- A Chinese PhD Thesis Sheds Important New Light On The Origin of the COVID-19 Coronavirus
Posted by Gerard
on May 26, 2021, 7:07 pm
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"by Jonathan Latham, PhD and Allison Wilson, PhD One of the very earliest scientific papers from the COVID-19 pandemic era now has over 11,000 citations. Appearing in the scientific journal Nature on February 3rd 2020, Zhou et al., 2020 reported the genome sequence of a novel coronavirus isolated from patients with atypical pneumonia in Wuhan, China. Its senior author was leading coronavirus researcher Zheng-li Shi of the Wuhan Institute of Virology (the WIV). Along with what we now call SARS-CoV-2, her paper also reported the genome sequence of a closely related (96.2% identical) bat virus. The authors called this virus RaTG13. To this day RaTG13 is still the closest known viral genome by far to SARS-CoV-2. RaTG13 came from the freezers of the WIV. In one sense, there is nothing unusual about that. Researchers often have old samples stored away and the WIV has the largest collection of coronaviruses in the world. On the other hand, Wuhan is considered an unlikely locality for a coronavirus outbreak. However, the two sentences in Zhou et al., (2020) describing RaTG13 allayed any fears: “We then found that a short region of RNA-dependent RNA polymerase (RdRp) from a bat coronavirus (BatCoV RaTG13)–which was previously detected in Rhinolophus affinis from Yunnan province–showed high sequence identity to 2019-nCoV. We carried out full-length sequencing on this RNA sample (GISAID accession number EPI_ISL_402131).” This statement clearly implied that, prior to the pandemic, WIV researchers had only ever studied a ‘short’ fragment of RaTG13, that the fragment was unpublished (since no prior description was cited), and that no recent research had been carried out on RaTG13 or its sample. Consequently, a lab leak involving RaTG13 was implausible. But all these inferences turned out to be untrue. Zhou et al. was one of the pandemic’s key misinformation superspreaders. In August 2020, two researchers, Monali Rahalkar and Rahul Bahulikar, published a preprint in which they reported that they had accessed the underlying sequencing files for RaTG13. As first noticed by Twitter user Francisco A. de Ribeira, some were dated from 2017 and others from 2018. Moreover, these early RaTG13 sequences went far beyond a short fragment, encompassing most of the genome (Rahalkar and Bahulikar, 2020a). In November 2020 Nature published an addendum to Zhou et al. in which Zheng-li Shi and her co-authors conceded these points. They wrote: “In 2018…..we performed further sequencing of these bat viruses and obtained almost the full-length genome sequence (without the 5′ and 3′ ends) of RaTG13.” Thus the RaTG13 genome sequence was mostly deciphered in 2018 and not in January 2020. Ergo, the viral genome most similar to SARS-CoV-2 was being studied at the WIV before the pandemic broke out. But why hide this activity? The outbreak in the Mojiang Mine By the time of these revelations, yet other questions had arisen about RaTG13. It turned out that RaTG13 was an exact genetic match to an already published partial virus sequence called BtCoV/4991. BtCoV/4991 had been obtained by Zheng-li Shi’s group in 2013 from a mine in Yunnan Province, China (Ge et al., 2016). Furthermore, RaTG13 and BtCoV/4991 were from the same bat anal swab sample. In other words, from the data provided, the two were indistinguishable. Thus, RaTG13 did have a publishing history, but under the name BtCoV/4991 (Bengston, 2020). In addition to BtCoV/4991 another novel betacoronavirus was found at the same time. Their discoverers concluded the following: “Considering that the two highly pathogenic human coronaviruses (SARS-CoV and MERS-CoV) in this genus [the Betacoronaviruses] originated from bats (Ge et al., 2013; Lau et al., 2013; Corman et al., 2014), attention should be particularly paid to these lineages of bat coronaviruses.” (Ge et al., 2016) According to their own words, it would therefore be surprising had Zheng-li Shi’s group not gone on to study BtCoV/4991 aka RaTG13. Yet the discovery of this publication trail only deepened the mystery yet further. Though never mentioned by Ge et al., the ‘abandoned’ mine (which subsequently became known as the Mojiang mine) where BtCoV/4991 was found had recently been the site of a mystery disease outbreak. In April 2012, just two and a half months before the first WIV sampling trip, six miners had become sick and three of them had died. Indeed, the mine outbreak was presumably why the WIV researchers were sampling there (and the Zhou et al. addendum later confirmed this). The nature of the 2012 disease outbreak became much clearer with the discovery (by an anonymous Twitter user called @TheSeeker268) of a 2013 Chinese Master’s thesis. This thesis is titled “The Analysis of Six Patients With Severe Pneumonia Caused By Unknown Viruses“. Its abstract specifically mentions a possible outbreak of SARS-like coronaviruses. To learn more about the 2012 pneumonia outbreak, we arranged to have the Master’s thesis translated into English. The translation yielded a cornucopia of information. This began with the fact that the author of the thesis was the doctor who supervised the testing and treatment of the miners at the First Affiliated hospital of Kunming Medical University (Yunnan Province). According to the Master’s thesis, the miners had been shovelling bat guano. This implied that the mystery disease probably originated from bats. That, along with various test results and consultations led the author to conclude that the most likely cause of the outbreak was a coronavirus. But perhaps most startling of all the findings to emerge from the translation was that the symptoms of the miners closely resembled those of COVID-19 (Rahalkar and Bahulikar, 2020b). The Master’s thesis thus raised a host of questions. Why did the Ge et al. 2016 publication (from Zheng-li Shi’s lab), which sampled the mine on multiple occasions, make no mention of the outbreak that caused them to be sampling there in the first place? Why did Zheng-li Shi tell Scientific American in March 2020 that the miners died of a fungal infection? Why did her Zhou et al. 2020 publication rename BtCov/4991 as RaTG13 without explanation or even referencing the earlier work on BtCov/4991 or its mine origin? Especially, given that Zheng-li Shi and her corona-colleagues in China and elsewhere have constantly warned of coronavirus spillovers from bats (e.g. Zhou et al., 2018), why did no one seemingly prove or disprove the coronavirus theory in the Master’s thesis? Are we to presume that an apparent textbook case of a zoonotic spillover, significant enough at the time to be covered by Science magazine, was in the end simply ignored? So many interrelated errors and omissions present a conundrum. Are these concatenated oversights simply innocent happenstances? Or were they deliberate attempts to obscure the connections from RaTG13 back to BtCov/4991 and from there to the mine and thence to the mine outbreak; to thereby prevent anyone in 2020 linking SARS-CoV-2 and the mine outbreak in 2012? Is there something about the mine or the miners of deep significance to the current pandemic? If so, what?" Go to: https://www.independentsciencenews.org/commentaries/a-chinese-phd-thesis-sheds-important-new-light-on-the-origin-of-the-covid-19-coronavirus/ for full article. |