The coronavirus did not escape from a lab. Here's how we know.

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adam

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Are you saying RaTG13 is the precursor virus to sars-cov-2? It has been suggested that there is decades of natural evolution between the two so this scenario seems unlikely.
The info in the link I posted into the research by Dr J Latham (a virologist) and Allison Wilson, PhD - is very helpful in showing how the virus could have developed rapidly to Covid-19, and why the virus did not emerge before 2019 is also addressed as is the involvement of WuHan Institute of Virology / WIV and Professor Shi.

I will copy and paste in a separate answer - the start of a big section from their paper headed

Jonathan Latham, PhD and Allison Wilson, PhD

You can continue reading the rest in post with the peer reviewed links . The Q&A is also very good

The medical details were published in a 2013/2014 MA thesis (later a Phd) by the hospital Dr - Dr Xu

In April/May 2012 Dr Xu had 6 patients, who worked in the bat cave where the RaTG13 virus was later found. 3 patients died. This was initially treated as a potential SARS outbreak and hospital emergency.

Dr Xu's thesis links the miners deaths to an unknown SARS like bat virus from the caves. Some miners did test positive for a coronavirus and the ultimate conclusion of the thesis reads “the unknown virus [that] led to severe pneumonia could be: The SARS-like-CoV from the Chinese rufous horseshoe bat.”
 
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adam

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Jonathan Latham, PhD
and
Allison Wilson, PhD

We agree that ordinary rates of evolution would not allow RaTG13 to evolve into SARS-CoV-2 but we also believe that conditions inside the lungs of the miners were far from ordinary. Five major factors specific to the hospitalised miners favoured a very high rate of evolution inside them.

i) When viruses infect new species they typically undergo a period of very rapid evolution because the selection pressure on the invading pathogen is high. The phenomenon of rapid evolution in new hosts is well attested among corona- and other viruses (Makino et al., 1986; Baric et al., 1997; Dudas and Rambaut 2016; Forni et al., 2017).

ii) Judging by their clinical symptoms such as the CT scans, all the miner’s infections were primarily of the lungs. This localisation likely occurred initially because the miners were exerting themselves and therefore inhaling the disturbed bat guano deeply. As miners, they may already have had damaged lung tissues (patient 3 had suspected pneumoconiosis) and/or particulate matter was present that irritated the tissues and may have facilitated initial viral entry.

In contrast, standard coronavirus infections are confined to the throat and upper respiratory tract. They do not normally reach the lungs (Perlman and Netland, 2009). Lungs are far larger tissues by weight (kilos vs grammes) than the upper respiratory tract. There was therefore likely a much larger quantity of virus inside the miners than would be the case in an ordinary coronavirus infection.

Evolutionary change is in large part a function of the population size. The lungs of the miners, we suggest, supported a very high viral load leading to proportionately rapid viral evolution.

Furthermore, according to the Master’s thesis, the immune systems of the miners were compromised and remained so even for those discharged. This weakness on the part of the miners may also have encouraged evolution of the virus.

iii) The length of infection experienced by the miners (especially patients 2, 3 and 4) far exceeded that of an ordinary coronavirus infection. From first becoming too sick to work in the mine, patient 2 survived 57 days until he died. Patient 3 survived 120 days after stopping work. Patient 4 survived 117 days and then was discharged as cured. Each had been exposed in the mine for 14 days prior to the onset of severe symptoms; thus each presumably had nascent infections for some time before calling in sick (See Table 2 of the thesis).

In contrast, in ordinary coronavirus infections the viral infection is cleared within about ten to fourteen days after being acquired (Tay et al., 2020). Thus, unlike most sufferers from coronavirus infection, the hospitalised miners had very long-term bouts of disease characterised by a continuous high load of virus. In the cases of patients 3 and 4 their illnesses lasted over 4 months.

iv) Coronaviruses are well known to recombine at very high rates: 10% of all progeny in a cell can be recombinants (Makino et al., 1986; Banner and Lai, 1991; Dudas and Rambaut, 2016). In normal virus evolution the mutation rate and the selection pressure are the main foci of attention. But in the case of a coronavirus adapting to a new host where many mutations distributed all over the genome are required to fully adapt to the new host, the recombination rate is likely to be highly influential in determining the overall speed of adaptation by the virus population (Baric et al., 1997).

Inside the miners a large tissue was simultaneously infected by a population of poorly-adapted viruses, with each therefore under pressure to adapt. Even if the starting population of virus lacked any diversity, many individual viruses would have acquired mutations independently but only recombination would have allowed these mutations to unite in the same genome. To recombine, viruses must be present in the same cell. In such a situation the particularities of lung tissues become potentially important because the existence of airways (bronchial tubes, etc.) allows partially-adapted viruses from independent viral populations to travel to distal parts of the lung (or even the other lung) and encounter other such partially-adapted viruses and populations. This movement around the lungs would likely have resulted in what amounted to a passaging effect without the need for a researcher to infect new tissues. Indeed, in the Master’s thesis the observation is several times made that areas of the lungs of a specific patient would appear to heal even while other parts of the lungs would become infected.

v) There were also a number of unusual things about the bat coronaviruses in the mine. They were abnormally abundant but also there were many different kinds, often causing co-infections of the bats (Ge et al., 2016). Viral co-infections are often more infectious or more pathogenic (Latham and Wilson, 2007).

As the WIV researchers remarked about the bats in the mine:

“we observed a high rate of co-infection with two coronavirus species and interspecies infection with the same coronavirus species within or across bat families. These phenomena may be owing to the diversity and high density of bat populations in the same cave, facilitating coronavirus intra- and interspecies transmissions, which may result in recombination and acceleration of coronavirus evolution.” (Ge et al., 2016).


PLEASE READ

Jonathan Latham, PhD and Allison Wilson, PhD

LINK below FOR THE REST

[/s][/s]
 
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efarina96

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If one has significant knowledge of virology and molecular biology, it would be obvious by a simple evaluation of the requirements that this virus was NOT "artificially created" in a lab, or anywhere else. Such manipulations are well beyond our current capabilities. We are simply not that clever, yet.

"Altering" or "isolating" an existing strain is another story. While it has no doubt been covered in the many posts before these, a viral isolate from the wild, by itself or by isolating it from "downstream" serial infections, could have been produced in a lab, and somehow got into humans. This is not "artificially created". It is using strictly natural processes, albeit with human assistance.

Many of these viruses are replicating in all kinds of animals at very low levels, and may never infect humans unless they are amplified and allowed sufficient exposure to human hosts. There is every reason to believe that direct transfer to humans from either an animal, or a lab isolate from an animal (or cell culture), is the source of the original strain now brutalizing the world.
While I believe you are probably correct, the question I have asked is very simple and remains unanswered. Consider that it is well established that our government employs the use of secret technology, such as the technology used to improve the resolution of a photo Robert Ballard used in the search for Amelia Earhart. I believe it to be highly likely that the government is hiding significantly more advanced technology. Is it not even remotely possible that the Chinese or another government could use some form of anticipatory mutation, releasing a virus into the wild that is designed to mutate in a specific way and to be highly transmissible? Isn't it at least remotely possible that there is some other means by which a bad actor could cover their tracks using sufficiently advanced secret technology? The idea that the tech the public is aware of constitutes the epitomy of modern advancement seems pretty absurd to me. The Manhattan project outlined the manner in which strategic division of labor can be used to mask the true purpose of government funded research, aw practice which it would be highly logical to think might continue to this day, and the government has a well known tendency to hide essentially any information they are not physically forced to share so long as that information gives them a perceived edge against their rivals. here is just one example: https://www.livescience.com/64292-military-classified-geoscience.html
 
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Jonathan Latham, PhD
and
Allison Wilson, PhD

We agree that ordinary rates of evolution would not allow RaTG13 to evolve into SARS-CoV-2 but we also believe that conditions inside the lungs of the miners were far from ordinary. Five major factors specific to the hospitalised miners favoured a very high rate of evolution inside them.

i) When viruses infect new species they typically undergo a period of very rapid evolution because the selection pressure on the invading pathogen is high. The phenomenon of rapid evolution in new hosts is well attested among corona- and other viruses (Makino et al., 1986; Baric et al., 1997; Dudas and Rambaut 2016; Forni et al., 2017).

ii) Judging by their clinical symptoms such as the CT scans, all the miner’s infections were primarily of the lungs. This localisation likely occurred initially because the miners were exerting themselves and therefore inhaling the disturbed bat guano deeply. As miners, they may already have had damaged lung tissues (patient 3 had suspected pneumoconiosis) and/or particulate matter was present that irritated the tissues and may have facilitated initial viral entry.

In contrast, standard coronavirus infections are confined to the throat and upper respiratory tract. They do not normally reach the lungs (Perlman and Netland, 2009). Lungs are far larger tissues by weight (kilos vs grammes) than the upper respiratory tract. There was therefore likely a much larger quantity of virus inside the miners than would be the case in an ordinary coronavirus infection.

Evolutionary change is in large part a function of the population size. The lungs of the miners, we suggest, supported a very high viral load leading to proportionately rapid viral evolution.

Furthermore, according to the Master’s thesis, the immune systems of the miners were compromised and remained so even for those discharged. This weakness on the part of the miners may also have encouraged evolution of the virus.

iii) The length of infection experienced by the miners (especially patients 2, 3 and 4) far exceeded that of an ordinary coronavirus infection. From first becoming too sick to work in the mine, patient 2 survived 57 days until he died. Patient 3 survived 120 days after stopping work. Patient 4 survived 117 days and then was discharged as cured. Each had been exposed in the mine for 14 days prior to the onset of severe symptoms; thus each presumably had nascent infections for some time before calling in sick (See Table 2 of the thesis).

In contrast, in ordinary coronavirus infections the viral infection is cleared within about ten to fourteen days after being acquired (Tay et al., 2020). Thus, unlike most sufferers from coronavirus infection, the hospitalised miners had very long-term bouts of disease characterised by a continuous high load of virus. In the cases of patients 3 and 4 their illnesses lasted over 4 months.

iv) Coronaviruses are well known to recombine at very high rates: 10% of all progeny in a cell can be recombinants (Makino et al., 1986; Banner and Lai, 1991; Dudas and Rambaut, 2016). In normal virus evolution the mutation rate and the selection pressure are the main foci of attention. But in the case of a coronavirus adapting to a new host where many mutations distributed all over the genome are required to fully adapt to the new host, the recombination rate is likely to be highly influential in determining the overall speed of adaptation by the virus population (Baric et al., 1997).

Inside the miners a large tissue was simultaneously infected by a population of poorly-adapted viruses, with each therefore under pressure to adapt. Even if the starting population of virus lacked any diversity, many individual viruses would have acquired mutations independently but only recombination would have allowed these mutations to unite in the same genome. To recombine, viruses must be present in the same cell. In such a situation the particularities of lung tissues become potentially important because the existence of airways (bronchial tubes, etc.) allows partially-adapted viruses from independent viral populations to travel to distal parts of the lung (or even the other lung) and encounter other such partially-adapted viruses and populations. This movement around the lungs would likely have resulted in what amounted to a passaging effect without the need for a researcher to infect new tissues. Indeed, in the Master’s thesis the observation is several times made that areas of the lungs of a specific patient would appear to heal even while other parts of the lungs would become infected.

v) There were also a number of unusual things about the bat coronaviruses in the mine. They were abnormally abundant but also there were many different kinds, often causing co-infections of the bats (Ge et al., 2016). Viral co-infections are often more infectious or more pathogenic (Latham and Wilson, 2007).

As the WIV researchers remarked about the bats in the mine:

“we observed a high rate of co-infection with two coronavirus species and interspecies infection with the same coronavirus species within or across bat families. These phenomena may be owing to the diversity and high density of bat populations in the same cave, facilitating coronavirus intra- and interspecies transmissions, which may result in recombination and acceleration of coronavirus evolution.” (Ge et al., 2016).


PLEASE READ

Jonathan Latham, PhD and Allison Wilson, PhD

LINK below FOR THE REST

[/s][/s]

The miners may have had a sars-like coronavirus, or may have had a fungal infection; it seems that the actual cause of death wasnt confirmed either way. So as a starting point to this proposal, there is uncertainy. If the assumption is that it was a sars-like coronavirus, it may have been any of the variety of coronaviruses that the cave was found to have hosted. The authors to this lab escape theory have assumed that it was RaTG13 and then rely on further hypothetical assumptions of fact to support their theory. They may be correct, but their hypothesis seems unlikely to me -relying on theoretical possibilities, assumption and exceptional circumstance -and contradicts the various lineage studies that have proposed decades of evolution separating the two viruses in question. They insist that the WIV must have performed human cell passage experiments because the opportunity would be too tempting to miss, and from there an accidental release occured. Shi Zheng Li has stated that they only sequenced RaTG13 and did not isolate it, and so such experiments would not have been possible, and indeed havent been reported. It may be theoretically possible, but i dont buy it.
 
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If the assumption is that it was a sars-like coronavirus, it may have been any of the variety of coronaviruses that the cave was found to have hosted.
This is quite true. It is clear that many viruses replicate in wild animals (and humans) at low levels to escape immune elimination, and their ability to infect new hosts presents itself over time. A large number of viruses are of this nature. It is how they survive.

If a sufficient dose of virus is obtained by a human from a wild animal, and takes hold as an active infection, it could lead to a global pandemic, or a local sniffle and disappear.

One thing that certainly seems likely. There are others lurking that could be worse than what we are seeing now. People fooling around with these viruses and amplifying them better know what they are doing, and eliminate any chance of an outbreak.

The spread to humans from wild sources must be minimized by highly enforced regulations. People may simply have to stop eating certain "foods".
 
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This is quite true. It is clear that many viruses replicate in wild animals (and humans) at low levels to escape immune elimination, and their ability to infect new hosts presents itself over time. A large number of viruses are of this nature. It is how they survive.

If a sufficient dose of virus is obtained by a human from a wild animal, and takes hold as an active infection, it could lead to a global pandemic, or a local sniffle and disappear.

One thing that certainly seems likely. There are others lurking that could be worse than what we are seeing now. People fooling around with these viruses and amplifying them better know what they are doing, and eliminate any chance of an outbreak.

The spread to humans from wild sources must be minimized by highly enforced regulations. People may simply have to stop eating certain "foods".
Whilst I agree that work with live isolates of viruses with high human pathogenic potential should be practised under the highest standards of lab safety, I believe that the greater threat is posed by viruses naturally emerging from nature, given the seemingly accelerating frequency at which they are occurring. I think that it is hard to deny that this is a result of human behaviours that give increased opportunity to zoonotic events, such as industrialised livestock farming and deforestation [see research on how loss of biodiversity increases likelihood of future pandemics]. This is why a focus on a lab escape theory without clear evidence is unhelpful and obstructs our ability to recognise our collective liability for this dreadful situation, ultimately hindering our ability to prevent future similar events. Its not a lab in Wuhan; its not a bat in a seafood market; its everything: its energy consumption; its climate change; its war; its mass consumption economics and associated culture etc. If we continue to treat the delicate and intricately inter-connected ecosystem with the same reckless indifference, we should only expect more of the same.
 

adam

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While I believe you are probably correct, the question I have asked is very simple and remains unanswered. Consider that it is well established that our government employs the use of secret technology, such as the technology used to improve the resolution of a photo Robert Ballard used in the search for Amelia Earhart. I believe it to be highly likely that the government is hiding significantly more advanced technology. Is it not even remotely possible that the Chinese or another government could use some form of anticipatory mutation, releasing a virus into the wild that is designed to mutate in a specific way and to be highly transmissible? Isn't it at least remotely possible that there is some other means by which a bad actor could cover their tracks using sufficiently advanced secret technology? The idea that the tech the public is aware of constitutes the epitomy of modern advancement seems pretty absurd to me. The Manhattan project outlined the manner in which strategic division of labor can be used to mask the true purpose of government funded research, aw practice which it would be highly logical to think might continue to this day, and the government has a well known tendency to hide essentially any information they are not physically forced to share so long as that information gives them a perceived edge against their rivals. here is just one example: https://www.livescience.com/64292-military-classified-geoscience.html
As far as controlled bio weapons if they exist we would not know about them until after they were used - if at all.

As far as Covid-19 goes it does seem there is some data missing between its nearest wild virus from the 2012 bat caves and Covid-19 (or an alternative wild source).

If that 2012 wild virus from the Chinese bat caves is its origin and it mutated naturally we should either see some genetic markers - plus animals who were more or equally prone to it as humans, or were virus carriers or some earlier human version of the virus.

So far nothing.

The fact that China will not allow outside observers access and has destroyed evidence is not good, but does not imply pre planning - just the opposite a cover up.

The fact that Prof Shi says the miners died in 2012 from a deadly fungal infection is not credible because -

if it really was the case that a deadly new fungus with SARS like symptoms was a possible cause of the deaths there would have been

lots of experts on fungal infections visiting the caves multiple times not bat coronavirus researchers and

the dead mens Dr would have written his medical thesis on their deaths based on a fungal infection not a new unknown coronavirus SARS

Finally Prof Shi says the fungal infection was caught in the bat caves where she found in bats a new strain of SARS - but also that the men would have anyway caught the bat virus if they had worked longer in the caves. This implies lots of knowledge - which she has of coronaviruses.

This new bat related SARS is genetically linked to human SARS and she said is the only one found in the caves she classified as of beta/human pandemic potential.

One other beta coronavirus was found in the caves but was not closely linked to any human version of SARS etc

There were many other coronaviruses also found in the bats but they were alpha viruses meaning very very unlikely to infect humans

The hospital Dr also sent blood and tissue to Wuhan 1,000 miles away, for Prof Shi's colleagues and other to test and consulted with the top SARS expert - plus the men were in hospital for up to six months or died so had lots of time to study them unlike Prof Shi ?

While none of this proves that the men died of a SARS related coronavirus - it seems more likely than a fungal infection with SARS like symptoms - at least based on what is currently known.

Either way none of the above proves Dr Latham's theory about Covid-19s development in humans, however it opens up an understanding of how human gain of function could be done in a lab in a petri dish using human tissue from the miners or elsewhere, and with other viruses - so avoiding gene splicing and making rapid and natural like mutations and not requiring a prior animal host.

I will try and write more in answer to other peoples messages another time
 
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Coronaviruses closely related to the pandemic virus discovered in Japan and Cambodia

Two lab freezers in Asia have yielded surprising discoveries. Researchers have told Nature they have found a coronavirus that is closely related to SARS-CoV-2, the virus responsible for the pandemic, in horseshoe bats stored in a freezer in Cambodia. Meanwhile, a team in Japan has reported the discovery of another closely related coronavirus — also found in frozen bat droppings.

The virus in Cambodia was found in two Shamel’s horseshoe bats (Rhinolophus shameli) captured in the country’s north in 2010. The virus’s genome has not yet been fully sequenced — nor its discovery published — making its full significance to the pandemic hard to ascertain.

That is the case with the other virus, called Rc-o319, identified in a little Japanese horseshoe bat (Rhinolophus cornutus) captured in 2013. That virus shares 81% of its genome with SARS-CoV-2, according to a paper1 published on 2 November — which makes it too distant to provide insights into the pandemic’s origin, says Edward Holmes, a virologist at the University of Sydney in Australia.
 

Finch

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A persistent coronavirus myth that this virus, called SARS-CoV-2, was made by scientists and escaped from a lab in Wuhan is completely unfounded. Here's how we know.

The coronavirus did not escape from a lab. Here's how we know. : Read more
You do not know this, we also do not know that covid 19 was not first discovered in 2012 in a bat cave 1000 miles from Wuhan. Also there is no need to create a new virus in the lab, simply letting an existing one go is good enough.
 

adam

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You do not know this, we also do not know that covid 19 was not first discovered in 2012 in a bat cave 1000 miles from Wuhan. Also there is no need to create a new virus in the lab, simply letting an existing one go is good enough.
These comments make sense - though there is data missing on how covid-19 developed from the 2012 miners coronavirus.

To recap there were 2 SARS type betacoronaviruses discovered by Professor Shi from the Wuhan Institute of Virology (WIV) in 2012 in the caves she visited after the miners died in 2012 from an infection by an unknown coronavirus with SARS/covid-19 like symptoms.

WIV was consulted about the miners unknown coronavirus in 2012 and records show WIV tested the miners blood. Other tests on human tissue from the miners also took place.

Also in 2020 Prof Shi made misleading or very unscientific comments about the miners deaths and her discovery in 2012 of the betacoronavirus RaTG13 despite publishing papers on it in 2016. Prof Shi implied the work and/or discovery of RaTG13 was very recent and made no reference to her previous papers and work on RaTG13

Note - many other viruses were also found in the same caves by Prof Shi in 2012 these other corona viruses had no meaningful genetic link to covid-19 unlike RaTG13, or to possible human infection in the future, and were not betacoronaviruses

So RaTG13 is confirmed by Prof Shi in a 2016 published paper (linked below and previously) as having been discovered by her in 2012 in caves (that miners caught and died of an unknown coronavirus) and Prof Shi states in 2016 that it has human SARS like pandemic potentional as a betacoronavirus and we now know is also the closest coronavirus yet found with an over 96%+ genetic match to covid-19

Prof Shi indicates that the other betacoronavirus discovered in the mine had only a very distant link to SARS and none to human SARS, and was considered very very unlikely to be able to infect peopl e- this other coronavirus had about an 80% genetic match to existing non human SARS viruses

Please read the quotes below and for further full info and see all the research papers quoted and linked in the links below


the "Shi lab found that bat coronaviruses were unusually abundant in the mine (Ge at al., 2016). Among their findings were two betacoronaviruses, one of which was RaTG13 (then known as BtCoV/4991). In the coronavirus world betacoronaviruses are special in that both SARS and MERS, the most deadly of all coronaviruses, are both betacoronaviruses. Thus they are considered to have special pandemic potential, as the concluding sentence of the Shi lab publication which found RaTG13 implied: “special attention should particularly be paid to these lineages of coronaviruses” "

"in a letter obtained by us Zheng-li Shi confirmed to a virology database that BtCoV/4991 and RaTG13 are both from the same bat faecal sample and the same mine" in 2012
 
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adam

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I do not think that anyone has properly explained the origins of Covid-19 and that is a problem

It is clear China stopped internal travel but allowed international travel so knowingly allowed covid-19 to spread internationally and China has withheld info on a big scale.

My comments are just a recap
To recap there were 2 SARS type betacoronaviruses discovered by Professor Shi from the Wuhan Institute of Virology (WIV) in 2012 in the caves she visited after the miners died in 2012 from an infection by an unknown coronavirus with SARS/covid-19 like symptoms.

WIV was consulted about the miners unknown coronavirus in 2012 and records show WIV tested the miners blood. Other tests on human tissue from the miners also took place.

Also in 2020 Prof Shi made misleading or very unscientific comments about the miners deaths and her discovery in 2012 of the betacoronavirus RaTG13 despite publishing papers on it in 2016. Prof Shi implied the work and/or discovery of RaTG13 was very recent and made no reference to her previous papers and work on RaTG13

Note - many other viruses were also found in the same caves by Prof Shi in 2012 these other corona viruses had no meaningful genetic link to covid-19 unlike RaTG13, or to possible human infection in the future, and were not betacoronaviruses

So RaTG13 is confirmed by Prof Shi in a 2016 published paper (linked below and previously) as having been discovered by her in 2012 in caves (that miners caught and died of an unknown coronavirus) and Prof Shi states in 2016 that it has human SARS like pandemic potentional as a betacoronavirus and we now know is also the closest coronavirus yet found with an over 96%+ genetic match to covid-19

Prof Shi indicates that the other betacoronavirus discovered in the mine had only a very distant link to SARS and none to human SARS, and was considered very very unlikely to be able to infect peopl e- this other coronavirus had about an 80% genetic match to existing non human SARS viruses

Please read the quotes below and for further full info and see all the research papers quoted and linked in the links below

the "Shi lab found that bat coronaviruses were unusually abundant in the mine (Ge at al., 2016). Among their findings were two betacoronaviruses, one of which was RaTG13 (then known as BtCoV/4991). In the coronavirus world betacoronaviruses are special in that both SARS and MERS, the most deadly of all coronaviruses, are both betacoronaviruses. Thus they are considered to have special pandemic potential, as the concluding sentence of the Shi lab publication which found RaTG13 implied: “special attention should particularly be paid to these lineages of coronaviruses” "

"in a letter obtained by us Zheng-li Shi confirmed to a virology database that BtCoV/4991 and RaTG13 are both from the same bat faecal sample and the same mine" in 2012
We know RaTG13 is 96%+ genetically linked to Covid-19 and is the closest known virus to covid-19 ; so they either have a common earlier link or RaTG13 was mutated into Covid-19.

Natural mutation of RaTG13 into Covid-19 has been ruled out and no earlier link has yet been found.

So whatever people think info is missing

This linked research paper is the best independent Phd professional research summary I have seen to date of the public data available currently on Covid-19 origins - see the link below.

Prof Shi's 2020 comments on Covid-19 do not line up with her earlier research into RaTG13 which highlight its human pandemic SARS related potential.

It shows when and what Prof Shi discovered about RaTG13 since 2012 and the 2013/14 paper written by the hospital Dr of the miners who died in 2012 of the unknown coronavirus with Covid-19/SARS like symptoms which has not been much discussed

The links between Prof Shi, the miners deaths and Wuhan/WIV are also set out

Its difficult to find the info in one place with all the data and links


https://www.independentsciencenews.org/commentaries/a-proposed-origin-for-sars-cov-2-and-the-covid-19-pandemic/
 
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adam

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Here are further links on FOIA requests, FOIA legal action against the NIH, related to info on Covid-19 origins recently made/taken plus conflicts of interest highlighted by U.S. Right to Know a non profit pressure group

This action does not seem to be getting reported in main stream media or any obvious press coverage

From USRTK web site some info below

In July 2020, U.S. Right to Know began submitting public records requests in pursuit of data from public institutions in an effort to discover what is known about the origins of the novel coronavirus SARS-CoV-2, which causes the disease Covid-19.

On Nov. 5, U.S. Right to Know filed a lawsuit against the National Institutes of Health (NIH) for violating provisions of the Freedom of Information Act. The lawsuit, filed in U.S. District Court in Washington, D.C., seeks correspondence with or about organizations such as the Wuhan Institute of Virology and the Wuhan Center for Disease Control and Prevention, as well as the EcoHealth Alliance, which partnered with and funded the Wuhan Institute of Virology.

U.S. Right to Know is a nonprofit investigative research group focused on promoting transparency for public health.

The public and global scientific community have a right to know what data exists about these matters. We will report here any useful findings that may emerge from our research.

U.S. Right to Know is an investigative research group focused on promoting transparency for public health.

We are concerned that the national security apparatuses of the United States, China and elsewhere, and the university, industry and governmental entities with which they collaborate, may not provide a full and honest picture of the origins of SARS-CoV-2 and the dangers of gain-of-function research.







Note research paper

 
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An alternate postulate that I am not sure has been presented on this thread is that the current virus actually arose inside a human host in China from a non-pathogenic coronavirus strain obtained from a bat, and may have been present for quite some time, replicating and mutating at a low level until the "final" mutant SARS-CoV-2 was formed. There must be "local" coronavirus variants in areas of China quite dissimilar than our own.

Sequence differences should rule out the potential for this source of the virus. If it did arise from a human source, sufficient mutations allowed it to evade immune surveillance, thus permitting it to expand in numbers and infect other animals and/or people.

This is a certainly possible since related coronaviruses that cause the common cold do the same thing. Once they are "gone" and no longer circulate causing cold symptoms, they are not really gone. They are suppressed, and still exist at low levels, in humans or animals humans interact with, all the while mutating in order to allow the next season's cold viruses to emerge. Tracking mutations and how they impact pathogenicity of a viral strain is the key to understanding these pandemics, and perhaps in eliminating them.
 
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An alternate postulate that I am not sure has been presented on this thread is that the current virus actually arose inside a human host in China from a non-pathogenic coronavirus strain obtained from a bat, and may have been present for quite some time, replicating and mutating at a low level until the "final" mutant SARS-CoV-2 was formed. There must be "local" coronavirus variants in areas of China quite dissimilar than our own.

Sequence differences should rule out the potential for this source of the virus. If it did arise from a human source, sufficient mutations allowed it to evade immune surveillance, thus permitting it to expand in numbers and infect other animals and/or people.

This is a certainly possible since related coronaviruses that cause the common cold do the same thing. Once they are "gone" and no longer circulate causing cold symptoms, they are not really gone. They are suppressed, and still exist at low levels, in humans or animals humans interact with, all the while mutating in order to allow the next season's cold viruses to emerge. Tracking mutations and how they impact pathogenicity of a viral strain is the key to understanding these pandemics, and perhaps in eliminating them.
This seems a very likely scenario to me, considering the suggestion from one research paper that pangolins captured in March 2019 with a virus with high sequence homology in the RBD to sars-cov-2, most likely caught the virus from their human captors -which perhaps indicates an evolutionary path moving between species until the emergence of the human pandemic virus in oct/nov; this hypothesis is perhaps given credence by considering the wide variety of animal species that are susceptible to sars-cov-2 infection. It is noted that virus epidemic outbreaks often occur at a different location to their original emergence which leads to the conclusion that the pandemic virus was brought into Wuhan after previous adaptation in humans, perhaps via the pathway suggested here.
 

adam

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Its known that many researchers have looked at pre 2020 human blood samples to see if they can identify the origins of Covid-19 and when it started.

In Europe research found positive Covid-19 results were in late 2019 blood samples and Chinese studies indicate Oct/Nov 2019 as the start of Covid-19.

This research process would have identified a genetically similar virus to Covid-19 if it existed in the human population before Oct 2019 and mutated - even if it were also carried by other animals as well.

Zoonotic beta coronaviruses that infect animals birds bats etc and humans have not been common, and would also need to be highly infectious to mutate as suggested between animals and humans or even just between humans.

No such highly infectious genetic markers have been publically declared found outside Covid-19 or in any other human or animal virus or blood tested linked to Covid-19


SARS and MERS were not highly infectious.

China certainly would like such a path to be found for covid-19 as it would help limit the Wuhan Institute of Virology (WIV) from being labeled a potential source of Covid-19

Jonathan Latham, PhD and Allison Wilson, PhD in their independent research paper previously linked in above posts and again below reviews some different routes for how Covid-19 developed but does not conclude any natural route has been identified

 
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adam

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Its good to keep reviewing the origins of Covid-19

However as part of this review we need answers to existing questions about known human deaths from any unknown SARS like coronavirus.

This happened in 2012 when Chinese miners died of what their hospital Dr believed was an unknown SARS like coronavirus contracted from bats in the caves where coronavirus RaTG13 was found by Prof Shi / WIV.

RaTG13 is Covid-19s closest known beta coronavirus at 96%+ why is it not being studied

The Drs 2013 research paper on the miners deaths says that it was from SARS like symptoms probably caught from a bat coronavirus

The Dr makes reference to such a SARS like coronavirus being found before the 28th May 2013 in the RaTG13 caves where the miners worked and as being the main focal point of his medical research

This indicates the Dr was aware of Prof Shi's findings about RaTG13 before late May 2013


See page 8 of the 66 page thesis linked above

Also note on page 64 the list of reference papers includes work by Prof Shi from 2005 on bats and coronaviruses as well as other works on SARS and bat coronaviruses etc

It is of note

1. the miners blood was sent 1,000 miles to the Wuhan Institute of Virology (WIV) to research.

2. in late 2012 or early 2013 Prof Shi of the WIV found and then officially registered a new genetic code for a new SARS betacoronavirus genetically linked to human SARS - RaTG13 - in the same caves the dead miners worked in

3. no meaningful human research follow up has been made available other than a limited review by the patients hospital Dr in around 2013 which was removed from the internet in 2020

4. that Prof Shi stated in 2020 about the dead miners that

"it would have been only a matter of time before they caught the coronaviruses" in the caves.


5. there was only one coronavirus RaTG13 that was identified by Prof Shi as being likely to infect humans

6. Prof Shi admits taking human blood samples in another area so it seems odd she would not have a similar interest in doing so in an area where RaTG13 was discovered and she did not follow up on or look into the human blood samples sent to WIV from the sick/dead miners in 2012

"In October 2015 Shi’s team collected blood samples from more than 200 residents in four of those villages. It found that six people, or nearly 3 percent, carried antibodies against SARS-like coronaviruses from bats—even though none of them had handled wildlife or reported SARS-like or other pneumonia like symptoms."


7. in 2013 in the same RaTG13 caves some tests on rats etc were later done by another research group but it never found the rats etc were infected with RaTG13 - the new human SARS like coronavirus that Prof Shi discovered.

See rat etc focused research below from 2014

"June 2012, in Mojiang Hani Autonomous County, Yunnan Province, China, severe pneumonia without a known cause was diagnosed in 3 persons who had been working in an abandoned mine; all 3 patients died. Half a year later, we investigated the presence of novel zoonotic pathogens in natural hosts in this cave"


Simply put we have RaTG13 found via Prof Shi/WIV in 2012/13 with a 96%+ genetic match to Covid-19 which did not infect rats etc living in the caves - and Prof Shi stated in 2020 that coronaviruses in the RaTG13 caves would infect humans when exposed to them for a short time as quoted previously above. She did not appear to make this claim about any other bat caves.

However Prof Shi also tried to claim the miners died of a fungal infection -

There is no evidence this is true, or that any later researchers looked for or found any deadly fungal infections, rather later researchers looked for a zoonotic virus related to the miners deaths and Prof Shi went to these caves 4 times in about 6 months

The dead mens hospital Dr cited no fungal link as a cause of death

Please see my previous posts for other links and research quoted

Recent 2020 references to new research on old 2010 etc virus samples from bats now being studied to find where Covid-19 came from makes sense - but lets focus first on the known 2012 high risk case with a known human death link and exclude it as well as studying the human populations from which in 2015 human blood samples were taken and bat coronavirus antibodies were
found

Why this has not happened already should be of very serious concern - but no one is asking why ?

More evidence they need to ban exotic wild life consumption.

The mutation rate in this virus is relatively high. An article (1) from the nih.gov website indicates that the spike protein alone has undergone over 8000 mutations (since the date of this publication's sequence availability). There are many more by now.

The article indicates that some of the mutations which might occur in the receptor binding domain (RBD) of the spike protein are more likely to increase its infectivity. Moreover, the mutation rate in the RBD appears to occur at a higher rate than other mutations in the spike protein.

The take home message is that the more this virus spreads, the more infective it appears to become. While this is not yet confirmed, it is certainly a good reason to limit its replication. Faster spread means more misery and potentially more lethal strains The higher mutation rate may be helping to derive strains with a greater rate of infectivity and mortality. One shouldn't need much schooling to know that is not a good thing.

Everyone should do whatever they can to eliminate these mutants!


"Mutations Strengthened SARS-CoV-2 Infectivity"

1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7375973/
The missing step in passive human development or any other route for Covid-19 is clear - so where is the proof of any earlier genetic code for any previous earlier non lethal versions of Covid-19?

Its not there

It should show up in old stored blood or virus samples reviewed but this has not yet been found - so looks unlikely for now


The link above to independent Phd research explains how the virus RaTG13 might have mutated in the miners lungs in 2012 to become Covid-19 and not been spread before 2019.

You can read how mutations that take many years could have happened over the six months or so some of the miners were in hospital - this is partly based on the limited medical records found in the 2013 medical research paper

It states 50% of the miners died in 2012 from SARS like symptoms probably from an unknown coronavirus caught in the RaTG13 bat caves. Have the 3 miners who lived been traced and researched - if not why not?

This proposed human covid-19 mutation process is similar to a live animal gain of function process / lab research and would appear totaly natural

However this 2012 RaTG13 human hospital route requires that some human actor stored the human blood with the virus between 2012 and 2019/2020

There is no evidence this happened. If it happened it was hidden.

Another alternative is that secret gain of function research was done on the human blood etc or the bat RaTG13 derived virus samples in a lab by using ferrets or mink etc or by repeatedly mixing human cells and viruses with RaTG13 in many petri dishes to create a "natural" recombined virus as opposed to a lab spliced virus.

No human intervention could obviously be seen by such a process

We know Prof Shi collected and tested human blood for bat derived coronavirus antibodies etc.

Given the USA stopped much live animal and other gain of function work from around 2015 it is possible others in China continued unofficially to do the work.

The Chinese have a history of acting without due care in medical matters - hiding SARS outbreaks, stealing cancer research and covid-19 vaccine data etc





Prof Shi was involved in gain of function research from around 2013 or earlier.

The link below is to gain of function work published in 2015 about research on mice and in test tubes which involved Prof Shi and bat coronaviruses plus also refers to earlier studies by Prof Shi

- 2015 -

A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence

"Here we examine the disease potential of a SARS-like virus, SHC014-CoV, which is currently circulating in Chinese horseshoe bat populations. Using the SARS-CoV reverse genetics system, we generated and characterized a chimeric virus expressing the spike of bat coronavirus SHC014 in a mouse-adapted SARS-CoV backbone.."

"On the basis of these findings, we synthetically re-derived an infectious full-length SHC014 recombinant virus and demonstrate robust viral replication both in vitro and in vivo. Our work suggests a potential risk of SARS-CoV re-emergence from viruses currently circulating in bat populations."


So to date the rapid mutation of RaTG13 to covid-19 or what link exists between RaTG13 and another virus and covid-19 is has remained unexplained.

However we do know the miners medical records show their human blood samples were sent to the Wuhan Institute of Virology (WIV) in 2012 to look for the SARS like coronavirus that was killing the miners, that these WIV blood tests showed a coronavirus was present and that other tests were done on the miners tissue, that human glands which filter and store viruses were removed. See the linked research papers for Chinese research paper.

Also we know that the WIV / Prof Shi visited the bat caves after the miners were infected and died in 2012 and then WIV stored samples of what the WIV and Prof Shi have set out in published research papers was a very rare new SARS like coronavirus with a close genetic link to human SARS and which had human pandemic potential. This being RaTG13 which was genetically identified and recorded around 2013 by Prof Shi but that research data findings were not published until 2016 (with Prof Shi identified as the contact person)

- 2016 -

Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft

"the surveillance identified two unclassified betacoronaviruses, one new strain of SARS-like coronavirus, and one potentially new betacoronavirus species."


If Covid-19 developed naturally in humans it seems likely that there would be human blood samples that are stored with a virus genetically similar to Covid-19 and with SARS like betacoronavirus genetics. This has not been found.

To date the closest genetic virus to covid-19 is RaTG13 - 96%+

RaTG13 has clear links going back to 2012 to the Wuhan Institute of Virology / WIV, Prof Shi and also to the miners who died from an unknown coronavirus caught in the same caves that RaTG13 was found .

In 2020 Prof Shi hid or at least was not open about her work on RaTG13 from 2012 onwards, failed to provide guidance about the coronavirus medical research papers on the dead miners, tried to implicate the deaths on a fungal infection but also said the miners would have soon caught a bat coronavirus in the caves had the caves not been shut (which implies she knew they could be transmitted to humans - though only one coronavirus RaTG13 came within that criteria) and she did not disclose her involvement in gain of function and other studies linked to bat coronaviruses using mice etc or RaTG13

The info is also covered by Jonathan Latham, PhD and Allison Wilson, PhD independent research which sets out the links to info and documents going back to 2012


From the limited info on the miners medical records it is clear that Prof Shi visited the caves after the miners died and almost certainly after the Wuhan Institute of Virology carried out blood tests on the miners blood. Other tests and operations on the miners human tissue were also carried out

As this virus is the closest link to Covid-19 and was probably involved in human deaths in 2012 it is obvious research should be done and published to prove or disprove any connection.

This has not happened

The existing human and some other research related to WIV, the dead miners and RaTG13 and/or its previous name has been removed or hidden from the public domain - why?

Still no answers and still no public research
 
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Zoonotic beta coronaviruses that infect animals birds bats etc and humans have not been common, and would also need to be highly infectious to mutate as suggested between animals and humans or even just between humans.

No such highly infectious genetic markers have been publicly declared found outside Covid-19 or in any other human or animal virus or blood tested linked to Covid-19

The ability to detect and sequence coronavirus variants is not as easy as some might think. Many persist at very low levels, and such "strains" would have to be amplified even to detect them, much less sequence them. It is how they persist within a host. Low enough levels to replicate but not high enough to prompt an immune response. This allows a virus to mutate "under the radar", and never be detected by assay without considerable effort.

It should also be realized that there are over 7 billion people on the planet, some living in isolated areas and who do not interact with the "general population". Such people would not necessarily be part of a massive screen of coronaviruses in search of any initial human source.

Despite noted references to other potential sources of the virus, its low level of replication could easily have prevented its detection in earlier studies, regardless of "host" source.

Taken from an article on ScienceAlert (1):

Quote:

"With 'laboratory experiment gone wrong' out of the way, the team explored two viable hypotheses. First, that the natural selection occurred in an animal host before the virus was transmitted to humans. The team explains that although samples of coronaviruses in bats and pangolins have shown similar genomes, none of them fit perfectly just yet.

"Although no animal coronavirus has been identified that is sufficiently similar to have served as the direct progenitor of SARS-CoV-2, the diversity of coronaviruses in bats and other species is massively undersampled," the researchers write. (emphasis mine)

The second hypothesis is that the natural selection happened in humans - after the virus was transmitted from an animal host.

"The second scenario is that the new coronavirus crossed from animals into humans before it became capable of causing human disease," director of the National Institute of Health, Francis Collins explains on the NIH blog.

"Then, as a result of gradual evolutionary changes over years or perhaps decades, the virus eventually gained the ability to spread from human-to-human and cause serious, often life-threatening disease."

end quote.

Again, these viruses do not need to be highly infectious to mutate. They are actually capable of surviving in many species without being eliminated, all the while mutating and reproducing at a low level. This is probably why Collins mentioned "gradual evolutionary changes over years or perhaps decades". It cannot be ruled out that the original strain arose in humans at a level that has not been detected as yet.


Reference:

"The COVID-19 Virus May Have Been in Humans For Years, Study Suggests"

1. https://www.sciencealert.com/the-new-coronavirus-could-have-been-percolating-innocently-in-humans-for-years
 
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adam

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Thank you for the info.

Have you read Prof Shi's
strange November 2020 updates on Covid-19 etc?

See later below

Nothing is ruled out yet but there is no evidence for any under the radar process - there is "real" evidence of RaTG13 linking to Covid-19

All the obvious sources of Covid-19s origin need also to be explored and RaTG13 is a big unanswered question

Professor Shi has just provided some very strange new updates on the origins of Covid-19, the Wuhan Institute of Virology / WIV role and RaTG13 etc


Nine months after her disclosures about coronavirus RaTG13 and Covid-19 Prof Shi updated the info including confirming the 2020 existence of human hospital samples from the 2012 dead miners, 8 new undisclosed SARS betacoronaviruses from 2013 on found at the RaTG13 cave and other strange disclosures etc

This info was something that should be normally known to Prof Shi in early 2020 and much of it before - its all very strange

1. Comment - RaTG13 the genetically closest registered virus to Covid-19 has only been found once in the wild in July 2013 and there is no other proof it exists - no lab samples now exist

Comment - Prof Shi now says 8 other SARS linked betacoronaviruses were also discovered with RaTG13 but not disclosed or registered. No gene sequence has yet been provided on these 8 this could help with a cure etc - why no disclosure ?

2. Blood or other tests were recently done in 2020 on 2012 blood / serum samples from the miners who died in 2012 etc of an unknown SARS coronavirus caught in caves where RaTG13 plus 8 other SARS viruses were found.

Prof Shi says the 2020 test show the miners did not die in 2012 from Covid-19

Comment - did they test for all types of SARS etc, no evidence is provided about the 2020 tests done
or state of the 2012 samples or why this was not done before.

Comment - MA 2013 and Phd 2016 studies on the 2012 dead miners from show that the miners blood tested positive for SARS and other coronavirus antibodies - tests by the WIV in 2012 with one miner already dead on testing. The Phd supervisor is now head of Chinese CDC

Comment - now Prof Shi says the miners did not die from a fungal infection which she claimed in early 2020.

Also Prof Shi now says that till 2015 she and others searched for the zoonotic source that killed the miners.

Why did Prof Shi lie in early 2020 about all this and not disclose?

3. There is much more please read links below from peer-reviewed Rahalkar and Bahulikar


Peer Reviewed Study

See info from link above author of peer reviewed

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 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 Naturearticle 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 theseviruses (plural), which means they also could have the whole genome of the other viruses. They released only the RaTG13 sequence.”[ENDS UPDATE]

A member of the DRASTIC team, who tweets under the handle @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.




None of the information in the Nov Addendum was unknown to Prof Shi 9 months ago






 
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there is no evidence for any under the radar process
There likely never would be evidence found in a random, broad sampling. The intermediate strains leading to the current version are probably historical, and would never reappear to reveal the way it arose now. Unless, perhaps you could find the precise location of its origin (if in humans). If Collins is right and it took years/decades in humans to evolve into the current form, almost all of what you will likely find in most people now would be the current form.

However, it is possible that a major sampling within the Chinese population might reveal some interesting sequences, using all the approaches required to detect all present coronaviruses of interest. If it arose in humans, it did not happen all over the world, but in a single. possibly isolated, location.

Have you read Prof Shi's strange November 2020 updates on Covid-19 etc?
I have read some of her comments in the news, but nothing directly from her. The comments were enough. There is not a lot out of Chinese researchers which I accept as being totally factual. There is a high risk for censorship and manipulation. Tend to stick with data from the West - more reliable.

Why did Prof Shi lie in early 2020 about all this and not disclose?
A cover-up comes to mind. Which is why I do not trust most data or commentary coming out of China. If they have hard data of a scientific nature, that may be acceptable. But their '"commentary" and lies and distortions about what has happened do not usually find their way into my reading stream.
 
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Observer

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Thanks Adam for this real and proven data about whats going on

Theory is great and hard facts are better still

As these facts come from the journal Nature and other peer reviewed or serious research sources its something everyone should read


Prof Shi and the Chinese are now confirming through this Nature official update of previous Chinese publications in Nature that they withheld data for many years including 2020 about 8 SARS viruses they found and data on human blood tests from 2012 which are all in some way connected to RaTG13 and so to covid19 and there is more

Professor Shi has now proved some of what she said in early 2020 was untrue and that she knew people really died in 2012 of a covid type virus not a fungus

Nine months after her disclosures about coronavirus RaTG13 and Covid-19 Prof Shi updated the info including confirming the 2020 existence of human hospital samples from the 2012 dead miners, 8 new undisclosed SARS betacoronaviruses from 2013 on found at the RaTG13 cave and other strange disclosures etc
Why is media not reporting this?

The Chinese officially admit they have blood from 2012 with links to RaTG13 and so to covid19 which they just tested for covid19 and they still dont provide any medical data on the tests or the 8 SARS beta corona viruses they found near the RaTG13 location

How can 2020 blood tests of 2012 blood samples show no trace of SARS or coronaviruses when published research from 2012 and 2016 shows that SARS and coronavirus antibodies were found by the Wuhan Institute of Virology in the same blood in 2012 ?

1. Comment - RaTG13 the genetically closest registered virus to Covid-19 has only been found once in the wild in July 2013 and there is no other proof it exists - no lab samples now exist

Comment - Prof Shi now says 8 other SARS linked betacoronaviruses were also discovered with RaTG13
So does this mean RaTG13 may not exist as only one sample was ever found and nothing is left and the Chinese say they have 8 other SARS viruses they have not disclosed!?

Could this mean RaTG13 was never a wild zoonotic virus. We only have Prof Shi's word about the source of the registered genetic code

No other researchers have found RaTG13 in any bats or animals and its full registration was made in parts over many years.

This really sounds so strange am I missing something?

The closest virus to covid19 was only ever found once and by the lab in the city where covid started

These same researchers first say in 2020 the 2012 miners died from a fungus infection and now in 2020 say death was from a virus and they spent years looking for the virus in the place RaTG13 was found!

3. There is much more please read links below from peer-reviewed Rahalkar and Bahulikar
Why is no one looking into this?

The Chinese chief bat coronavirus person Professor Shi is admitting to withholding new SARS information for years and has still not provided the research and blood test data and this is ignored.

Come on this is crazy stuff from the head of a top security bat coronavirus research lab and no one "bats" an eye ?

I dont get it ??

Thanks for putting this out there with all the published research data linked

Fact certainly looks stranger than fiction!

Thank you for the info.

Have you read Prof Shi's
strange November 2020 updates on Covid-19 etc?

See later below

Nothing is ruled out yet but there is no evidence for any under the radar process - there is "real" evidence of RaTG13 linking to Covid-19

All the obvious sources of Covid-19s origin need also to be explored and RaTG13 is a big unanswered question

Professor Shi has just provided some very strange new updates on the origins of Covid-19, the Wuhan Institute of Virology / WIV role and RaTG13 etc


Nine months after her disclosures about coronavirus RaTG13 and Covid-19 Prof Shi updated the info including confirming the 2020 existence of human hospital samples from the 2012 dead miners, 8 new undisclosed SARS betacoronaviruses from 2013 on found at the RaTG13 cave and other strange disclosures etc

This info was something that should be normally known to Prof Shi in early 2020 and much of it before - its all very strange

1. Comment - RaTG13 the genetically closest registered virus to Covid-19 has only been found once in the wild in July 2013 and there is no other proof it exists - no lab samples now exist

Comment - Prof Shi now says 8 other SARS linked betacoronaviruses were also discovered with RaTG13 but not disclosed or registered. No gene sequence has yet been provided on these 8 this could help with a cure etc - why no disclosure ?

2. Blood or other tests were recently done in 2020 on 2012 blood / serum samples from the miners who died in 2012 etc of an unknown SARS coronavirus caught in caves where RaTG13 plus 8 other SARS viruses were found.

Prof Shi says the 2020 test show the miners did not die in 2012 from Covid-19

Comment - did they test for all types of SARS etc, no evidence is provided about the 2020 tests done
or state of the 2012 samples or why this was not done before.

Comment - MA 2013 and Phd 2016 studies on the 2012 dead miners from show that the miners blood tested positive for SARS and other coronavirus antibodies - tests by the WIV in 2012 with one miner already dead on testing. The Phd supervisor is now head of Chinese CDC

Comment - now Prof Shi says the miners did not die from a fungal infection which she claimed in early 2020.

Also Prof Shi now says that till 2015 she and others searched for the zoonotic source that killed the miners.

Why did Prof Shi lie in early 2020 about all this and not disclose?

3. There is much more please read links below from peer-reviewed Rahalkar and Bahulikar


Peer Reviewed Study

See info from link above author of peer reviewed

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 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.


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


“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).


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.


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.


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 theseviruses (plural), which means they also could have the whole genome of the other viruses. They released only the RaTG13 sequence.”[ENDS UPDATE]

A member of the DRASTIC team, who tweets under the handle @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.


@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.







None of the information in the Nov Addendum was unknown to Prof Shi 9 months ago




 
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Observer

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Aug 15, 2020
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Links to published papers and references at the end

As I understand it

1. Scientists from a range of leading universities published a paper stating that to date computer modeling and research shows bats cannot get infected by RaTG13 the nearest virus to Covid19.

2. To date there is no proof bats carry RaTG13

3. Prof Shi from Wuhan Institute of Virology who discovered RaTG13 has only found it on one occasion in July 2013 despite Prof Shi and others looking in the same bat cave location many times over several years after 3 miners died in the First Affiliated Hospital of Kunming Medical University of an unknown SARS like infection caught in the same caves near Kunming, Yunnan Province, which is 1000 miles from Wuhan.

3a. There are no samples of the RaTG13 virus left to look at or study or prove it exists

4. No one else apart from Prof Shi has ever discovered a sample of RaTG13 anywhere

5. it is odd that RaTG13 was allegedly not pursued or studied by the Prof Shi group for a period of nearly seven years, to further characterize their S proteins as it was identified by Prof Shi in a published paper in 2016 as a rare SARS virus with human pandemic potential.

Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft

7. In 2013, Prof Shi's group published an article in Nature describing the discovery of two SARS bat [beta] coronaviruses, Rs3367 and SHC014

7a. Prof Shi found these other beta coronaviruses rs3367 and SHC014 in the same area near Kunming, Yunnan Province, before RaTG13 was found.

Viruses were collected over a span of 5 years from the same cave near Kunming, Yunnan Province, where the Shi group originally found Rs3367 and RsSHC014 and used in experiments to make them able to infect humans

7b. Prof Shi now admits in her recent Nature article update on RaTG13 that she also found 8 other bat SARS viruses that she did not publish or declare anything about and still has not done so

7c. SHC014 was genetically modified in a US lab to allow it to infect humans. Prof Shi was involved with this work

8. Prof Shi and the University of North Carolina at Chapel Hill and the Wuhan Institute of Virology conducted research showing the virus SHC014 could be made to infect the human HeLa cell line, through the use of reverse genetics to create a chimeric virus consisting of a surface protein of SHC014 and the backbone of a SARS virus

9. Prof Shi has made many conflicting comments about what she knew about miners deaths in 2012. For example Prof Shi stated in 2020 that they died of a fungal infection.
In the 2020 Scientific American interview, Dr. Zhengli Shi outlines that fungus was responsible for pneumonia in the miners

However in the recent Narture update she says it was an unknown virus.

10. Prof Shi failed to disclose that 2012 blood tests by
Wuhan Institute of Virology showed a coronavirus was present in the dead miners. A 2016 Phd thesis states tests showed a SARS Virus was discovered in the blood tests. A 2013 MA thesis just says a coronavirus was identified. See previous posts for link to MA and Phd data.

Instead Prof Shi listed specific viruses tested for and not present including various SARS viruses

Links below


it is odd that RaTG13 or BtCoV/4991 was allegedly not pursued by the Shi group for a period of nearly seven years, to further characterize their S proteins. In 2013, her group published an article in Nature describing the discovery of two bat coronaviruses, Rs3367 and SHC014



Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft



RaTG13 was found in feces of the intermediate horseshoe bat (Rhinolophus affinis) (1), but to our knowledge this virus has not been shown to bind to ACE2 of R. affinis or any other bat species. In addition, RaTG13 was reported not to infect human cells expressing Rhinolophus sinicus ACE2 in a recent study (65).





further: instead of using human immunodeficiency viruses (HIV) pseudo‐viruses with bat CoV spike proteins, a live chimeric CoV was created. Following the experiments of their 2007 WIV colleagues, the Baric group used a bat SARS‐like CoV as a backbone and replaced its RBD with the RBD from human SARS.[30]

In 2015, the Shi and Baric groups joined forces and published probably the most famous gain‐of‐function virology paper, which described the creation of another synthetic chimeric virus.[19] This time the RBD of a mouse‐adapted SARS backbone (SARS‐MA15) was replaced by the RBD of RsSHC014, a bat strain previously isolated from Yunnan bats in 2011 by the Shi group. In 2016, the Baric group repeated their 2015 experiment using the same SARS‐MA15 backbone and the RBD from Rs3367,[31] a close relative of RsSHC014 also previously found in Yunnan by WIV and renamed “WIV1” after live culturing.[17]

Probably the largest reported number of novel chimeric viruses created was described in a 2017 paper from the Shi group at WIV,[15] in which the authors reported creating eight chimeric viruses using WIV1 as a backbone and transplanting into it various RBDs from bat SARS‐like viruses. These viruses were collected over a span of 5 years from the same cave near Kunming, Yunnan Province, where the Shi group originally found Rs3367 and RsSHC014. Only two of the eight live chimeric viruses were successfully rescued, and those two strains were found to possess the ability to bind to the human ACE2 receptor, as confirmed by experiments in hACE2‐expressing HeLa cells and RT‐PCR quantification of viral RNA.

 
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A persistent coronavirus myth that this virus, called SARS-CoV-2, was made by scientists and escaped from a lab in Wuhan is completely unfounded. Here's how we know.

The coronavirus did not escape from a lab. Here's how we know. : Read more
it did originate in china - in a wuhan market - -bats also carried it

the spreaders of it over in th UK are the rule breaking younger generation who are selfish & dont care about their own health , their significant others in their families health or friends or anyones -all they care about is going out in crowds & getting boozed up & bunching up-& I ahve a diary full of evidence pictures to prove it
 

adam

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Jul 2, 2020
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The CDC sets out there is no evidence that bats host, carry or spread covid19 or can even catch covid19. See CDC and other links later below

More importantly no one in the media has made clear or discussed that the closest linked virus to covid19 RaTG13 which was discovered by Prof Shi from Wuhan Institute of Virology (WIV) in 2013 has the following issues

"Unfortunately, the RaTG13 sample has been exhausted and it is no longer available for external examination,"


1. RaTG13 - no sample exists anywhere in the world that can be viewed or studied

2. RaTG13 - the virus was only EVER found ONCE in 2013 in one bat, so no independent verification it existed has been possible.

3. RaTG13 - despite many years of searching the same caves and general area (both before and after 2013) plus looking in many other caves etc no other sample of the RaTG13 virus has ever been found in any bat or animal anywhere in the world

4. Prof Shi is the only person to have seen or studied RaTG13 so there is no independent verification RaTG13 existed in a lab or in a bat or of the quality and origin of any sample

5. Prof Shi has changed her story several times in 2020 on the RaTG13 virus, the miners who died in 2012 from an unknown virus caught in the location of the caves RaTG13 was found in, she failed to discuss the 2020 WIV blood tests carried out on the 2012 dead miners blood until November 2020 or to discuss that the 2012 blood tests carried out by Prof Shi's colleagues in the WIV labs where she is based showed that a coronavirus / a SARS type virus was present.

Neither has Prof Shi provided the results of the blood and other tests on human tissue and scans done in 2012 which are quoted in an MA paper and later Phd research on the same miners killed in 2012 by an unknown virus which it was believed came from bats in the caves RaTG13 was found

See links below and in previous posts.

Prof Shi has left out all this info or hidden it.

For example by listing numerous specific viruses tested for in the 2012 miners blood including MERS and then saying they did not find MERS or other specific viruses Prof Shi appears to indicate no coronavirus was present so the miners medical data does not need to be researched by others.

However the MA and Phd work makes clear non specific virus blood tests showed a coronavirus specifically a SARS virus was present but not what it was.

Either Prof Shi does not understand why this info and the tests need to be disclosed for transparent research or she has been hiding the info since early 2020 till now.

It is unlikely Prof Shi is acting on her own on these matters.

If Prof Shi and those who control and direct her do not understand why disclosure of the information is necessary then her abilities as a researcher carrying out gain of function work enabling bat viruses to transmit easily amongst humans should be cause for great concern, if Prof Shi and others are hiding the info then that is not a positive indicator of transparency.

Will we have to wait another 9 months for more information?

Either way Prof Shi and those researchers not asking normal questions come out looking strange and unprofessional with all that it implies.

Without meaningful communication and full transparent disclosure about the known information about the 2012 miners deaths, or the missing WIV lab worker legitimate doubt will remain as to Prof Shi's and the WIVs role in Covid-19.

It should be very simple to produce the missing lab worker whose research work profile was deleted from the WIV website but we are advised now having completed her studies now works elsewhere in China.

Professor Edward Holmes makes various comments in support of Professor Shi about [4991 the previous name of] RaTG13 that need clarification given Prof Shi stated in a published 2016 paper that RaTG13 was a potentially human pandemic SARS beta coronavirus needing to be researched and only one other beta coronavirus had been found in the 100+ samples collected at the sample time. The other viruses being alpha viruses

Prof Holmes states

That's “a very logical explanation,” says Edward Holmes, an evolutionary biologist at the University of Sydney. Shi's reply also clarified to him why 4991 [RaTG13] held such little interest to her team that they didn't even bother to sequence it fully until recently: That short genetic sequence was very different from SARS-CoV, the virus that caused the 2003 outbreak. “In reading this the penny dropped: Of course, they would have been mainly interested in bat viruses closely related to SARS-CoV … not some random bat virus that is more distant,” Holmes says.

[However the partial gene sequence of RaBtCoV/4991 (GenBankKP876546) the previous name of RaTG13 had already been registered by Prof Shi at Genbank in 2016 (see NIH link below) ie prior to 2020 by Prof Shi and this was independently brought to Prof Shi's attention by other Chinese researchers who were then punished. 4991 as a partial sequence had a 98% match with Covid-19. Dr Latham's research includes a copy of email correspondence with GenBank confirming they were advised by Prof Shi BtCoV/4991 and RaTG13 were from the same sample]

LOCUS KP876546 370 bp RNA linear VRL 02-MAR-2016
DEFINITION Rhinolophus bat coronavirus BtCoV/4991 RNA-dependent RNA polymerase
(RdRp) gene, partial cds.
ACCESSION KP876546
VERSION KP876546.1
KEYWORDS .
SOURCE Rhinolophus bat coronavirus BtCoV/4991





Thank you for the info.

Have you read Prof Shi's
strange November 2020 updates on Covid-19 etc?

See later below

Nothing is ruled out yet but there is no evidence for any under the radar process - there is "real" evidence of RaTG13 linking to Covid-19

All the obvious sources of Covid-19s origin need also to be explored and RaTG13 is a big unanswered question

Professor Shi has just provided some very strange new updates on the origins of Covid-19, the Wuhan Institute of Virology / WIV role and RaTG13 etc


Nine months after her disclosures about coronavirus RaTG13 and Covid-19 Prof Shi updated the info including confirming the 2020 existence of human hospital samples from the 2012 dead miners, 8 new undisclosed SARS betacoronaviruses from 2013 on found at the RaTG13 cave and other strange disclosures etc

This info was something that should be normally known to Prof Shi in early 2020 and much of it before - its all very strange

1. Comment - RaTG13 the genetically closest registered virus to Covid-19 has only been found once in the wild in July 2013 and there is no other proof it exists - no lab samples now exist

Comment - Prof Shi now says 8 other SARS linked betacoronaviruses were also discovered with RaTG13 but not disclosed or registered. No gene sequence has yet been provided on these 8 this could help with a cure etc - why no disclosure ?

2. Blood or other tests were recently done in 2020 on 2012 blood / serum samples from the miners who died in 2012 etc of an unknown SARS coronavirus caught in caves where RaTG13 plus 8 other SARS viruses were found.

Prof Shi says the 2020 test show the miners did not die in 2012 from Covid-19

Comment - did they test for all types of SARS etc, no evidence is provided about the 2020 tests done
or state of the 2012 samples or why this was not done before.

Comment - MA 2013 and Phd 2016 studies on the 2012 dead miners from show that the miners blood tested positive for SARS and other coronavirus antibodies - tests by the WIV in 2012 with one miner already dead on testing. The Phd supervisor is now head of Chinese CDC

Comment - now Prof Shi says the miners did not die from a fungal infection which she claimed in early 2020.

Also Prof Shi now says that till 2015 she and others searched for the zoonotic source that killed the miners.

Why did Prof Shi lie in early 2020 about all this and not disclose?

3. There is much more please read links below from peer-reviewed Rahalkar and Bahulikar


Peer Reviewed Study

See info from link above author of peer reviewed

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 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.


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


“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).


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.


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.


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 theseviruses (plural), which means they also could have the whole genome of the other viruses. They released only the RaTG13 sequence.”[ENDS UPDATE]

A member of the DRASTIC team, who tweets under the handle @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.


@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.







None of the information in the Nov Addendum was unknown to Prof Shi 9 months ago







The CDC states
there is currently no evidence that the virus that causes COVID-19 is present in any free-living wildlife in the United States, including bats.


Also see



Since the early days of the coronavirus pandemic, reports have suggested that SARS-CoV-2 (the virus that causes COVID-19) jumped from animals to humans in Wuhan's Huanan Seafood Wholesale Market. Now, experts at the Wuhan Institute of Virology (WIV) have said publicly that the theory was wrong, and that the virus must have originated elsewhere, according to a Wall Street Journal report.

"I haven't seen anything that makes me feel, as a researcher who studies zoonotic disease, that this market is a likely option," said Colin Carlson, a professor at Georgetown Ukniversity who studies the spread of such zoonotic viruses, which transmit between animals and humans. Carlson does not work for the WIV.

 
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