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Wednesday, May 26, 2021

The SARS-CoV-2 reference genome

Chinese scientists isolated virus particles from a patient admitted to hospital on December 26, 2019 in Wuhan, China. The RNA genome was sequenced and the sequence was immediately distributed to interested scientists around the world. It was submitted to GenBank on January 5, 2020 and appeared as entry NC_045512 on January 13, 2020 [Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1, complete genome].

The original GenBank record was annotated and updated by NIH staff on January 17, 2020 and now appears as updated locus NC_045512 last modified on July 18, 2020 now called SARS-CoV-2 [Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome].

The sequence was extensively mapped and analyzed by Chinese scientists in Shanghai, Wuhan, and Beijing, and Ed Holmes in Sydney, Australia and the results were submitted to Nature on January 7, 2020 and published on February 3, 2020.

Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., Yuan, M.-L., Zhang, Y.-L., Dai, F.-H., Liu, Y., Wang, Q.-M., Zheng, J.-J., Xu, L., Holmes, E.C. and Zhang, Y.-Z. (2020) A new coronavirus associated with human respiratory disease in China. Nature 579:265-269. [doi: 10.1038/s41586-020-2008-3]

Emerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health1–3. Despite intense research efforts, how, when and where new diseases appear are still a source of considerable uncertainty. A severe respiratory disease was recently reported in Wuhan, Hubei province, China. As of 25 January 2020, at least 1,975 cases had been reported since the first patient was hospitalized on 12 December 2019. Epidemiological investigations have suggested that the outbreak was associated with a seafood market in Wuhan. Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing of a sample of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae, which is designated here ‘WH-Human 1’ coronavirus (and has also been referred to as ‘2019-nCoV’). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China. This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans.

The Nature paper notes that this is a novel coronavirus related to known bat coronaviruses but it's exact origin remains unclear. The authors also mention that the origin of other disease-causing coronavirus-like viruses is also unknown.

Coronaviruses are associated with a number of infectious disease outbreaks in humans, including SARS in 2002–2003 and Middle East respiratory syndrome (MERS) in 2012. Four other coronaviruses—human coronaviruses HKU1, OC43, NL63 and 229E—are also associated with respiratory disease. Although SARS-like coronaviruses have been widely identified in mammals including bats since 2005 in China, the exact origin of human-infected coronaviruses remains unclear. Here we describe a new coronavirus—WHCV—in the BALF from a patient who experienced severe respiratory disease in Wuhan, China. Phylogenetic analysis suggests that WHCV is a member of the genus Betacoronavirus (subgenus Sarbecovirus) that has some genomic and phylogenetic similarities to SARS-CoV1, particularly in the RBD of the spike protein. These genomic and clinical similarities to SARS, as well as its high abundance in clinical samples, provides evidence for an association between WHCV and the ongoing outbreak of respiratory disease in Wuhan and across the world. Although the isolation of the virus from only a single patient is not sufficient to conclude that it caused these respiratory symptoms, our findings have been independently corroborated in further patients in a separate study.

The identification of multiple SARS-like CoVs in bats have led to the idea that these animals act as hosts of a natural reservoir of these viruses. Although SARS-like viruses have been identified widely in bats in China, viruses identical to SARS-CoV have not yet been documented. Notably, WHCV is most closely related to bat coronaviruses, and shows 100% amino acid similarity to bat SL-CoVZC45 in the nsp7 and E proteins (Supplementary Table 3). Thus, these data suggest that bats are a possible host for the viral reservoir of WHCV. However, as a variety of animal species were for sale in the market when the disease was first reported, further studies are needed to determine the natural reservoir and any intermediate hosts of WHCV.

Subsequent work suggests that the virus did not originate in the Wuhan market but was circulating in Wuhan in November 2019 among a small number of people who were not associated with the market. It looks like market workers were the source of superspreader event.

It's important to keep in mind that the exact origin of several other viral diseases has never been determined. This is quite normal so don't be fooled by people who think that the mysterious origin of SARS-CoV-2 demands an immediate explanation. That's likely not going to happen no matter how many outside investigators go snooping around Wuhan looking for clues to support their favorite conspiracy theory.


26 comments :

  1. Contrary to political statements by US interest groups, the Chinese scientific community promptly reported on the virus. If anyone was negligent and tardy, it was the outside world, in particularly the US government and government scientists, in not recognizing and responding to the threat. The Chinese had sent out warnings of a new circulating virus at the end of 2019, published the RNA genome online by Jan. 13, 2020, and put one of the country's largest cities on lockdown January 23 (I read about one day later on Yahoo). President Xi contacted President Trump shortly afterwards and explained the threat in words that even Trump could understand. It took a lot of incompetence by the West, the United States and its leadership in particular, not to have foreseen and prepared for what was clearly in the cards.

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  2. Thanks for your 3 posts (so far) on the anti-China Wuhan lab propaganda campaign. I predict this conspiracy garbage will go the way of the earlier anti-Soviet "Yellow Rain" hysteria claiming chemical warfare in SE Asia by evil communists. It turned out to be bee shite for the alleged victims and propaganda shite for the American state department. https://www.jstor.org/stable/1148733?origin=crossref&seq=1#metadata_info_tab_contents.

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  3. "That's likely not going to happen no matter how many outside investigators go snooping around Wuhan looking for clues to support their favorite conspiracy theory."

    Millions have died and billions have been affected. The costs of our public health measures will be passed on to our grandchildren. It's not unreasonable to ask for an open and transparent investigation, especially considering the abundance of evidence that the Chinese government has covered up some aspects of the pandemic, and the lab in question has put out misleading and false statements.

    To shut down discussion and label hypotheses from other scientists as conspiracies is completely antithetical to science. We're supposed to ask questions and even give consideration to ideas that we find unlikely or unpleasant. Moreover, the last sentence that you quoted shows exactly why we shouldn't limit debate on this subject. Early on it seemed highly likely that the Wuhan market was the source of the spillover, but that has now been disproven. This is an unprecedented event and a little intellectual humility is warranted.

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    1. " Early on it seemed highly likely that the Wuhan market was the source of the spillover, but that has now been disproven."

      How was it disproven?

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    2. "How was it disproven?"

      None of the animals sampled from the market tested positive. Other Covid cases were later found that preceded the event at the market and these patients didn't come into contact with it. The market was a super spreader event.

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    3. Thanks. But I'm unclear on some of the things you mention.

      You say none of the animals tested from the market tested positive. Okay, but when were they tested relative to when the pandemic is first thought to have begun? I have to assume there's been some lag-period between the realization that a pandemic had started, and someone going to the market to test animals there. It's in principle possible the whole thing started with an animal that was previously sold there, which then spread to people working there, without getting back into other animals sold later. Have ALL the animals sold there been tested? So it not being found in animals at a later time I don't think does much to rule out the market hypothesis.

      Another thing. You speak of an "event" at the market, and that the market was "a super spreader event". That seems to imply a rather narrow window of time for the market to have become a source of new infections. When was this and how does it relate in time to estimates of the beginning of the pandemic?

      A third point is that the market doesn't really need to be the particular geographical location where the zoonotic transmission first occurred. A person having contact with market workers (for example delivering animal products to the market for sale there) can have carried the virus there after him/herself having first suffered transmission elsewhere while catching, or transporting wild animals to the market.

      This whole things is a lot more complicated and nuanced than a "market source of first zoonotic event" vs "lab escape". That seems like an overly simplistic false dichotomy.

      I'm not sure what you're referring to with "other covid cases" that preceded "the event at the market", either. What event at the market, and what covid cases?

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    4. Chinese scientists have scoured the hospital records and identified case from early December where the patients have no connection to the Wuhan market. That's why they now believe that the virus did not originate in the market.

      The earliest case in the scientific literature is from Dec. 1, 2019 but there are substantiated reports of earlier cases in November that have been published in Chinese newspapers.

      https://doi.org/10.1126/science.abf8003

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    5. @Skeletor

      I'm not objecting to a reasonable an open investigation but it has to be based on evidence and not just on a mistrust of the Chinese.

      So far there's not one shred of evidence that the researchers at the Wuhan Institute of Virology were working with SARS-CoV-2 before the pandemic began. Until such evidence is presented there's no reason to assume that all of the world-renowned scientists at WIV are lying and covering up the fact that they were working with SARS-CoV-2 and accidentally allowed it to escape from the lab.

      Transparency is often used as a synonym for opaqueness and that's exactly how you're using it here. So far it's transparent that the lab leak conspiracy theory is a farse but you want to promote a very dark and mysterious explanation that's the exact opposite of transparent.

      You say,

      "To shut down discussion and label hypotheses from other scientists as conspiracies is completely antithetical to science."

      In order for the lab leak conspiracy theory to be correct it MUST require that the scientists at WIV are lying and covering up their role in the pandemic. That, by definition, is a conspiracy. Furthermore, it's a ridiculous conspiracy because it involves dozens or hundreds of conspirators whose reputations are vouched for by lots of scientists from other countries.

      "We're supposed to ask questions and even give consideration to ideas that we find unlikely or unpleasant."

      Exactly, and now is a good time for you to begin taking your own advice.

      "Moreover, the last sentence that you quoted shows exactly why we shouldn't limit debate on this subject. Early on it seemed highly likely that the Wuhan market was the source of the spillover, but that has now been disproven."

      Exactly. The Chinese scientists kept on the case and after a thorough investigation they ruled out the Wuhan market as the source of the pandemic. They have also been doing extensive field work in order to discover the real source of the virus and they have ruled out some early speculations. This is how scientists are supposed to behave. They follow the EVIDENCE and not their biases and suspicions.

      "This is an unprecedented event and a little intellectual humility is warranted."

      Yep. You can start any time.

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    6. "I'm not objecting to a reasonable an open investigation but it has to be based on evidence and not just on a mistrust of the Chinese."

      This statement is inconsistent with how you've smeared lab leak proponents as racists and conspiracy theorists. Moreover, the lab leak proponents have correctly pointed out that the WIV has collaborated with American scientists and even received funding from the US. They have also pointed out that past lab leaks have occurred in a variety of countries including Russia, the US, and the UK. Believing that the lab leak is a viable does not require one to have an axe to grind with China.

      "So far there's not one shred of evidence that the researchers at the Wuhan Institute of Virology were working with SARS-CoV-2 before the pandemic began. Until such evidence is presented there's no reason to assume that all of the world-renowned scientists at WIV are lying and covering up the fact that they were working with SARS-CoV-2 and accidentally allowed it to escape from the lab."

      We do know that they have been working with SARS related viruses and that they have been working with hundreds of viruses that they haven't disclosed yet. The lab in question has had multiple biosafety violations and was working with coronaviruses under BSL-2 conditions. The WIV scientists have also put out multiple inconsistent statements and omissions about other viruses they had collected that are the most closely related to SARS-CoV-2. For example, they renamed BtCov/4991 as RaTG13 without disclosing that they did so or referencing their previous work. In their 2020 paper, it seemed that they only performed whole genome sequencing on RatG13 after finding a match between RdRp region in SARS-CoV-2 and RaTG13. Alina Chan, a molecular biologist, pointed out that they already performed whole genome sequencing of the virus, which they later admitted in an addendum.

      More importantly, RaTG13 was collected from a mine Mojiang in 2013 where six miners had developed severe pneumonia in 2012. Dr. Zhong Nanshan (a pulmonologist and SARS expert) concluded that the pneumonia way likely a viral pneumonia, primarily from SARS-like coronaviruses and a secondary fungal infection. Four of these patients tested positive for SARS virus IgG antibodies (https://www.frontiersin.org/articles/10.3389/fpubh.2020.581569/full).

      Why didn't Dr. Shi and her colleagues reference the miners, the renaming of RaTG13, or that they had been with this several virus years before the pandemic when they published their first paper on Covid-19 in 2020? She is even on record as stating that the miners became sick from a fungal infection rather than a SARS-like virus (https://www.scientificamerican.com/article/how-chinas-bat-woman-hunted-down-viruses-from-sars-to-the-new-coronavirus1/). It's noteworthy that the link to a SARS-like virus and the miners has only come to attention because some people found the case studies in one of her student's theses.

      We also know that they took the WIV virus database in September 2019. This database contained data and sequences on over 1,400 bat viruses from over 15,000 samples. The official explanation is that they did this due to hackers, but that is a poor excuse. There are numerous biological databases online, as well as measures for dealing with hackers. There's no reason why they couldn't share this database with the rest of the research community without putting it online. This clearly shows an unwillingness to make crucial data accessible and open to the scientific community.

      Delete
    7. PART TWO

      Yes, the evidence is circumstantial, which is why I have never stated that a lab leak is a certainty or is even the most likely explanation, but we haven't been given access to the data that would rule it out in the first place. That's why I am arguing for a more open and transparent investigation. We can't collect evidence when we are denied the means to do so. This would be like denying a grant because there isn't direct evidence that supports the hypothesis.

      "Transparency is often used as a synonym for opaqueness and that's exactly how you're using it here. So far it's transparent that the lab leak conspiracy theory is a farse but you want to promote a very dark and mysterious explanation that's the exact opposite of transparent."

      Huh? Transparency is the opposite of opaqueness. I have no idea what you're trying to argue here. My arguments for transparency are consistent with the principles of open science, such as the open and accessible dissemination of information. Hiding databases and obfuscating names is not consistent with transparency or openness.


      "To shut down discussion and label hypotheses from other scientists as conspiracies is completely antithetical to science."

      In order for the lab leak conspiracy theory to be correct it MUST require that the scientists at WIV are lying and covering up their role in the pandemic. That, by definition, is a conspiracy. Furthermore, it's a ridiculous conspiracy because it involves dozens or hundreds of conspirators whose reputations are vouched for by lots of scientists from other countries."

      As I've noted repeatedly, you continue to evade the sociopolitical situation that these scientists are in. The Chinese government arrested whistleblowers, sanctioned the scientist who published the first SARS-CoV-2 genome. To this date, they are engaging in censorship of discussions surrounding the pandemic and have placed gag orders on scientists. This is not a situation where people are likely to tell the truth. If the pandemic resulted from a leak, I wouldn't expect the WIV scientists to be truthful considering the personal risk that they would face. Scientists from other countries aren't relevant in this discussion because they haven't been given access to the data. The WHO team, for example, had to take the conclusions from the WIV scientists at face value. They are on record as stating that they were not given access to the raw data and the entire investigation was supervised by the Chinese government. As I mentioned above, the WIV scientists have removed access to crucial data and have made inconsistent statements and omissions.

      Delete
  4. PART THREE


    "We're supposed to ask questions and even give consideration to ideas that we find unlikely or unpleasant."

    "Exactly, and now is a good time for you to begin taking your own advice."

    "This is an unprecedented event and a little intellectual humility is warranted."

    "Yep. You can start any time."

    You can do better than petty insults. I have only argued for two points: that we shouldn't dismiss the lab leak hypothesis, and that the sociopolitical situation in China calls into question the reliability of some the information coming from the WIV scientists and the WHO report. I haven't once stated that the lab leak is the most probable cause or that the natural origin is unlikely. I am open to both possibilities and find neither of them to be unpleasant. I have also been modest about my own knowledge. I have deliberately avoided discussing the virology because I am untrained in that area. In your previous posts, I referenced well-regarded sources that backed up the problems that I raised surrounding the WHO report and how the Chinese government has interfered in the dissemination of information surrounding the pandemic. I haven't made any definitive statements that I know the cause of the pandemic or that people who I disagree with are racist or conspiracy theorists.

    Recently some very important people have stated that a lab leak cannot be ruled out. This includes Dr. Fauci, Francis Collins, Tedros Adhanom, Ralph Baric (who collaborated with the WIV), and other respected scientists (https://science.sciencemag.org/content/372/6543/694.1). Are they also conspiracy theorists?

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    1. I'm done with you.

      You have no evidence to support your lab leak conspiracy theory and every time you post you bring up your mistrust of the Chinese. It's clear that your main motive for supporting your conspiracy theory is the "sociopolitical situation in China" and not scientific facts.

      You say,

      "I have only argued for two points: that we shouldn't dismiss the lab leak hypothesis, and that the sociopolitical situation in China calls into question the reliability of some the information coming from the WIV scientists and the WHO report."

      That's only one point. The only reason for keeping the lab leak conspiracy theory alive is because you support the conspiracy.

      Delete
  5. Scientists support leak from lab version:

    https://science.sciencemag.org/content/372/6543/694.1

    https://www.washingtonpost.com/politics/2021/05/25/timeline-how-wuhan-lab-leak-theory-suddenly-became-credible/

    It is NOT CONSPIRACIES THEORY. And data also support it:


    https://link.springer.com/article/10.1007/s10311-021-01211-0

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    1. P.S.
      BioEssays also published articles on lab leak version:

      https://onlinelibrary.wiley.com/doi/full/10.1002/bies.202000240

      https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.202100015

      Delete
    2. In the first paper from November 2020 the authors point to the furin cleavage site in SARS-CoV-2 and note that it is not found in other coronaviruses. This raises suspicion so they postulate that it might have arisen by genetic manipulation.

      In the second paper by the same authors (May 2021) they admit that furin cleavage sites are fairly common in coronavisuses but they question the alignment and sequencing studies of an unrelated paper suggesting "possible contamination."

      This is typical conspiracy theory behavior. First you claim that the furin cleavage site is clear evidence of genetic manipulation and then when that theory is refuted you find something else to raise suspicion.

      Here's a paper on the presence of furin cleavage sites in a variety of different coronaviruses.

      Furin cleavage sites naturally occur in coronaviruses
      https://doi.org/10.1016/j.scr.2020.102115

      And here's a recent preprint from the "Bat Lady" (Zheng-Li Shi) at the Wuhan Institute of Virology. They show the alignment of recently sequenced bat genomes and note the these viruses do not have the furin cleavage site. But that lack of a furin cleavage site is just what the BioEssay authors were complaining about in their second paper. So what's the problem?

      Identification of a novel lineage bat SARS-related coronaviruses that use bat ACE2 receptor
      https://doi.org/10.1101/2021.05.21.445091

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  6. I am not in a position to evaluate the accuracy of this article. It is not from a scientific source, but from Newsweek. It is relevant to the argument on this comment thread. https://www.newsweek.com/exclusive-how-amateur-sleuths-broke-wuhan-lab-story-embarrassed-media-1596958

    I don't know if these "amateur sleuths" dug out something real or connected dots inappropriately.

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    Replies
    1. And obviously, whether true or not it doesn't establish the origin of the virus causing COVID-19.

      Delete
    2. I am in a position to evaluate the accuracy of that article. It's bullshit.

      You should have been suspicious when you read ...

      "The people responsible for uncovering this evidence are not journalists or spies or scientists. They are a group of amateur sleuths, with few resources except curiosity and a willingness to spend days combing the internet for clues. Throughout the pandemic, about two dozen or so correspondents, many anonymous, working independently from many different countries, have uncovered obscure documents, pieced together the information, and explained it all in long threads on Twitter—in a kind of open-source, collective brainstorming session that was part forensic science, part citizen journalism, and entirely new. They call themselves DRASTIC, for Decentralized Radical Autonomous Search Team Investigating COVID-19."

      Delete
    3. Perhaps, Newsweek is bullshit, but if you read the related article in Vanity Fair, it points out some of the various backgrounds of DRASTIC members. Included in that group are Gilles Demaneuf, a data scientist with the Bank of New Zealand; Rodolphe de Maistre, a laboratory project director based in Paris who had previously studied and worked in China; "Some were cutting-edge scientists at prestigious research institutes. Others were science enthusiasts."

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    4. Dr. Moran, Thank you. It didn't seem plausible, but the source is not as prone to silly conspiracy theories as many are. I thought, hoped, that they would check it out. Sigh.

      Delete
  7. "I am in a position to evaluate the accuracy of that article. It's bullshit."

    If you are going to argue from your self-appointed authority, could you please tell us why the following facts are bullshit?

    1. RaTG13 was previously described in earlier papers under a different name. Shi's team renamed this sample in their earlier paper in the early stage of the pandemic. Should they have mentioned the name change and cited the earlier work in their paper?

    2. In the annotation for RaTG13 found in online databases, the sample source was changed from bronchoalveolar lavage to a bat fecal swab. Misannotations are common in databases like those at NCBI, but are you at least concerned about the quality of their record keeping? Do you think that they should have explained why this was changed, considering how important the data provenance is for this record?



    3. RaTG13 was sampled from a mine, where 6 miners got sick from a SARS-like virus. 3 of them died. Shi's team omitted this from their paper. More importantly, Shi told Scientific American that the miners died from a fungal infection. The DRASTIC team uncovered the details of the illness in one of the WIV student's theses. The illness was diagnosed as a SARS-like illness (with a secondary fungal infection) based on the diagnosis (including antibody testing) from a top SARS expert. Should they have disclosed this link? Do you believe that Shi was being truthful in her statements to Scientific American?

    4. In September 2019, the WIV took down their public database that contained thousands of records describing the viruses in their collection. Shi said that they took it down during the pandemic due to hackers. How do you make sense of this discrepancy? Moreover, why haven't they shared this database with the rest of the scientific community privately?

    Now, none of these findings proves that a lab leak occurred. However, I can't see how you can just dismiss them as bullshit.

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    1. From the Vanity Fair article: "Shi Zhengli had stated that the WIV took down the database due to hacking attempts during the pandemic. 'Absolutely reasonable,' Daszak said. 'And we did not ask to see the data…. As you know, a lot of this work has been conducted with EcoHealth Alliance…. We do basically know what’s in those databases. There is no evidence of viruses closer to SARS-CoV-2 than RaTG13 in those databases, simple as that.'

      In fact, the database had been taken offline on September 12, 2019, three months before the official start of the pandemic, a detail uncovered by Gilles Demaneuf and two of his DRASTIC colleagues."

      Delete
    2. Shi Zhengli and her group have published dozens of papers on naturally occurring coronaviruses and in every case that I could find they deposited the sequences in GenBank. Here's an example of the study of bat viruses from a cave in Yunnan. It was published in 2017.

      Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus.
      https://doi.org/10.1371/journal.ppat.1006698

      Lots of other sequences were obtained by other labs in China and they were all deposited in GenBank.

      What was in the database that you are referring to? Was there stuff that hasn't been published? If so, what was it and why is it so important to you?

      Prior to 2019 do you have any evidence to suggest that these Chinese scientists were hiding something? To me their work looks as open and transparent as the work from labs in America or anywhere else. It's pretty obvious that they were tracking down bat coronaviruses that could have been responsible for MERS and SARS and they made significant progress. Do you honestly believe that everything changed in September 2019 when they decided to coverup work on a new virus and then, coincidentally, allowed it to escape from their lab?

      And how do you account for the fact that other workers in the field who knew them all vouch for their honesty and sincerity? ... Oops, I forgot. Those other scientists from the USA, Australia, and Europe are part of the conspiracy, right?


      Delete
  8. "Shi Zhengli and her group have published dozens of papers on naturally occurring coronaviruses and in every case that I could find they deposited the sequences in GenBank. Here's an example of the study of bat viruses from a cave in Yunnan. It was published in 2017."

    I just sorted her publications in PubMed by publication date, and the 2nd most recent paper had performed sequencing:

    Serological investigation of asymptomatic cases of SARS-CoV-2 infection reveals weak and declining antibody responses(https://www.tandfonline.com/doi/full/10.1080/22221751.2021.1919032)

    I don't see any mention of the data being available publicly. If you search for the paper in NCBI, there are links to it in PubMed and PubMed Central, but no links to any of the genomic databases:

    https://www.ncbi.nlm.nih.gov/search/all/?term=Serological%20investigation%20of%20asymptomatic%20cases%20of%20SARS-CoV-2%20infection%20reveals%20weak%20and%20declining%20antibody%20responses

    That's besides the point though. Of course they have shared some data, but the more important questions are how much unpublished data do they have and why did they obfuscate data that is of key importance to our understanding of the pandemic? It's clear that they have a lot of data that is unpublished.

    Let's look at RaTG13, which I've already mentioned. Here's the link for the BioProject: https://www.ncbi.nlm.nih.gov/bioproject/606165

    They uploaded two SRA datasets for the RatG13 sample, both in 2020. Now, the biosample shows that the virus was collected in 2013! This clearly shows that they have data that they sit on for years before publication. It's also noteworthy that they tried to obfuscate the history of this virus by renaming it and by omitting it's origin.

    The deleted databases (there are actually multiple) also show that they have a lot of data that is not available the rest of the community.

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  9. PART TWO

    "What was in the database that you are referring to? Was there stuff that hasn't been published? If so, what was it and why is it so important to you?"

    Yes, there was unpublished data in that database, including data of clear importance. The database is described as follows:

    "It contains data on seasonal epidemics of viruses crossing the species barrier, data not provided by DBatVir or DRodVir. This makes it potentially the best database for investigating whether the theory of natural spillover of SARS-CoV-2 is plausible.It held more than 22,000 samples and sequence records, including for all WIV sampling trips going back many years, plus some data from external DBs (namely DBatVir (bats) and DRodVir (rodents), managed by the Institute of Pathogen Biology in Beijing - both still available). The WIV had collected over 15,000 such samples from bats (amongst the 22,000 samples records in the DB), covering over 1,400 distinct bat viruses

    Most importantly, the example virus given in the table shows that it includes samples and sequences of bat betacoronaviruses gathered by the WIV on trips to Yunnan including Mojiang (where RaTG13 was sampled), sequences that have not all been made public"

    It's also noteworthy that Shi Zhengli was the admin of this database.


    https://www.researchgate.net/publication/349073738_An_investigation_into_the_WIV_databases_that_were_taken_offline


    Prior to 2019 do you have any evidence to suggest that these Chinese scientists were hiding something? To me their work looks as open and transparent as the work from labs in America or anywhere else. It's pretty obvious that they were tracking down bat coronaviruses that could have been responsible for MERS and SARS and they made significant progress.

    Their transparency before the pandemic is irrelevant because they had no incentive to obfuscate data or to mislead the rest of the world then. That's like saying that a murder suspect had good interactions with the police before they were suspected of a crime. You're also phrasing this as if there is no reason to question the credibility of information coming from China when their track record proves otherwise. We know that the CCP tried to cover it up, censored and punished doctors and scientists, have enacted a country-wide censorship program surrounding the pandemic, and to date control what scientists can discuss or publish. The CCP has recently jailed reporters for years for the crime of questioning the official numbers surrounding the pandemic deaths. It boggles my mind how you can dismiss all of this and treat the data coming from China as reliable.

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  10. PART THREE

    "Do you honestly believe that everything changed in September 2019 when they decided to coverup work on a new virus and then, coincidentally, allowed it to escape from their lab?"

    I have no evidence of a lab-leak, but there is undeniable evidence that the data coming from China is unreliable. I do believe that the burden of proof is now on the CCP to prove that they are providing credible data. Despite of numerous lies, misdirection, and demonstrable coverups, the world has been extremely charitable towards the Chinese government during this pandemic. I'm running out of charitable explanations to account for how they obfuscated data, lied about the miner's deaths, and deleted a key database a few months before the world became aware of the pandemic and later lied about the reason for doing so.

    "And how do you account for the fact that other workers in the field who knew them all vouch for their honesty and sincerity? ... Oops, I forgot. Those other scientists from the USA, Australia, and Europe are part of the conspiracy, right?"

    I've given you multiple examples of how the Chinese authorities covered up the pandemic, censored and persecuted those who spoke out, how crucial data was obfuscated or made unavailable, etc. You continue to evade these issues and respond with an argument from authority (that these scientists are very respected). I've given you concrete examples of Shi Zhengli lying or contradicting herself. Rather than appeal to her reputation, why don't you address her inaccurate statements? Her being well regarded isn't necessarily mutually exclusive with her being an unreliable source of information (which should be obvious considering her statements that would charitably described as inaccurate or misleading). After all, she is living under a totalitarian government that has demonstrated that they will persecute those who contradict the government's statements. There is some reason to believe that she has tried to be more transparent in the past, but the Chinese authorities aren't allowing her to:

    "But her ascent came at a cost. There is reason to believe she was hardly free to speak her mind or follow a scientific path that didn’t conform to China’s party line. Though Shi had planned to share isolated samples of the virus with her friend James LeDuc in Galveston, Beijing officials blocked her. And by mid-January, a team of military scientists led by China’s top virologist and biochemical expert, Major General Chen Wei, had set up operations inside the WIV."

    https://www.vanityfair.com/news/2021/06/the-lab-leak-theory-inside-the-fight-to-uncover-covid-19s-origins

    Can you please explain to me how I Chinese scientist could contradict the party line?

    Also, you continue to assert that scientists from other countries would need to be involved in a coverup. There is no reason to believe this. The rest of the world hasn't been given access to the required data. All publications and statements about the pandemic require CCP approval. The WHO team were not given the authority to review raw data or conduct private interviews:

    "In my discussions with the team, they expressed the difficulties they encountered in accessing raw data. I expect future collaborative studies to include more timely and comprehensive data sharing."

    https://www.who.int/director-general/speeches/detail/who-director-general-s-remarks-at-the-member-state-briefing-on-the-report-of-the-international-team-studying-the-origins-of-sars-cov-2

    "Dominic Dwyer, an Australian infectious disease expert who was part of the team, said they had requested raw patient data but were only given a summary.

    Dwyer told Reuters on Saturday that sharing anonymised raw data is “standard practice” for an outbreak investigation. "

    https://www.theguardian.com/world/2021/feb/14/who-investigator-claims-china-refused-to-hand-over-key-covid-information


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