Communist China's clampdown on information about the Wuhan covid outbreak undermines its claim that nothing untoward occurred. The world's experts lack basic information about the Wuhan outbreak, according to numerous published reports.
For example,
The chief scientist at the Wuhan Institute of Virology, Shi Zhengli, has said she had reviewed her notes and found nothing amiss, but evidently they have not been scrutinized by her U.S. or other foreign colleagues.
A recent U.S. intelligence assessment says,
https://www.dni.gov/files/ODNI/documents/assessments/Unclassified-Summary-of-Assessment-on-COVID-19-Origins.pdf
The intelligence units, as quoted by the summary, do not suggest that China's secrecy tends to undercut its stance that no lab leak occurred.
The summary, from the national intelligence director's office, says that one intelligence unit was moderately confident that the pandemic was sparked by a lab leak. It adds that four intelligence units and the National Intelligence Council leaned toward the "leap from an animal" theory. But they were extremely unsure of that scenario, for which they had only "low confidence." Analysts at three other intelligence units, the summary says, were divided between the "animal leap" and lab accident scenarios.
The summary explains that differences of opinion stem largely from the methods each agency uses to sift and analyze information. It avoids raising the possibility of undue political influence from the China lobby, which consists of American investors eager for "engagement" riches and Chinese communist-backed operatives.
Reporters Without Borders, an international activist group, reports that a Chinese journalist, imprisoned for her early pandemic reporting, is now near death. The group documents a number of other cases of China's harsh treatment of journalists who do not toe the party line.
Chinese covid reporter's harsh treatment
https://rsf.org/en/news/china-rsf-urges-release-covid-19-reporter-who-faces-impending-death
Drastic -- an acronym for 'Decentralized Radical Autonomous Search Team Investigating COVID-19' -- is a loose collection of internet activists investigating the origins of covid. The dogged information-mining of these activists has drawn both admiration and scorn from scientists. Yet, there is little doubt that the collective's work has knocked out the oft repeated charge that the lab leak scenario was merely an alt right "conspiracy theory" (as if communists would never conspire).
Drastic home page
https://drasticresearch.org/
Drastic's cyber activities are assuredly a menace to the desire of governments to control information. We can be sure that Beijing views Drastic with the same dim view that the U.S. and British governments have of Wikileaks. And, considering the complicity of major elements of the U.S. press and government in shielding communist China from criticism in the Wuhan matter, it is only a matter of time before the CIA is weighing measures for shutting down Drastic as a spy shop for a foreign government while the Justice Department obtains indictments of its leadership for the "crime" of Assange-style journalism.
Free press coalition opposes Assange extradition
https://invisiblepaul.blogspot.com/p/free-press-coalition-opposes-assange.html
Below is Drastic's summary of its case.
The Lab Leak Hypothesis
Virologists study dangerous viruses. They collect them from the wild, they study them in labs, and they genetically engineer them. One goal of their research is to help prevent future pandemics.
However, viruses have escaped from laboratories around the world on several occasions. New techniques for bioengineering can enable dangerous viruses to be created in research laboratories.
Previous pandemics such as SARS and MERS have arisen naturally as viruses jump from species to species and evolve through natural selection. The lab leak hypothesis proposes that the SARS-COV-2 virus responsible for Covid-19 did not arise naturally but escaped from a virology laboratory, the Wuhan Institute of Virology (WIV) [Segreto20] [Deigin21].
The Importance of the Hypothesis
If SARS-COV-2 did result from a lab leak then such research needs to be much more carefully controlled in order to prevent any future outbreak of an even more potent virus.
There is no suggestion that the leak was deliberate. The Wuhan Institute of Virology published their impressive results and collaborated openly with other virologists around the world. For example, their chief scientist Shi Zhengli collaborated closely with Ralph Baric of the University of North Carolina. The Wuhan Institute of Virology is a well respected member of the international community of virologists.
Until recently, any suggestion of a laboratory leak was discounted as an unsubstantiated far right conspiracy theory. However, as more and more evidence has accumulated many leading scientists now consider the theory plausible if not proven.
This paper should not be viewed as an attack on China. But rather, it provides a strong motivation to review the practice of virology internationally.
Beyond Reasonable Doubt
There will never be a mathematical proof that SARS-COV-2 is the result of a laboratory leak.
However there is now a large body of evidence to support a leak hypothesis. Taken collectively we believe that it proves the hypothesis well beyond any reasonable doubt. But the reader is encouraged to review the evidence and draw their own conclusions.
There is no absolute proof. But there is most certainly plenty of evidence.
Summary of the Evidence
Geography
The outbreak of a bat coronavirus occurred in the city which hosted the world’s leading bat coronavirus laboratory. This does not prove anything, but it certainly warrants investigation.
Moreover, the relevant horseshoe bats live 1500 kilometers from the laboratory. No explanation has been offered as to how the virus traveled to Wuhan. The Chinese CDC and WIV chief scientist Shi Zhengli have stated that the “wet markets” that sell exotic animals were not the source of the virus.
Natural precursors
A natural virus takes some time to adapt to a new host, as SARS-1 and MERS did. But SARS-COV-2 arose suddenly, fully formed and functional. Early genomes showed minimal variation, and it took many months and billions of infections in order for it to substantially improve upon the first variant (with the Beta and then Delta strains).
The virus is not particularly infectious to bats. So any natural evolution would require some other unknown intermediate host animal. (The coronavirus’s critical spike protein is very host species dependent.)
The WHO report stated that none of the hospitals in Hubei Province (in which Wuhan is located) reported any SARS-like viruses in the months before December 2019, so it is unlikely to have matured in humans. No other natural precursor has been found, despite an extensive search. (The direct precursors to SARS-1 and MERS were identified within several months of their outbreaks.)
The only currently known potential intermediate host is laboratory cell cultures and genetically engineered “humanized” mice which are commonly used for research into coronaviruses.
Laboratory Leaks
Laboratory leaks have occurred many times around the world. Examples include leaks of SARS-1 from Singapore and Taiwan in 2003 and Beijing in 2004, Foot and Mouth from the USA in 2004, Ebola from Germany in 2009, and Brucellosis from China in 2016.
A review of the WIV in 2017 by the US embassy had concerns about the institute’s biosecurity protocols. To their credit, the WIV had asked for help in improving their biosecurity.[Rogin21][Pompeo21][Liu20]
SARS-COV viruses were not considered particularly dangerous before 2020, and published papers indicate that much of the research both at the WIV and the University of North Carolina was conducted at Biosecurity Levels 2 and 3 (BSL-2, BSL-3). The WIV’s new high security BSL-4 facility was used for more dangerous viruses such as Ebola.
Chimera
The virus appears to be 96.1% similar to a genome RaTG13 which was released by the WIV in January 2020, after the outbreak.
The genome suggests that SARS-COV-2 was a chimera, a mixture between two or more viruses. This is because the “body” of the SARS-COV-2 is 98% similar to RaTG13 while the “head” of the virus (the tip of the spike protein) is significantly different.
Such chimeras do occur naturally. However, the two viruses need to infect the same cells in the same animal. No host has been found or proposed. (Evidence that pangolins were involved is now discounted.)
Modern technology makes it relatively easy to create such chimera’s in the laboratory, and this is often performed. They leave no obvious trace that the genome has been manipulated. There is no doubt that the WIV was engineering many such chimeras because they proudly published their results. Shi in 2007 and Baric in 2008 created chimeric viruses based on the SARS virus, with the most influential paper being [Menachery15]. A 2017 WIV paper reported eight chimeric viruses [Hu17].
Furin Cleavage Site
SARS-COV-2 has a “S1/S2 furin cleavage site” that had been known to greatly increase the potency of coronaviruses. This is not found naturally in other beta coronaviruses like SARS-COV-2 yet it is essential for SARS-COV-2 to be able to infect humans. Further, the actual genome that represents the cleavage site is unusual for a coronavirus, but is commonly used in the laboratory.
SARS-1 did not have a furin cleavage site.
Both the very effective spike protein and the furin cleavage site might possibly have arisen naturally. However, it seems extremely unlikely that both would have arisen together without any intermediate virus being discovered. The virus would need to win the genetic lottery twice while being restricted to a small, unknown population. Perhaps this is why it is the most infectious coronavirus in 100 years (much more infectious than SARS or MERS).
2013 Sick Bat Guano Miners
In 2013 six bat guano miners in Mojiang, Yunnan province became very ill with a SARS-like virus, and three died. This was well documented in a recently discovered master’s thesis published at the time by Li Xu [Latham20].
Samples of the virus were sent to the WIV, as they should have been, and some 293 other coronaviruses were then sampled around the cave. It seems likely that one of these formed the basis of SARS-COV-2 and is related to RaTG13.
Chief scientist Shi Zhengli had stated that the miners had died from a fungal infection [Qui20]. However, the subsequent discovery of Li’s thesis makes it clear that it was not a fungal infection. And SARS-1 was never prevalent in Yunnan.
Database Removal and Obfuscation
The WIV had published an important database of virus genetic sequences. However, in September 2019 they removed this database with the excuse that it was subject to cypher attacks, and they have not made it available to any researchers [Bostickson21]. This makes it impossible to determine the exact path of the development of SARS-COV-2.
In 2018 the WIV published the partial genome of BtCoV/4991 from the Mojiang caves. When RaTG13 was subsequently published in 2020, it was discovered to be an exact match. This shows that RaTG13 is the same as BtCoV/4991 and that the WIV had been studying the virus since at least 2018.
Sick WIV Workers
The U.S. government stated there was evidence that several workers at the WIV had become ill enough to require hospitalization in December 2019 [State21]. It is possible that they were infected with SARS-COV-2.
Shi said she was unaware of any sick workers at that time which would be untrue if the US government source is correct. She also said that serum samples were taken from workers around March 2020 and all proved negative for any SARS virus, but no verifiable details have been released. Given the general prevalence of Covid-19 in Wuhan by then that seems most unlikely even if the WIV is not the source of SARS-COV-2 [Quay21].
Eco Health Alliance and NIH Research Grants
The WIV was partially funded from the US Government via the Eco Health Alliance (EHA). EHA’s CEO Peter Daszak explained that it was relatively easy to add a different spike protein to a coronavirus, which was a useful way to study their potential for pandemics [Daszak19].
In 2018 the EHA applied for a Darpa [Defense Advanced Research Projects Agency] grant to develop novel chimeras and specifically to add furin cleavage sites [Drastic21]. That grant was declined due to Gain of Function concerns. They subsequently received smaller grants from the U.S. National Institutes of Health.
Early Contact Tracing
The WHO report described searches of hospital records and other sources and determined the beginning of the outbreak to be early December 2019 [WHO20]. However, there does not appear to have been any follow up on the earliest cases to test those people’s close contacts for SARS antibodies. This contact tracing has been very effective in containing outbreaks in Australia and elsewhere, and should be able to push the source back to a small number of initial cases.
The director of WIV biosafety, Yuan Zhiming, said that zero staff tested positive for antibodies, which would actually be surprising given that the virus was so prevalent in Wuhan [Global21]. ON 3 January 2019, the head of the CDC Robert Redfield offered to send a US team to help identify the origins of SARS-COV-2, but this was declined.
One explanation for these observations is that the Chinese government already knew the source, namely the WIV. Not proof, but yet more evidence.
Chinese Reaction
The Chinese government has reacted angrily to any suggestion of a laboratory leak and has obstructed any investigation. They have prevented laboratory workers from being interviewed, or their laboratory notes being reviewed by external parties.
Further, the Chinese government has forbidden other Chinese researchers from publishing any papers relating to the origins SARS-COV-2 [Kirchgaessner21].
The Chinese government has conducted their own investigation which includes the sampling of some 80,000 animals. They would certainly refute the lab leak hypothesis if they could.
Rebuttal of the Lab Leak Hypothesis
Linage A and B
An unusual feature of SARS-COV-2 is that all samples appear to be a direct descendant of a single case, a 39 year old man seen at a Wuhan PLA Hospital.
But Nature published an article claiming that there were in fact two distinct lineages A and B of SARS-COV-2 prior to 28 February 2019 [Mallapaty21]. They assert that this could only happen if there were not one but two different laboratory leaks, and so “puts a dagger through the heart” of the laboratory leak hypothesis. Strong words indeed.
However, this article is based on an unreviewed preprint on a discussion board. The difference in the lineages is based on just two nucleotides C8782 and T28144, which could have easily evolved naturally after a lab leak in October or November. Indeed, [WHO21] estimates that the most recent common ancestor was 11 December 2019, well after the beginning of the outbreak in late November.
RaTG13 is Too Different
RaTG13 has over 1000 different bases than SARS-COV-2 and it has been argued that there are too many scattered differences to be the result of genetic engineering. However, most of the differences are concentrated in the spike protein “head” area, and not the “body” of the virus which suggests a chimera, whether man made or natural.
The intermediate virus may then have had many generations in cell cultures and humanized mice which would have introduced random changes throughout the virus. Such changes are known to happen at a faster rate than in natural evolution.
The significance of RaTG13 is to show that the virus is a chimera, and that it arose in the Mojiang caves which the WIV had studied. But the actual source may actually be some other closely related virus known only to the WIV. The DARPA grant application says that they had “>180 SARSr-CoV strains sequenced”, most unpublished.
RaTG13 is just a series of letters in a text file that was published after the outbreak. It might not even be the exact genome of any virus and it has not been independently verified. [Deigin21a] (Steven Carl presents evidence that RaTG13 was indeed fabricated [Carl21], [Zhang20], [Rahalkar20].)
The Furin Cleavage Site Encoding
The unusual CGG encoding within the furin cleavage site does occur naturally in about 5% of the arginine’s amino acid codons. There are two of them, so that is 0.25% likely, and certainly not impossible. It is only evidence, not proof.
The Furin cleavage site was also inserted out of frame, meaning that it was inserted in the middle of an existing three nucleotide codon. That excludes certain natural processes, but could have been manipulated. Regardless, it evidently works very well.
What is certain is that having both the furin site and the effective spike protein is very unusual.
Engineering SARS-COV-2 is Beyond Current Technology
It is now relatively easy to engineer a virus to produce any desired protein, but it is extremely difficult to engineer a protein that will have a particular function. In particular, to design a spike protein from first principles that fits snugly into the human ACE2 receptor is beyond current technology. So it is argued that it could not have been engineered.
In 2007 Shi’s group determined that a relatively short part of the spike protein is responsible for binding to different species [Segreto20]. New models to predict human ACE2 affinity have been developed. Subsequent reproduction in cell cultures or humanized mice could refine that sequence to produce SARS-COV-2.
What is certain is that laboratories regularly create chimeras that would be unlikely to occur naturally.
The WIV Cannot Disprove a Leak
Shi Zhengli has complained that it is unreasonable to expect the lab to prove that something did not happen. To prove the non-existence of an event.
However, a lab leak is likely if and only if the WIV was working on or had created a virus that was very similar to the initial SARS-COV-2. Evidence of that would be in their lab notes. Indeed, Shi had earlier said that she had carefully reviewed all lab notes and said “none of the sequences matched those of the viruses her team had sampled from bat caves” (emphasis added). Note that she did not say that there were no engineered sequences that matched SARS-COV-2. An independent review of those same notes would help resolve the issue.
Shi had made misleading statements about the miner’s disease being fungal as well as the source of RaTG13. Peter Daszak had also stated that no bats were kept at the institute, even though there were published videos showing such bats.
Further reading
Expert urges end to 'pandemic virus' research
https://washingtonpost.com/opinions/2021/10/07/manipulating-viruses-risking-pandemics-is-too-dangerous-its-time-stop/
That writer's profile
http://www.sculptingevolution.org/kevin-m-esvelt
Newsweek: Drastic's probe of Wuhan virus lab
https://www.newsweek.com/exclusive-how-amateur-sleuths-broke-wuhan-lab-story-embarrassed-media-1596958
For example,
✓ No record exists of an international scientific review of critical Wuhan virus lab notes that were made during the runup to the outbreak of covid.Though initially soft on the Chinese information gap, the World Health Organization's director, Tedros Adhanom Ghebreyesus, has called for audits of Wuhan laboratories, including the Wuhan Institute of Virology, which some scientists believe may be the source of the virus that caused the first infections in China.
✓ A crucial lab database that could have bolstered a truthful claim that no lab leak had occurred was taken offline shortly before the pandemic came to public attention.
✓ China refuses international on-site investigations.
✓ Chinese authorities have classified as secret a trove of Wuhan virus papers written by Chinese scientists.
The chief scientist at the Wuhan Institute of Virology, Shi Zhengli, has said she had reviewed her notes and found nothing amiss, but evidently they have not been scrutinized by her U.S. or other foreign colleagues.
A recent U.S. intelligence assessment says,
China’s cooperation most likely would be needed to reach a conclusive assessment of the origins of COVID-19. Beijing, however, continues to hinder the global investigation, resist sharing information and blames other countries, including the United States.The summary then went on to excuse the communist clampdown:
These actions reflect, in part, China’s government’s own uncertainty about where an investigation could lead as well as its frustration [that] the international community is using the issue to exert political pressure on China.Unclassified summary of intel report
https://www.dni.gov/files/ODNI/documents/assessments/Unclassified-Summary-of-Assessment-on-COVID-19-Origins.pdf
The intelligence units, as quoted by the summary, do not suggest that China's secrecy tends to undercut its stance that no lab leak occurred.
The summary, from the national intelligence director's office, says that one intelligence unit was moderately confident that the pandemic was sparked by a lab leak. It adds that four intelligence units and the National Intelligence Council leaned toward the "leap from an animal" theory. But they were extremely unsure of that scenario, for which they had only "low confidence." Analysts at three other intelligence units, the summary says, were divided between the "animal leap" and lab accident scenarios.
The summary explains that differences of opinion stem largely from the methods each agency uses to sift and analyze information. It avoids raising the possibility of undue political influence from the China lobby, which consists of American investors eager for "engagement" riches and Chinese communist-backed operatives.
Reporters Without Borders, an international activist group, reports that a Chinese journalist, imprisoned for her early pandemic reporting, is now near death. The group documents a number of other cases of China's harsh treatment of journalists who do not toe the party line.
Chinese covid reporter's harsh treatment
https://rsf.org/en/news/china-rsf-urges-release-covid-19-reporter-who-faces-impending-death
Drastic -- an acronym for 'Decentralized Radical Autonomous Search Team Investigating COVID-19' -- is a loose collection of internet activists investigating the origins of covid. The dogged information-mining of these activists has drawn both admiration and scorn from scientists. Yet, there is little doubt that the collective's work has knocked out the oft repeated charge that the lab leak scenario was merely an alt right "conspiracy theory" (as if communists would never conspire).
Drastic home page
https://drasticresearch.org/
Drastic's cyber activities are assuredly a menace to the desire of governments to control information. We can be sure that Beijing views Drastic with the same dim view that the U.S. and British governments have of Wikileaks. And, considering the complicity of major elements of the U.S. press and government in shielding communist China from criticism in the Wuhan matter, it is only a matter of time before the CIA is weighing measures for shutting down Drastic as a spy shop for a foreign government while the Justice Department obtains indictments of its leadership for the "crime" of Assange-style journalism.
Free press coalition opposes Assange extradition
https://invisiblepaul.blogspot.com/p/free-press-coalition-opposes-assange.html
Below is Drastic's summary of its case.
The Lab Leak Hypothesis
Virologists study dangerous viruses. They collect them from the wild, they study them in labs, and they genetically engineer them. One goal of their research is to help prevent future pandemics.
However, viruses have escaped from laboratories around the world on several occasions. New techniques for bioengineering can enable dangerous viruses to be created in research laboratories.
Previous pandemics such as SARS and MERS have arisen naturally as viruses jump from species to species and evolve through natural selection. The lab leak hypothesis proposes that the SARS-COV-2 virus responsible for Covid-19 did not arise naturally but escaped from a virology laboratory, the Wuhan Institute of Virology (WIV) [Segreto20] [Deigin21].
The Importance of the Hypothesis
If SARS-COV-2 did result from a lab leak then such research needs to be much more carefully controlled in order to prevent any future outbreak of an even more potent virus.
There is no suggestion that the leak was deliberate. The Wuhan Institute of Virology published their impressive results and collaborated openly with other virologists around the world. For example, their chief scientist Shi Zhengli collaborated closely with Ralph Baric of the University of North Carolina. The Wuhan Institute of Virology is a well respected member of the international community of virologists.
Until recently, any suggestion of a laboratory leak was discounted as an unsubstantiated far right conspiracy theory. However, as more and more evidence has accumulated many leading scientists now consider the theory plausible if not proven.
This paper should not be viewed as an attack on China. But rather, it provides a strong motivation to review the practice of virology internationally.
Beyond Reasonable Doubt
There will never be a mathematical proof that SARS-COV-2 is the result of a laboratory leak.
However there is now a large body of evidence to support a leak hypothesis. Taken collectively we believe that it proves the hypothesis well beyond any reasonable doubt. But the reader is encouraged to review the evidence and draw their own conclusions.
There is no absolute proof. But there is most certainly plenty of evidence.
Summary of the Evidence
Geography
The outbreak of a bat coronavirus occurred in the city which hosted the world’s leading bat coronavirus laboratory. This does not prove anything, but it certainly warrants investigation.
Moreover, the relevant horseshoe bats live 1500 kilometers from the laboratory. No explanation has been offered as to how the virus traveled to Wuhan. The Chinese CDC and WIV chief scientist Shi Zhengli have stated that the “wet markets” that sell exotic animals were not the source of the virus.
Natural precursors
A natural virus takes some time to adapt to a new host, as SARS-1 and MERS did. But SARS-COV-2 arose suddenly, fully formed and functional. Early genomes showed minimal variation, and it took many months and billions of infections in order for it to substantially improve upon the first variant (with the Beta and then Delta strains).
The virus is not particularly infectious to bats. So any natural evolution would require some other unknown intermediate host animal. (The coronavirus’s critical spike protein is very host species dependent.)
The WHO report stated that none of the hospitals in Hubei Province (in which Wuhan is located) reported any SARS-like viruses in the months before December 2019, so it is unlikely to have matured in humans. No other natural precursor has been found, despite an extensive search. (The direct precursors to SARS-1 and MERS were identified within several months of their outbreaks.)
The only currently known potential intermediate host is laboratory cell cultures and genetically engineered “humanized” mice which are commonly used for research into coronaviruses.
Laboratory Leaks
Laboratory leaks have occurred many times around the world. Examples include leaks of SARS-1 from Singapore and Taiwan in 2003 and Beijing in 2004, Foot and Mouth from the USA in 2004, Ebola from Germany in 2009, and Brucellosis from China in 2016.
A review of the WIV in 2017 by the US embassy had concerns about the institute’s biosecurity protocols. To their credit, the WIV had asked for help in improving their biosecurity.[Rogin21][Pompeo21][Liu20]
SARS-COV viruses were not considered particularly dangerous before 2020, and published papers indicate that much of the research both at the WIV and the University of North Carolina was conducted at Biosecurity Levels 2 and 3 (BSL-2, BSL-3). The WIV’s new high security BSL-4 facility was used for more dangerous viruses such as Ebola.
Chimera
The virus appears to be 96.1% similar to a genome RaTG13 which was released by the WIV in January 2020, after the outbreak.
The genome suggests that SARS-COV-2 was a chimera, a mixture between two or more viruses. This is because the “body” of the SARS-COV-2 is 98% similar to RaTG13 while the “head” of the virus (the tip of the spike protein) is significantly different.
Such chimeras do occur naturally. However, the two viruses need to infect the same cells in the same animal. No host has been found or proposed. (Evidence that pangolins were involved is now discounted.)
Modern technology makes it relatively easy to create such chimera’s in the laboratory, and this is often performed. They leave no obvious trace that the genome has been manipulated. There is no doubt that the WIV was engineering many such chimeras because they proudly published their results. Shi in 2007 and Baric in 2008 created chimeric viruses based on the SARS virus, with the most influential paper being [Menachery15]. A 2017 WIV paper reported eight chimeric viruses [Hu17].
Furin Cleavage Site
SARS-COV-2 has a “S1/S2 furin cleavage site” that had been known to greatly increase the potency of coronaviruses. This is not found naturally in other beta coronaviruses like SARS-COV-2 yet it is essential for SARS-COV-2 to be able to infect humans. Further, the actual genome that represents the cleavage site is unusual for a coronavirus, but is commonly used in the laboratory.
SARS-1 did not have a furin cleavage site.
Both the very effective spike protein and the furin cleavage site might possibly have arisen naturally. However, it seems extremely unlikely that both would have arisen together without any intermediate virus being discovered. The virus would need to win the genetic lottery twice while being restricted to a small, unknown population. Perhaps this is why it is the most infectious coronavirus in 100 years (much more infectious than SARS or MERS).
2013 Sick Bat Guano Miners
In 2013 six bat guano miners in Mojiang, Yunnan province became very ill with a SARS-like virus, and three died. This was well documented in a recently discovered master’s thesis published at the time by Li Xu [Latham20].
Samples of the virus were sent to the WIV, as they should have been, and some 293 other coronaviruses were then sampled around the cave. It seems likely that one of these formed the basis of SARS-COV-2 and is related to RaTG13.
Chief scientist Shi Zhengli had stated that the miners had died from a fungal infection [Qui20]. However, the subsequent discovery of Li’s thesis makes it clear that it was not a fungal infection. And SARS-1 was never prevalent in Yunnan.
Database Removal and Obfuscation
The WIV had published an important database of virus genetic sequences. However, in September 2019 they removed this database with the excuse that it was subject to cypher attacks, and they have not made it available to any researchers [Bostickson21]. This makes it impossible to determine the exact path of the development of SARS-COV-2.
In 2018 the WIV published the partial genome of BtCoV/4991 from the Mojiang caves. When RaTG13 was subsequently published in 2020, it was discovered to be an exact match. This shows that RaTG13 is the same as BtCoV/4991 and that the WIV had been studying the virus since at least 2018.
Sick WIV Workers
The U.S. government stated there was evidence that several workers at the WIV had become ill enough to require hospitalization in December 2019 [State21]. It is possible that they were infected with SARS-COV-2.
Shi said she was unaware of any sick workers at that time which would be untrue if the US government source is correct. She also said that serum samples were taken from workers around March 2020 and all proved negative for any SARS virus, but no verifiable details have been released. Given the general prevalence of Covid-19 in Wuhan by then that seems most unlikely even if the WIV is not the source of SARS-COV-2 [Quay21].
Eco Health Alliance and NIH Research Grants
The WIV was partially funded from the US Government via the Eco Health Alliance (EHA). EHA’s CEO Peter Daszak explained that it was relatively easy to add a different spike protein to a coronavirus, which was a useful way to study their potential for pandemics [Daszak19].
In 2018 the EHA applied for a Darpa [Defense Advanced Research Projects Agency] grant to develop novel chimeras and specifically to add furin cleavage sites [Drastic21]. That grant was declined due to Gain of Function concerns. They subsequently received smaller grants from the U.S. National Institutes of Health.
Early Contact Tracing
The WHO report described searches of hospital records and other sources and determined the beginning of the outbreak to be early December 2019 [WHO20]. However, there does not appear to have been any follow up on the earliest cases to test those people’s close contacts for SARS antibodies. This contact tracing has been very effective in containing outbreaks in Australia and elsewhere, and should be able to push the source back to a small number of initial cases.
The director of WIV biosafety, Yuan Zhiming, said that zero staff tested positive for antibodies, which would actually be surprising given that the virus was so prevalent in Wuhan [Global21]. ON 3 January 2019, the head of the CDC Robert Redfield offered to send a US team to help identify the origins of SARS-COV-2, but this was declined.
One explanation for these observations is that the Chinese government already knew the source, namely the WIV. Not proof, but yet more evidence.
Chinese Reaction
The Chinese government has reacted angrily to any suggestion of a laboratory leak and has obstructed any investigation. They have prevented laboratory workers from being interviewed, or their laboratory notes being reviewed by external parties.
Further, the Chinese government has forbidden other Chinese researchers from publishing any papers relating to the origins SARS-COV-2 [Kirchgaessner21].
The Chinese government has conducted their own investigation which includes the sampling of some 80,000 animals. They would certainly refute the lab leak hypothesis if they could.
Rebuttal of the Lab Leak Hypothesis
Linage A and B
An unusual feature of SARS-COV-2 is that all samples appear to be a direct descendant of a single case, a 39 year old man seen at a Wuhan PLA Hospital.
But Nature published an article claiming that there were in fact two distinct lineages A and B of SARS-COV-2 prior to 28 February 2019 [Mallapaty21]. They assert that this could only happen if there were not one but two different laboratory leaks, and so “puts a dagger through the heart” of the laboratory leak hypothesis. Strong words indeed.
However, this article is based on an unreviewed preprint on a discussion board. The difference in the lineages is based on just two nucleotides C8782 and T28144, which could have easily evolved naturally after a lab leak in October or November. Indeed, [WHO21] estimates that the most recent common ancestor was 11 December 2019, well after the beginning of the outbreak in late November.
RaTG13 is Too Different
RaTG13 has over 1000 different bases than SARS-COV-2 and it has been argued that there are too many scattered differences to be the result of genetic engineering. However, most of the differences are concentrated in the spike protein “head” area, and not the “body” of the virus which suggests a chimera, whether man made or natural.
The intermediate virus may then have had many generations in cell cultures and humanized mice which would have introduced random changes throughout the virus. Such changes are known to happen at a faster rate than in natural evolution.
The significance of RaTG13 is to show that the virus is a chimera, and that it arose in the Mojiang caves which the WIV had studied. But the actual source may actually be some other closely related virus known only to the WIV. The DARPA grant application says that they had “>180 SARSr-CoV strains sequenced”, most unpublished.
RaTG13 is just a series of letters in a text file that was published after the outbreak. It might not even be the exact genome of any virus and it has not been independently verified. [Deigin21a] (Steven Carl presents evidence that RaTG13 was indeed fabricated [Carl21], [Zhang20], [Rahalkar20].)
The Furin Cleavage Site Encoding
The unusual CGG encoding within the furin cleavage site does occur naturally in about 5% of the arginine’s amino acid codons. There are two of them, so that is 0.25% likely, and certainly not impossible. It is only evidence, not proof.
The Furin cleavage site was also inserted out of frame, meaning that it was inserted in the middle of an existing three nucleotide codon. That excludes certain natural processes, but could have been manipulated. Regardless, it evidently works very well.
What is certain is that having both the furin site and the effective spike protein is very unusual.
Engineering SARS-COV-2 is Beyond Current Technology
It is now relatively easy to engineer a virus to produce any desired protein, but it is extremely difficult to engineer a protein that will have a particular function. In particular, to design a spike protein from first principles that fits snugly into the human ACE2 receptor is beyond current technology. So it is argued that it could not have been engineered.
In 2007 Shi’s group determined that a relatively short part of the spike protein is responsible for binding to different species [Segreto20]. New models to predict human ACE2 affinity have been developed. Subsequent reproduction in cell cultures or humanized mice could refine that sequence to produce SARS-COV-2.
What is certain is that laboratories regularly create chimeras that would be unlikely to occur naturally.
The WIV Cannot Disprove a Leak
Shi Zhengli has complained that it is unreasonable to expect the lab to prove that something did not happen. To prove the non-existence of an event.
However, a lab leak is likely if and only if the WIV was working on or had created a virus that was very similar to the initial SARS-COV-2. Evidence of that would be in their lab notes. Indeed, Shi had earlier said that she had carefully reviewed all lab notes and said “none of the sequences matched those of the viruses her team had sampled from bat caves” (emphasis added). Note that she did not say that there were no engineered sequences that matched SARS-COV-2. An independent review of those same notes would help resolve the issue.
Shi had made misleading statements about the miner’s disease being fungal as well as the source of RaTG13. Peter Daszak had also stated that no bats were kept at the institute, even though there were published videos showing such bats.
Further reading
Expert urges end to 'pandemic virus' research
https://washingtonpost.com/opinions/2021/10/07/manipulating-viruses-risking-pandemics-is-too-dangerous-its-time-stop/
That writer's profile
http://www.sculptingevolution.org/kevin-m-esvelt
Newsweek: Drastic's probe of Wuhan virus lab
https://www.newsweek.com/exclusive-how-amateur-sleuths-broke-wuhan-lab-story-embarrassed-media-1596958
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