotic reservoir (bats), at sites of high risk for emergence (wildlife markets) in an emerging disease hotspot (China)”.

He said: “Predictive models of host range (i.e. emergence potential) will be tested experimentally using reverse genetics, pseudovirus and receptor binding assays, and virus infection experiments across a range of cell cultures from different species and humanised mice.”

Writing in Science magazine on April 30, Meredith Wadman and Jon Cohen said that Daszak, with NIH vetting and approval, provided Zhengli with $599,000 out of a total of $3.1 million in grant funding to use lab sequencing techniques to identify bat coronaviruses that were at high risk of jumping to humans.

“The grant has also supported blood testing of people who live near bat caves in southern China to see whether they carried antibodies indicating they had been infected with a bat coronavirus,” Wadman and Cohen reported.

According to Wadman and Cohen, Zhengli and her colleagues collected some 15,000 biological samples in the field from bats.

The director of the WIV, Wang Yanyi, told the Beijing-based English-language news channel CGTN, in an interview published on May 25, 2020: “Many people might misunderstand that since our institute reported the RaTG13’s genomic similarity to SARS-CoV-2, we must have the RaTG-13 virus in our lab.

“In fact, that’s not the case. When we were sequencing the genes of this bat virus sample, we got the genome sequence of the RaTG13 but we didn’t isolate nor obtain the live virus of RaTG13. Thus, there is no possibility of us leaking RaTG13.”

Asked about speculation that SARS-CoV-2 leaked from the WIV, Wang Yanyi said: “This is pure fabrication. Our institute first received the clinical sample of the unknown pneumonia on December 30 last year. After we checked the pathogen within the sample, we found it contained a new coronavirus, which is now called SARS-CoV-2.

“We didn’t have any knowledge before that, nor had we ever encountered, researched or kept the virus. In fact, like everyone else, we didn’t even know the virus existed. How could it have leaked from our lab when we never had it?”

Watson says that, throughout the progression of the SARS-CoV-2 pandemic, there have been consistent efforts by officials and the mainstream media to repress factual information about the severity, transmission dynamics, origins, and physiological effects of SARS-CoV-2 and Covid-19.

“On January 21, President Xi Jinping asked the director-general of the WHO, Dr Tedros Adhanom, to withhold information about person-to-person transmission of the virus, as well as pandemic classification. Likely as a consequence, pandemic classification of the virus was delayed four to six weeks.”

HIV assertion

Luc Montagnier, who was joint winner of the 2008 Nobel Prize for discovery of the human immunodeficiency virus (HIV), has caused controversy with his assertion that some nucleotide sequences of HIV-1 have been found in the SARS-CoV-2 genome. Other scientists have challenged Montagnier’s assertion, saying that each of these sequences also appears in other viruses.

Montagnier (pictured left) also puts forward the theory that SARS-CoV-2 came from the Wuhan laboratory, escaping in an “industrial accident” when Chinese scientists were attempting to develop a vaccine against HIV.

Montagnier says that the sequences he asserts are HIV inserts must have been added to SARS-CoV-2 and that this could not have happened naturally. It is meticulous, professional work, Montagnier says.

Detractors say that a tiny bit of the SARS-CoV-2 genome is about 85% similar to part of the HIV-1 genome, but that the sequence can be found in other viruses.

A paper by Indian scientists who said there were four unique inserts in the 2019-nCoV (SARS-CoV-2) spike glycoprotein that were not present in any other coronavirus reported to date was retracted by the authors.

The paper had been published as a preprint on bioRxiv on January 31. It was stated on bioRxiv that the authors intended to revise the paper “in response to comments received from the research community on their technical approach and their interpretation of the results”.

Prashant Pradhan et al. had said the inserts were either identical or similar to the motifs in the highly variable (V) regions (V1, V4 and V5) in the envelope glycoprotein or in the Gag protein of some unique HIV-1 strains from three different countries (Thailand, Kenya and India).

They speculated that these motif insertions sharing similarity with HIV-1 proteins could provide an enhanced affinity towards host cell receptors and increase the range of host cells of 2019-nCoV. The study implied that 2019-nCoV might be generated by gaining gene fragments from the HIV-1 genome.

In a paper published on February 14 on PubMed Central (PMC), Chuan Xiao et al. discuss the Indian scientists’ assertions and their own examination of the sequences of 2019-nCoV, other CoV viruses and HIV-1 as well as the GenBank database.

Chuan Xiao et al. say their results demonstrate no evidence that the sequences of the four inserts are HIV-1 specific or that 2019-nCoV obtained these insertions from HIV-1.

“First, the results of blast search of these motifs against GenBank shows that the top 100 identical or highly homologous hits are all from host genes of mammalian, insects, bacterial and others,” Chuan Xiao et al. said.

“There are only a few hits on coronaviruses, but none of them are HIV-1 related.”

Chuan Xiao et al. say the insertion sequences in question exist widely in all kinds of viruses.

“While the 100% match between the insertion 1 and 2 sequences and the HIV sequences were found in 19 entries, the matches between the insertion 3 and 4 sequences and HIV-1 sequences were rather poor (from 42% to 88%).

“Sequences that completely match the insertion 3 and 4 sequences were not found in any HIV-1 sequences. This clearly shows that these insertion sequences are widely present in living organisms including viruses, but not HIV-1 specific.”

In an article published in July in the International journal of research-GRANTHAALAYAH, Montagnier and retired interdisciplinary researcher Jean-Claude Perez write that 16 fragments from different strains, “both diversified and very recent”, of the HIV-1, HIV-2, and SIV retroviruses have a “high percentage of homology” with parts of the SARS-CoV-2 genome.

Each of these elements is made up of 18 or more nucleotides and therefore may have a function, the two researchers say.

The Exogenous Informative Elements (EIE) include 12 that are concentrated in a very small region of the SARS-CoV-2-19 genome – “length less than 900 bases, i.e. less than 3% of the total length of this genome”, they write. Also, the EIE are positioned in two functional genes of SARS-CoV-2: the ORF1ab and S spike genes.

Perez and Montagnier cite the following two facts that they say contribute to their hypothesis that the SARS-CoV-2 genome is partially synthetic:

• There is a contiguous region representing 2.49% of the whole SARS-CoV-2 genome, of which 40.99% is made up of 12 diverse fragments originating from various strains of HIV/SIV retroviruses, and
• some of the 12 EIE appear concatenated (linked together in a chain or series).

Notably, the researchers say, the retroviral part of these regions, which consists of eight elements from various strains of HIV-1, HIV-2, and SIV covers a length of 275 contiguous bases of SARS-CoV-2.

The cumulative length of these eight HIV/SIV elements represents 200 bases, Perez and Montagnier say, and, consequently, the HIV/SIV density rate of the region of SARS-CoV-2 in question is 200/275, i.e. 72.73%.

A major part of the 16 EIE already existed in the first SARS genomes as early as 2003, but a new region including 4 HIV-1/HIV-2 EIE radically distinguishes all SARS-CoV-2 strains from all SARS and bat strains, with the exception of Bat RaTG13, Perez and Montagnier say.

Comparing the spikes of SARS-CoV-2 and RaTG13, Perez and Montagnier noted two abnormalities:

• the insertion of four contiguous PRRA amino acids in the middle of the spike, and
• an abnormal distribution of synonymous codons in the spike’s second half.

They say there is insertion in the spike region of a significant pair of EIE from Plasmodium yoelii “and a possible HIV-1 EIE with a crucial spike mutation”.

Plasmodium yoelii is a rodent parasite commonly used as a model to study malaria infection.

Evidence that SARS-CoV-2 didn’t develop naturally

Andre Watson explains that there is a way that small sequences of HIV may have been inserted into SARS-CoV-2 that would have made the manipulation less noticeable. There could, he says, have been a forensic cover-up.

Watson says it’s very odd that all four of the inserts in question have been found on the surface of the SARS-CoV-2 spike protein.

“One thing that has made this forensically difficult to investigate is that the genomic sequences don’t match. If you line up the RNA letters in those inserts with HIV, they don’t match.

“However, there is something called sense mutation. If I were trying to put a HIV sequence into something, and my job was to cover it up, I wouldn’t use the same genetic sequence, I would get the same protein sequence. I would change the genetic sequence.”

Three DNA or RNA letters create one amino acid, but there are multiple combinations of three that will create a given amino acid, Watson says. “So, you can scramble the genetic letters around and still get the same protein letters to come out.”

Two of the domains that have been found on the surface of the SARS-CoV-2 spike protein are also present in the HIV-1 gp120 surface domain, which, Watson says, is part of HIV’s “viral fusion machinery with CD4+T cells”. (T cells, also called T lymphocytes, are a type of white blood cell. They are an essential part of the body’s immune system.)

Watson says gp120 is known to interfere with dendritic cell function during HIV infections, and also modulates the activity of CD4+ T cells, which interact with dendritic cells to sense and respond to various pathogens.

“While I have yet to see structural modelling data of these domains interacting with known HIV binding motifs and this isn’t damning in and of itself, it does raise several questions, especially when coupled to the known immune-evasive properties of SARS-CoV-2, which includes T cell exhaustion and antibody avoidance in a number of patients,” Watson said.

Watson says he hasn’t a clue what the gp120 domains are doing, “but they are there”.

It’s also very strange, Watson says, to see a malaria sequence on the surface of the SARS-CoV-2 spike protein.

He says the malaria sequences don’t match the known binding domain of malaria to CD147 (malaria’s entry receptor into red blood cell precursor cells and red blood cells).

“However, there is speculation and computational modelling suggesting that SARS-CoV-2 also binds to CD147 and, in our own experiments, we have preliminarily seen some binding responses in the ~100–300 nanomolar range, which need to be further validated.

“What are the odds, if there was not laboratory manipulation, of having four little inserts that match protein sequences from HIV on solvent-accessible domains on the surface of the spike, along with a malaria sequence?”

Watson says he doesn’t want to make claims that cannot be proven, but the presence of the four inserts, and the malaria sequence, need to be investigated – and “certainly line up with the gain-of-function work that is suggested by the plasmid recombination experiments and insertion of higher binding affinity ACE2-binding spike proteins into infectious clones”.

It is important, Watson says, to remember that American and Chinese researchers were doing genetic engineering work in 2015, and admitted that they were doing it.

When a virus is randomly evolving, there is usually a fixed ratio of change if there is mutation, Watson says.

“In the case of SARS-CoV-2, when compared to the 2013 RaTG13 virus that was 96.11% similar to the current outbreak, there is an entire region where the virus has mutated in a way that is statistically impossible,” he said.

“It is virtually impossible for these particular mutations to have happened naturally. And this has happened in the same region of the virus – the spike protein – on which American and Chinese researchers have admitted doing recombination work.”

If SARS-CoV-2 were mutating accidentally, it would have a constant ratio of sense and missense mutations that is typically 5:1, Watson says.

“However, for nearly 2,100 RNA letters, there are virtually no missense mutations, as would be expected naturally between two viruses that are experiencing some form of genetic drift.

“The RNA letters are changing, but most of the protein letters are not – and it’s just in the part of the virus that was known to be spliced around in the SARS-related viral recombination experiments.”

The SARS-CoV-2 research was done in collaboration between the US and China, as well as other global actors, Watson points out.

“To say that we didn’t know what this was when it appeared in December is to outright lie about biological research that we knew was happening. We knew what SARS-CoV-1 did in 2003.”

In a paper published on the pre-print repository ViXr.org in May, independent researcher Murat Seyran from Vienna says that the host tropism (the infection specificity of certain pathogens to particular hosts and host tissues) and the infection pattern of SARS-CoV-2 have three fundamental differences compared to the previous six human pathogenic coronaviruses.

“The unnatural flat pattern of SARS-CoV-2 S protein NTD [N-terminal domain] is conflicting with the evolutionary host tropism strategy of not only the human CoVs but also many different human pathogenic viruses,” Seyran said.

Why have we not seen any pandemic caused by coronaviruses before? Seyran asks. Why did pandemics not emerge in places where people rely on water sources shared with bats or bats are consumed as bushmeat?

Seyran also says that, in the case of SARS-CoV-2, the S Protein RBD is not a high-frequency positive selection site, unlike in other coronaviruses.

The SARS-CoV-2 genome is almost identical to the bat coronavirus, but it is only mutated on the RBD, Seyran says. “Why only the RBD had mutations meanwhile the rest of the genome was almost unaltered?”

It is argued that the presence of a furin cleavage spike in SARS-CoV-2’s spike protein is evidence that the virus did not develop naturally.

A furin cleavage site is a segment of four amino acids that enables a virus to use furin in the human body as an enzyme to dissolve its coating so that it can release its genetic material to infect cells. Furin cleavage sites tend to be more infectious than cleavage sites that use other enzymes.

Seyran is one of 18 scientists who wrote a letter to the editor of the Journal of Medical Virology, which was published on September 3.

The scientists, who are from the US, Austria, Iran, Sudan, India, the UK, New Zealand, Egypt, Switzerland, and Jordan, wrote about the unnatural shape of SARS-CoV-2’s spike protein.

“The SARS-CoV-2 host tropism/adaptation pattern has significant discrepancies compared to other CoVs, raising questions concerning the proximal origin of SARSCoV-2,” Seyran et al. wrote.

“The flat and non-sunken surface of the sialic acid-binding domain of SARS-CoV-2 spike protein (S protein) conflicts with the general adaptation and survival pattern observed for all other CoVs.”

Seyran et al. say that SARS-CoV-2 recombination presumably occurred between the S1/S2 domains of the S protein, enabling host furin protease utilisation.

“Although millions of recorded cases have been recorded globally, SARS-CoV-2 S protein does not have any apparent further recombination, placing it in conflict with the recombination models of other CoVs,” the scientists wrote.

“Similarly, the S protein receptor-binding domain (RBD) of SARS-CoV-2 has not accumulated high-frequency non-synonymous substitutions, differentiating SARS-CoV-2 from other CoVs that have positive selection/adaptation mutations in their RBDs.”

Clinical SARS-CoV-2 isolates to date have only a single high frequency non-synonymous mutation, D614G, in their S protein, Seyran et al. say.

“Based on currently known mutation rates and patterns in clinical isolates of SARS-CoV-2, the S protein does not appear to be a mutational ‘hot spot’ for SARSCoV-2, unlike other human CoVs.”

Seyran et al. say that the furin recognition motif present at the SARS-CoV2 S1/S2 junction has no analogy in other “linage B” beta-coronaviruses, including neither pangolin-CoV nor RaTG13.

They say evidence suggests that the addition of a motif for S1/S2 site furin cleavage constituted a unique recombination occurrence.

“The CoV-unique insertion of 4 amino-acids creating a novel RRAR furin cleavage site introduces two arginine codons CGG-CGG, whose usage is extremely rare in CoVs, further supporting the hypothesis of a unique recombination occurrence.”

Andersen et al. say lab manipulation ‘improbable’

In their letter to the editor published in Nature Medicine, Kristian G. Andersen et al. say it is improbable that SARS-CoV-2 emerged through laboratory manipulation of a related SARS-CoV-like coronavirus.

“Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus,” the researchers said.

“It is improbable that SARS-CoV-2 emerged through laboratory manipulation of a related SARS-CoV-like coronavirus.”

Stuart Newman, who is a professor of cell biology and anatomy at New York Medical College, is quoted by GMWatch as saying that a key argument used to deny that SARS-CoV-2 could be a genetically engineered strain that escaped from a laboratory actually points to the exact opposite. In other words, he is quoted as saying, it indicates that SARS-CoV-2 could well be genetically engineered and that it could have escaped from a lab.

Andersen et al. say that, if genetic manipulation had been performed, one of the several reverse-genetic systems available for betacoronaviruses would probably have been used.

The genetic data irrefutably show that SARS-CoV-2 is not derived from any previously used virus backbone, they say.

Andersen et al. propose two scenarios they say can plausibly explain the origin of SARS-CoV-2: natural selection in an animal host before zoonotic transfer, and natural selection in humans following zoonotic transfer.

The researchers say the high-affinity binding of the SARS-CoV-2 spike protein to ACE2 “is most likely the result of natural selection on a human or human-like ACE2 that permits another optimal binding solution to arise”.

They say that, as many early cases of Covid-19 were linked to the Huanan market in Wuhan, it is possible that an animal source was present at this location.

“Given the similarity of SARS-CoV-2 to bat SARS-CoV-like coronaviruses, it is likely that bats serve as reservoir hosts for its progenitor,” they stated.

They add that Malayan pangolins (Manis javanica) illegally imported into Guangdong province contain coronaviruses similar to SARS-CoV-2.

Although the RaTG13 bat virus remains the closest to SARS-CoV-2 across the genome, some pangolin coronaviruses exhibit strong similarity to SARS-CoV-2 in the receptor-binding domain, the researchers say. This includes all six key RBD residues, they write.

According to Andersen et al., this clearly shows that the SARS-CoV-2 spike protein optimised for binding to human-like ACE2 is the result of natural selection.

It is possible, the researchers say, that a progenitor of SARS-CoV-2 jumped into humans, acquiring the genomic features described in their analysis through adaptation during undetected human-to-human transmission.

The researchers say that, although the evidence shows that SARS-CoV-2 is not a purposefully manipulated virus, it is currently impossible to prove or disprove the other theories of its origin described in their article.

However, they say, since they observed all notable SARS-CoV-2 features in related coronaviruses in nature, they do not believe that any type of laboratory-based scenario is plausible.

In an email interview with GMWatch, Stuart Newman said: “The Nature Medicine paper points to variations in two sites of the spike protein of the new coronavirus that the authors claim must have arisen by natural selection in the wild.

“However, genetic engineering of one of these sites, the ACE2 receptor binding domain, has been proposed since 2005 in order to help generate vaccines against these viruses. It is puzzling that the authors of the Nature Medicine commentary did not cite this paper, which appeared in the prominent journal Science.”

Newman also told GMWatch: “The second site that Andersen et al. assert arose by natural means, a target of enzyme cleavage not usually found in this class of viruses, was in fact introduced by genetic engineering in a similar coronavirus in a paper they do cite. This was done to explore mechanisms of pathogenicity.”

He added that he does not believe that changes were deliberately introduced to increase the pathogenicity of any single strain of SARS-CoV-2, but that the virus may have had genetically engineered components in its history before it was inadvertently introduced into the human population.

GMWatch also quoted the London-based molecular geneticist Michael Antoniou, who has also cast doubt on assertions that SARS-CoV-2 was not genetically engineered. Antoniou said that Andersen et al.’s reasoning was not conclusive because it was based largely on computer modelling, which, Antoniou says, is “not definitive but only predictive”.

Antoniou said that, while Andersen et al. may be correct in how they perceive SARS-CoV-2 to have arisen, the data they present “does not exclude the possibility that this new coronavirus variant could have been created through an in vitro, directed iterative evolutionary selection process”.

He added: “Using this method, a very large library of randomly mutagenised coronavirus spike proteins could be selected for strong binding to the ACE2 receptor and consequently high infectivity of human cells.

“The power of such directed evolution to select for optimal enzymatic and protein-protein interactions was acknowledged by the award of the Nobel Prize in Chemistry in 2018.”

GMWatch states: “Neither Dr Antoniou, nor Prof Newman, nor we ourselves make any suggestion that, in the event that genetic engineering was involved, the intention was to create a bioweapon. Such ‘enhanced infectivity’ research is carried out on viruses all over the world (and not just in China) to investigate their behaviour and to develop vaccines and other therapies, as well as for ‘biodefence’ purposes.

“But the question of whether genetic engineering did play a part in the emergence of SARS-CoV-2 must continue to be investigated so that humanity can place appropriate limits and safeguards on such research.”

‘Escapes’ from laboratories

Concerns about gain-of-function research erupted in 2011 when a team at the University of Wisconsin in the US and researchers at a laboratory at the Erasmus Medical Centre in Rotterdam in the Netherlands announced that they had modified the H5N1 bird flu virus to enable it to spread between ferrets.

The researchers had planned to publish their findings in Science and Nature, but the National Science Advisory Board for Biosecurity in the US asked the journals to refrain from publishing the methods the scientists had used.

The advisory board issued a statement that was published in Science and Nature saying that a pandemic or the deliberate release of a transmissible highly pathogenic influenza A/H5N1 virus “would be an unimaginable catastrophe for which the world is currently inadequately prepared”.

The board added: “Our concern is that publishing these experiments in detail would provide information to some person, organisation or government that would help them to develop similar mammal-adapted influenza A/H5N1 viruses for harmful purposes.”

During the SARS outbreak in 2003 and 2004, there were two separate ‘escapes’ of viruses from the same laboratory in Beijing, China.

The WHO described one of the Beijing incidents, along with two other incidents (one in Singapore and one in Taiwan), as being attributed to “breaches in laboratory biosafety”.

China

In a report in October 2004, the WHO said that two researchers at the National Institute of Virology (NIV) in Beijing, where experiments using live and inactivated forms of the SARS coronavirus were being carried out, developed SARS in late March and mid-April of that year. The outbreak was reported on April 22 and the institute was closed a day later.

In one of the cases, a nurse who had cared for a researcher at the NIV became ill in April 2004 and was diagnosed as being infected with the SARS virus. The researcher, who had worked at the institute for two weeks in March 2004, developed symptoms on March 25, 2004, and was diagnosed as being infected with the SARS virus. The researcher’s mother also became ill and died on April 19.

Another researcher who also worked at the Beijing virology institute developed SARS symptoms on April 17 and was hospitalised. Health authorities diagnosed him as a suspected SARS case.

The WHO said that many shortcomings in biosecurity were found at the NIV and added: “The specific cause of the outbreak was traced to an inadequately inactivated preparation of SARS virus that was used in general (that is, not biosecure) laboratory areas, including one where the primary cases worked.

“It had not been tested to confirm its safety after inactivation, as it should have been.”

The WHO had said on May 18, 2004, that investigators had serious concerns about biosafety procedures at the Beijing institute – including how and where procedures using the SARS coronavirus were carried out, and how and where SARS coronavirus samples were stored.

The organisation added: “WHO and Chinese authorities view with concern the occurrence of laboratory-associated SARS cases. WHO urges all member states to view this latest outbreak as an opportunity to review the biosafety practices of institutions and laboratories working with SARS coronavirus.”

During and after the SARS outbreak of 2003, a large number of specimens were collected from possible human cases, animals, and the environment, the WHO said.

“These specimens, which may contain live SARS coronavirus, are still kept in various laboratories around the world. Some of them are stored in laboratories at an inappropriate containment level.

“SARS coronavirus has also been propagated in reference and research laboratories, and distributed to other laboratories for research purposes. Research using live and inactivated SARS coronavirus – and other pathogens capable of causing serious illness – is being conducted in many laboratories.”

Singapore

In Singapore, in August 2003, a microbiology student who had been doing research on the West Nile virus at the country’s national university became ill. He tested positive for the SARS virus. The student has also been doing work on West Nile at Singapore’s Environmental Health Institute (EHI) laboratory, where others researchers were studying the SARS virus.

The Center for Infectious Disease Research and Policy (CIDRAP) at the University of Minnesota in the US reported on the incident in September 2003 and said an international committee concluded that the researcher had probably acquired the virus in the EHI laboratory.

“Inappropriate laboratory procedures and a cross-contamination of West Nile virus samples with SARS coronavirus in the laboratory led to the infection of the doctoral student,” the Singapore Ministry of Health said. “No evidence could be found of any other source of infection.”

The ministry said the committee determined that there was no evidence that the researcher, who recovered from his illness, transmitted the virus to anyone else.

CIDRAP reported that the international committee that investigated the incident also examined Singapore’s four laboratories rated as biosafety level 3 ((BSL-3), the second highest of four risk categories.

“The group found structural problems as well as training and record-keeping deficiencies at the environmental health lab and recommended that the lab not reopen until the problems are corrected,” CIDRAP reported. “Lesser problems were found at the Singapore General Hospital laboratory and the National University of Singapore laboratory.”

Taiwan

In December 2003, a scientist from Taiwan who had been doing research on SARS fell ill on a flight when returning from a meeting in Singapore and was diagnosed as positive for SARS infection. His 74 contacts in Singapore were quarantined, and none developed SARS. It was alleged in one press report that the scientist had handled leaking biohazard waste without gloves, a mask, or a gown.

Calls for augmented security

On December 18, 2003, the WHO called for augmented biosafety in laboratories where SARS-CoV specimens and cultures were being handled.

The WHO said it strongly recommended biosafety level 3 as the appropriate containment level for working with live SARS-CoV material.

“The possibility that a SARS outbreak could occur following a laboratory accident is a risk of considerable importance, given the relatively large number of laboratories currently conducting research using the SARS-CoV or retaining specimens from SARS patients,” the WHO said.

“These laboratories currently represent the greatest threat for renewed SARS-CoV transmission through accidental exposure associated with breaches in laboratory biosafety.

“Given the severity of the threat, WHO strongly recommends that national governments maintain a registry of laboratories that are approved to safely and securely hold and work with specimens of suspected or confirmed SARS patients or cultures containing SARS-CoV.”

Appropriate national authorities should provide guidelines for laboratories to catalogue and control the storage of cultures and specimens of SARS-CoV for periodic inspections, the WHO said.

The WHO also said it encouraged the destruction of unwanted or unneeded clinical and animal specimens that were suspected of, or were confirmed to contain, SARS-CoV, and/or of stocks of SARS-CoV that could not be kept under secure conditions.

In July 2018, the director of the biosafety laboratory at the WIV, Yuan Zhiming, and Shi Zhengli published a paper in ScienceDirect entitled ‘Quality management in a high-containment laboratory’.

The Wuhan Institute of Virology was accredited in 2017 by the China National Accreditation Service for Conformity Assessment, the scientists noted.

Zhiming and Zhengli said, however: “Because no international dedicated standard exists for biosafety level 4 (BSL-4) laboratories, this paper explains the desire of the laboratory’s director to set up a quality management system (QMS) to accredit this first level 4 containment laboratory in China …”

They added: “There are two international standards currently available, the choice of which depends on whether it is a laboratory intended for medical diagnoses … or a laboratory for both medical and environmental purposes …”

Both standards are recognised by the WHO, Zhiming and Zhengli noted. “Nonetheless, none of them has specific requirements for biorisks, i.e. biosafety and biosecurity.

“Although the 2017 version of ISO/IEC 17025:2017 takes into account risks in a general sense (clause 8.5), the management is free to use either another standard or any guidance more appropriate for the laboratory’s activity.”

Zhiming and Zhengli said that accreditation of a biocontainment laboratory in accordance with an international standard was a real challenge.

In the 14 countries hosting one or several BSL-4 laboratories, very few such laboratories had been accredited according to an international standard because there was no suitable international standard for accrediting the activities carried out at these laboratories, they added.

Writing in the Taiwan News, Keoni Everington relates how Chinese scientists used little or no personal protective equipment while handling bats in the wild and samples in the laboratory.

“A video released two years before the start of the Wuhan coronavirus pandemic shows Wuhan Institute of Virology (WIV) scientists being cavalier toward protective equipment and being bitten by bats that carry deadly viruses such as SARS, demonstrating a lax safety culture in the lab,” Everington wrote in an article published on January 15, 2021.

“From 4:45 to 4:56, a scientist can be seen holding a bat with his bare hands. Team members from 7:44 to 7:50 can be seen collecting potentially highly infectious bat faeces while wearing short sleeves and shorts and with no noticeable personal protective equipment (PPE) other than gloves.

“From 8:31 to 8:34, some team members can be seen wearing complete hazmat suits while many others are interacting with them in ordinary clothing and scrub caps and still others have no head covering at all.”

Everington adds: “From the 8:42-8:47 mark, one team member is wearing full scrubs, mask, and scrub cap, while another is in street clothes, scrub cap, and mask, and the third person, possibly Shi, is handing samples with her bare hands.”

Gain-of-function moratorium lifted

On December 19, 2017, federal officials in the US ended a moratorium that had been imposed three years earlier on the funding of gain-of-function research.

The head of the NIH, Francis S. Collins, said the research could only be done if a scientific panel decided that the benefits justified the risks.

Collins (pictured left) said that researchers would have to show that their studies were scientifically sound and that they would be done in a high-security lab.

The pathogen to be modified must pose a serious health threat, he said, and the work must produce knowledge that would benefit humans. In addition, there would have to be no safer way to do the research.

Collins said that the new regulations applied to any pathogen that could potentially cause a pandemic.

In October 2014, all federal funding had been halted for gain-of-function research on the flu virus and those causing Middle East respiratory syndrome (MERS) and SARS.

The NIH said that certain gain-of-function studies with the potential to enhance the pathogenicity or transmissibility of potential pandemic pathogens (PPPs) had raised biosafety and biosecurity concerns, “including the potential dual use risks associated with the misuse of the information or products resulting from such research”.

The White House Office of Science and Technology Policy launched a gain-of-function deliberative process to re-evaluate the potential risks and benefits associated with certain experiments.

During the process the government halted federal funding for gain-of-function studies that were aimed at enhancing the pathogenicity or transmissibility among mammals by respiratory droplets of influenza, MERS, or SARS viruses.

The National Science Advisory Board for Biosecurity (NSABB) finalised its recommendations on May 24, 2016. In January 2017, the US government released policy guidance for the review and oversight of research “anticipated to create, transfer, or use enhanced PPPs”.

A new framework was developed to guide funding decisions about proposed research involving pathogens with enhanced pandemic potential.

Writing in Lancet Infectious Diseases in February 2018 about the rescinding of the moratorium on gain-of-function experiments, Talha Burki referred to the suppression by the NSABB in 2011 of the two studies involving H5N1 viruses that had been modified to allow airborne transmission from ferret to ferret.

“They worried that malign actors could replicate the work to deliberately cause an outbreak in human beings,” Burki wrote.

The Department of Health and Human Services (HHS) issued guidelines for funding decisions on experiments likely to result in highly pathogenic H5N1 viruses transmissible from mammal to mammal via respiratory droplets, Burki reported. The guidelines were later expanded to include H7N9 viruses.

Burki reported that, in 2014, several breaches of protocol at US government laboratories brought matters to a head.

“The news that dozens of workers at the Centers for Disease Control and Prevention (CDC) might have been exposed to anthrax, that vials of smallpox virus had been left lying around in an NIH storeroom, and that the CDC had unwittingly sent out samples of ordinary influenza virus contaminated with H5N1, shook faith in the country’s biosafety procedures,” she wrote.

In July 2014 more than 200 scientists signed the Cambridge Working Group declaration in which they said that, for any experiment, the expected net benefits should outweigh the risks.

“Experiments involving the creation of potential pandemic pathogens should be curtailed until there has been a quantitative, objective and credible assessment of the risks, potential benefits, and opportunities for risk mitigation, as well as comparison against safer experimental approaches,” the scientists said.

“A modern version of the Asilomar process, which engaged scientists in proposing rules to manage research on recombinant DNA, could be a starting point to identify the best approaches to achieve the global public health goals of defeating pandemic disease and assuring the highest level of safety.

“Whenever possible, safer approaches should be pursued in preference to any approach that risks an accidental pandemic.”

The scientists said that “recent incidents involving smallpox, anthrax and bird flu in some of the top US laboratories remind us of the fallibility of even the most secure laboratories, reinforcing the urgent need for a thorough reassessment of biosafety”.

Such incidents had been accelerating, the scientists said and had been occurring on average more than twice a week with regulated pathogens in academic and government labs across the country.

“An accidental infection with any pathogen is concerning. But accident risks with newly created ‘potential pandemic pathogens’ raise grave new concerns.

“Laboratory creation of highly transmissible, novel strains of dangerous viruses, especially but not limited to influenza, poses substantially increased risks. An accidental infection in such a setting could trigger outbreaks that would be difficult or impossible to control.

“Historically, new strains of influenza, once they establish transmission in the human population, have infected a quarter or more of the world’s population within two years.”

Continuing investigations 

The DRASTIC team has explored, and continues to investigate, numerous hypotheses, ranging from the claim that SARS-CoV-2 is a Chinese or American bioweapon or was leaked from a laboratory to the “miners hypothesis”, the theory that the virus is “a vaccine gone wrong”, and the “serial passage” hypothesis.

“We question everything,” one member of the team, who prefers to remain anonymous, and tweets under the handle @BillyBostickson, said. “We have no fixed agenda.”

The team has put together a list of 260 questions that they say the WHO and specific scientists need to answer and is about to add more.

The questions cover an enormous amount of ground, and many are extremely technical.

They range from “Why did  Shi Zhengli alter keywords in the WIV database on December 30 when returning to Wuhan?” and “Why are the majority of Chinese viral pathogen databases now offline?” to “How did Shi Zhengli conclusively establish SARS-CoV-2 didn’t come from her lab?” and “When exactly did the first cases of viral pneumonia that are now known to be Covid-19 occur?”.

Other questions include “What was the increased activity (revealed by satellite images) at Wuhan hospitals in October 2019 due to?” and “Did the Wuhan Institute of Virology team newly extract RNA from the RaBtCoV/4991 physical sample or did they just sequence the stored RNA sample?”

One particular question that DRASTIC members want answered relates to a project at the WIV led by researcher Ben Hu entitled ‘Pathogenicity of two new bat SARS-related covs to transgenic mice expressing human ACE2’.

The DRASTIC team want to know which two bat SARS-related coronaviruses were used in the project.

The US State Department says WHO investigators must have access to the records of the WIV’s work on bat and other coronaviruses before the Covid-19 outbreak.

“As part of a thorough inquiry, they must have a full accounting of why the WIV altered and then removed online records of its work with RaTG13 and other viruses,” the department says in the fact sheet published on January 15.

“The CCP has prevented independent journalists, investigators, and global health authorities from interviewing researchers at the WIV, including those who were ill in the fall of 2019. Any credible inquiry into the origin of the virus must include interviews with these researchers and a full accounting of their previously unreported illness.”

Australia has called for an independent investigation into the origins and spread of SARS-CoV-2 and this has further soured its already tense relations with China.

The French news agency AFP reported that the Chinese ambassador in Canberra retaliated by threatening a widespread consumer boycott of Australian products and this was followed by a Chinese ban on imports from four major Australian beef producers.

 

1. The 26 scientists who have called for a new international investigation into the origins of Covid-19 include Alina Chan; Monali Rahalkar; Nikolai Petrovsky; professor of chemistry and chemical biology at Rutgers University in the US Richard Ebright; honorary professor at the National Centre for Epidemiology and Population Health in Canberra, Australia, Colin Butler; Rossana Segreto from the University of Innsbruck in Austria; data scientist Gilles Demaneuf from New Zealand; and ten scientists from France.