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Wednesday, June 09, 2021

Let's analyze the Newsweek lab leak conspiracy theory article

Lots of people have been sucked in to the lab leak conspiracy theory based on reporting in newspapers and magazines. One of the widely-cited sources is an article published in Newsweek on June 2, 2021. The focus of the article is on How Amateur Sleuths Broke the Wuhan Lab Story and Embarrassed the Media. Those "amateur sleuths" go by the name "Decentralized Radical Autonomous Search Team Investigating COVID-19" or DRASTIC. I'm not interested in them; I'm interested in scientific facts so let's look at all of the so-called "facts" in the Newsweek article. I'll leave it up to you, dear reader, to judge whether the media should be embarrassed by this story.

Newsweek statment #1: Thanks to DRASTIC, we now know that the Wuhan Institute of Virology had an extensive collection of coronaviruses gathered over many years of foraging in the bat caves, and that many of them—including the closest known relative to the pandemic virus, SARS-CoV-2—came from a mineshaft where three men died from a suspected SARS-like disease in 2012.

Some of this is correct. The WIV scientists and their collaborators have been collecting samples from bats all over China and Indochina for several years and many of them have been examined for the presence of coronaviruses. WIV scientists routinely sampled bats from the Yunnan mine cave from 2012 to 2015 after they were informed that four people had been admitted to hospital with severe respiratory disease in 2012 (one of them died). The workers tested negative for Ebola, Nipah virus, and coronavirus so the scientists were looking for a likely unknown virus that caused the infection. (The serum samples were subsequently tested for SARS-CoV-2 and they were negative.)

Several coronaviruses were detected in the bat samples based on short PCR sequences (370 bp) from the RdRp gene and they were classified as either alphacoronaviruses or betacoronaviruses. The data was published in 2016 (Ge et al., 2016) and the sequences were deposited in GenBank in 2016. Improvements in sequencing technology in 2018 prompted a re-examination of those bat samples and an almost full-length sequence of a betacoronavirus was obtained (missing the 5′ and 3′ ends). This virus was named RaTG13 and one of the short GenBank sequences identified as BtCoV/4491 (Accession #KP876546) comes from that virus (Zhou et al., 2020 Addendum).

The bat virus is RaTG13 and it is 96% similar in sequence to SARS-CoV-2—that means that they probably shared a common ancestor about 50 years ago (Zhou et al. 2020). The sequence was deposited in GenBank as Accession #Mn996532. There are parts of SARS-CoV-2 that are not closely related to RaTG13 and this includes the spike protein gene, which is essential for infecting humans. The spike gene sequence is most closely related to a coronavirus from pangolins, Pangolin-Cov.

The data is consistent with a recombination event between different strains of coronaviruses giving rise to SARS-CoV-2 or its immediate ancestors. Such recombinations are a common feature of coronavirus propagation in various animals, including bats. What's clear is that none of the currently known coronavirus sequences could possibly be the ancestors of SARS-CoV-2 so the hunt is on to locate those viruses.

Recently, the scientists at WIV and their collaboratore at the University of Chinese Academy of Sciences in Beijing looked at some of the other samples from bat anal swabs collected in Yunnan in 2015. This in depth analysis was prompted by the discovery of SARS-CoV-2 and the pandemic. They found a number of other bat coronavisus sequences and some of them were more closely related to SARS-CoV-2 in the ORF1b regions but not in other parts of the genome. Again, this is consistent with frequent recombination events that have been documented over the past few decades. Surprisingly, some of these new bat coronavisuses were able to use the bat angiotensin-converting enzyme 2 (ACE2) as a receptor, but they did not bind to human ACE2. (These assays take a lot of time and effort.) This and other data show that the evolution of ACE2 binding can occur in bats giving rise to a generalist virsus, SARS-CoV-2, than can bind to ACE2 from many different species. (MacLean et al., 2021; Guo et al., 2021).

A group of scientists from France, United States, Vietnam, and Cambodia looked at bat samples that were collected in Cambodia in 2010 and found coronaviruses from another species of bats that were cloesly related to SARS-CoV-2 across most of the genome except for a small region of the spike protein gene. In some parts of the genome (ORF1a and ORF8) these viruses were more closely related to SARS-CoV-2 than RATG13 (Hu et al. 2021). The evolutionary history of the Cambodian viruses indicate that they are mosaic viruses due to recombination events. This data indicates that SARS-CoV-2 related viruses are found in Southeast Asia as well as China—that's signficant since pangolins are only found in Southeast Asia and not in China.

SARS-CoV-2-like viruses have also been found in Thailand (Wacharapluesadee et al., 2021).

A group centered in Taian, China, has recently examined coronaviruses from bats at the botanical garden in Mengal county in Yunnan. They have identified four additional SARS-CoV-2 related viruses including one, RpYN06, that is the closest relative to SARS-CoV-2 outside of the spike gene. This is now the leading candidate for the "backbone" that might have given rise to the pandemic virus (Zhou et al., 2021).

CONCLUSION: The Newsweek statement is not wrong but it is highly misleading. The WIV labs had bat samples that contained coronaviruses but so did lots of labs all over the world. In that sense, these labs have an "extensive collection of coronaviruses" but they are stored in bat poop at -80° C! They identified two coronavirus, RaTG13 and RmYN02, by sequencing PCR fragments but the sequences were not complete. It's misleading for Newsweek to imply that the WIV labs had an RaTG13 coronavirus in their labs because that implies that they were working with active viruses. It's true that the RaTG13 virus came from a place where several workers had gotten sick with respiratory disease a few years before the sample was collected. One of these men died (not three) but none of the patients tested positive for coronavirus.

Newsweek statement #2: We know that the WIV was actively working with these viruses, using inadequate safety protocols, in ways that could have triggered the pandemic, and that the lab and Chinese authorities have gone to great lengths to conceal these activities.

CONCLUSION: This is misleading. As far as I know, the scientists are WIV were not actively working with the RaTG13 virus because they had never isolated that virus. Furthermore, it's almost impossible to create SARS-CoV-2 from RaTG13 [Could scientists use the bat coronavirus RaTG13 to engineer SARS-CoV-2, the virus that causes COVID-19, in a lab?]. They were working with other bat coronaviruses but none of them were closely related to SARS-CoV-2 so it's extremely misleading to imply that the escape of these viruses could have triggered the pandemic. They were not using inadequate safety protocols because all of the work with bat coronaviruses was carried out in level 2 labs, exactly as required. There's no evidence that the scientists at the WIV labs have concealed anything. You can only accuse someone of concealing something if you have strong evidence that they did something that they deny doing.

Newsweek statement #3: We know that the first cases appeared weeks before the outbreak at the Huanan wet market that was once thought to be ground zero.

CONCLUSION: This is correct. Chinese scientists and health workers identified a number of earlier cases that appear to be unrelated to the seafood market and they published their results in scientific journals over a year ago. They now conclude that the virus was circulating in the Wuhan population for more than a month before the superspreader event at the market ignited the pandemic. This appears to be a case where Newsweek trusts the work of Chinese scientists.

Newsweek statement #4: The Newsweek article talks a lot about the DRASTIC group as though they have uncovered a huge conspriacy theory. One of their "discoveries" relates to the bat coronavirus RaTG13 that's first mentioned in the paper where the SARS-CoV-2 sequence was published. Here's what Newsweek wrote: "The paper was vague about where RaTG13 had come from. It didn't say exactly where or when RaTG13 had been found, just that it had previously been detected in a bat in Yunnan Province, in southern China.

The paper aroused Deigin's suspicions. He wondered if SARS-CoV-2 might have emerged through some genetic mixing and matching from a lab working with RaTG13 or related viruses. His post was cogent and comprehensive. The Seeker posted Deigin's theory on Reddit, which promptly suspended his account permanently."

CONCLUSION: This is written like it's a big mystery that was uncovered by some clever sleuthing. It's true that the origin of RaTG13 was not discussed in the SARS-CoV-2 paper in January 2020 other than to say that it was found in a bat in Yunnan. I assume that the authors didn't think it was important (and still don't). The origin was explained in November 2020 in an Addendum to the Nature article (Zhou et al., 2020, Addendum). It was one of the viruses discoverd in the bats from the Yunnan mine cave and a partial sequence had been published earlier (Ge et al., 2016). It's not particulary close to SARS-CoV-2 and there's no reason to speculate that it was artificially created unless you are trying to create a conspiracy.

Newsweek statement #5: The key facts quickly came together. The genetic sequence for RaTG13 perfectly matched a small piece of genetic code posted as part of a paper written by Shi Zhengli years earlier, but never mentioned again. The code came from a virus the WIV had found in a Yunnan bat. Connecting key details in the two papers with old news stories, the DRASTIC team determined that RaTG13 had come from a mineshaft in Mojiang County, in Yunnan Province, where six men shoveling bat guano in 2012 had developed pneumonia. Three of them died. DRASTIC wondered if that event marked the first cases of human beings being infected with a precursor of SARS-CoV-2—perhaps RaTG13 or something like it.

In a profile in Scientific American, Shi Zhengli acknowledged working in a mineshaft in Mojiang County where miners had died. But she avoided connecting it to RaTG13 (an omission she had made in her scientific papers as well), claiming that a fungus in the cave had killed the miners.

This reads just like a typical conspiracy theory where "clever" sleuths (i.e. internet anateurs) uncover information that was hidden or covered up by those they are accusing. The origin of RaTG13 was explained in an addendum to the publication of the SARS-CoV-2 sequence in February 2020. The addendum was added in November 2020 in reponse to questions about the origin of RaTG13 but that information was widely known. The sequence of a short fragment of this virus was obtained earlier as explained above.

The WIV scientists were very concerned about the Yunnan mine workers because they had symptoms that were similar to those of SARS patients and that's why they tested serum from the patients. They were negative for all the viruses, including the original SARS-CoV-1. (The serum is also negative for SARS-CoV-2.) The WIV scientists were worried that the infections were due to an unknown virus that could cause a pandemic so they went back to the mine every year to collect samples from the bats. The RaTG13 sequence came from one of those samples but by then the scientists knew that there was no connection between the bat coronaviruses and the sick mine workers. (They were probably disappointed at the lack of connection because they were looking for the cause of the 2002 SARS outbreak.)

The WIV scientists now believe that the Yunnan mine workers had contracted a fungal infection from the fungus growing on the bat guano. There is no reason to connect RaTG13 to the mine workers because it's been known for many years that the workers were not infected with any coronavirus.

The RaTG13 virus is from the bat species Rhinolophus affinis (hence the designation "Ra") but up until the beginning of the pandemic the WIV scientists were much more interested in another cave in Yunnan populated by a number of different species. They reported that this cave represents the most diverse collection of bat coronaviruses in the world. Most of the ones that are SARS-like were from a different species of bat, Rhinolophus sinicus and many of these bound the same ACE2 receptor that SARS-CoV-1 used—the same one used by the more recent SARS-CoV-2 (Hu et al. 2017; Cui et al., 2019).

CONCLUSION: The Newsweek article is repeating innuendos and conspiracies that have been discredited in the past. The DRASTIC team is deliberately making up connections between coroanvirus and the mine workers but all of the data shows that there's no direct connection. It just happened that one of the bat coronaviruses collected in that mine happened to be the one closest to SARS-CoV-2, in part because that was a pretty extensive collection. The RaTG13 sequence is not similar enough to SAS-CoV-2 to be the direct ancestor and, besides, there are now known to be other virus sequences from as far away as Cambodia that are just as similar to SARS-CoV-2.

Newsweek statement #6: That explanation didn't sit well with the DRASTIC group. They suspected a SARS-like virus, not a fungus, had killed the miners and that, for whatever reason, the WIV was trying to hide that fact. It was a hunch, and they had no way of proving it.

At this point, The Seeker revealed his research powers to the group. In his online explorations, he'd recently discovered a massive Chinese database of academic journals and theses called CNKI. Now he wondered if somewhere in its vast circuitry might be information on the sickened miners.

Working through the night at his bedside table on phone and laptop, fueled by chai and using Chinese characters with the help of Google Translate, he plugged in "Mojiang"—the county where the mine was located—in combination with every other word he could think of that might be relevant, instantly translating each new flush of results back to English. "Mojiang + pneumonia"; "Mojiang + WIV"; "Mojiang + bats"; "Mojiang + SARS." Each search brought back thousands of results and half a dozen different databases for journals, books, newspapers, master's theses, doctoral dissertations. He combed through these results, night after night, but never found anything useful. When he ran out of energy, he broke for arcade games and more chai.

He was on the verge of calling it quits, he says, when he struck gold: a 60-page master's thesis written by a student at Kunming Medical University in 2013 titled "The Analysis of 6 Patients with Severe Pneumonia Caused by Unknown Viruses." In exhaustive detail, it described the conditions and step-by-step treatment of the miners. It named the suspected culprit: "Caused by SARS-like [coronavirus] from the Chinese horseshoe bat or other bats."

CONCLUSION: Move along folks; there's nothing to see here. The WIV scientists suspected that the miners were infected with an unknown virus and that's why they were concerned in 2012. They knew that coronavirus wasn't responsible and neither was any other known virus. This is why they went back every year to test the bats in the mine shaft. The know that the stored serum from these workers is negative for SARS-CoV-2, which is not a surprise. They now suspect that the mine workers had contracted a fungl infection and not a viral infection. It's not particulary surprising that a student reported the suspected cause of the symptoms back in the beginning of the investigation.

Newsweek statement #7: Ribera was responsible for solving another piece of the RaTG13 puzzle. Had the WIV been actively working on RaTG13 during the seven years since they discovered it? Peter Daszak said no: they had never used the virus because it wasn't similar enough to the original SARS. "We thought it's interesting, but not high-risk," he told Wired. "So we didn't do anything about it and put it in the freezer."

Ribera disproved that account. When a new science paper on genetics is published, the authors must upload the accompanying genetic sequences to an international database. By examining some metadata tags that had been accidentally uploaded by the WIV along with its genetic sequences for RaTG13, Ribera discovered that scientists at the lab had indeed been actively studying the virus in 2017 and 2018—they hadn't stuck it in a freezer and forgotten about it, after all.

I don't know what this means. The WIV scientists sequenced a bit of what turned out to be the RaTG13 virus when they catagorized all the other viruses back in 2012-2015 (Ge et al. 2016). They then completed an almost whole genome sequence later on in 2018 when their sequencing techniques improved. It's important keep in mind that the WIV never worked with the RaTG13 virus as emphasized by Frutos et al. (2021): "One must remember that SARS-CoV-2 was never found in the wild and that RaTG13 does not exist as a real virus but instead only as a sequence in a computer. It is a virtual virus which thus cannot leak from a laboratory." 1

CONCLUSION: The scientists at WIV were "working with" the RaTG13 PCR fragments in 2017 and 2018 as they assembled the whole genome sequence. They also assembled the sequences of seveal other viruses at the same time. To say that they were "actively studying" the virus is very misleading and to accuse Peter Daszek of lying is irresponsible.

Newsweek statement #8: In fact, the WIV had been intensely interested in RaTG13 and everything else that had come from the Mojiang mineshaft. From his giant Sudoku puzzle, Ribera determined that they made at least seven different trips to the mine, over many years, collecting thousands of samples. Ribera's guess is that their technology had not been good enough in 2012 and 2013 to find the virus that had killed the miners, so they kept going back as the techniques improved.

He also made a bold prediction. Cross-referencing snippets of information from multiple sources, Ribera guessed, in a Twitter thread dated August 1, 2020, that a cluster of eight SARS-related viruses mentioned briefly in an obscure section of one WIV paper had actually also come from the Mojiang mine. In other words, they hadn't found one relative of SARS-CoV-2 in that mineshaft; they'd found nine. In November 2020, Shi Zhengli confirmed many of DRASTIC's suspicions about the Mojiang cave in an addendum to her original paper on RaTG13 and in a talk in February 2021.

The mine shaft is located in Mojiang county, Yunnan—a map of the location was published in Ge et al. (2016). It contains six different bat species and many of them were infected with coronaviruses. The WIV scientists collected many samples over a number of years in order to determine the phylogeny of the viruses and which species were infected. They also did longitudinal studies to see if the different virus variants changed over time and to see if the infection rates of the various bat species were different from year to year. They also wanted to see if they could detect recombinations between different virus groups.

They obtained 152 partial sequences and then picked 12 of them for more detailed analysis in order to construct a phylogenetic tree from 816 bp of the RNA-dependent RNA polymerase (RdRp) gene. Anyone can read the Ge et al. (2016) paper to see why they were doing these experiments. There's nothing mysterious or unusual about their approach. It's the same one they took with the viruses from the other site (cave) in Yunnan where they identified the two bat coronaviruses that are most closely related to the original SARS virus (Ge et al., 2013) (see: SARS ouotbreak linked to Chinese bat cave)

CONCLUSION: The Newsweek article is making a huge mountain out of a molehill and it's misrepresenting the work of the "amateur sleuths." It's not a secret or a mystery that the WIV scientists were studying the coronaviruses from the mine shaft. That's what they do and they publish in journals that are easy to access.

Newsweek statement #9: "Other databases yielded other clues. In the WIV's grant applications and awards, The Seeker found detailed descriptions of the Institute's research plans, and they were damning: Projects were underway to test the infectivity of novel SARS-like viruses they'd discovered in human cells and in lab animals, to see how they might mutate as they crossed species, and to genetically recombine pieces of different viruses—all being done at woefully inadequate biosecurity levels. All the elements for a disaster were on hand."

CONCLUSION: It's true that the WIV scientists were looking at SARS-like coronavisuses and they were testing for infectivity in humanized mouse cells. The goal was to look for new coronaviruses that could bind ACE2 and they found quite a few of them. In many cases, they expressed the spike protein in recombinant viruses and plasmids just as you would expect them to do if they were looking for the source of the original SARS virus (SARS-CoV-1). All this is described in their grant applications and in their publications. Looks like they didn't make much of an attempt to hide this research. All the experiments were done under the appropriate biosafety measures as specified by international inspectors who visited the lab on several occasions. None of this has anything to do with the pandemic because they were not working with SARS-CoV-2 or any close relative.

The rest of the Newsweek article consists mostly of praise for the DRASTIC heros and the excellent work they have done in uncovering a huge conspiracy to cover up the fact that the WIV scientists started a pandemic. However, one embarrassing fact remains: there is not a shred of evidence that the lab was working with SARS-CoV-2 before the pandemic started. In the absence of such evidence it is irresponsible to accuse these reputable scientists of lying.

1. One could quibble slightly about the accuracy of this statment since there might be RaTG13 virus particles in the bat fecal samples that are stored in the -80°C freezer.

Cui, J., Li, F. and Shi, Z.-L. (2019) Origin and evolution of pathogenic coronaviruses. Nature Reviews Microbiology 17:181-192. doi: [doi: 10.1038/s41579-018-0118-9]

Severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) are two highly transmissible and pathogenic viruses that emerged in humans at the beginning of the 21st century. Both viruses likely originated in bats, and genetically diverse coronaviruses that are related to SARS-CoV and MERS-CoV were discovered in bats worldwide. In this Review, we summarize the current knowledge on the origin and evolution of these two pathogenic coronaviruses and discuss their receptor usage; we also highlight the diversity and potential of spillover of bat-borne coronaviruses, as evidenced by the recent spillover of swine acute diarrhoea syndrome coronavirus (SADS-CoV) to pigs.

Hu, V., Delaune, D., Karlsson, E.A., Hassanin, A., Tey, P.O., Baidaliuk, A., Gámbaro, F., Tu, V.T., Keatts, L. and Mazet, J. (2021) A novel SARS-CoV-2 related coronavirus in bats from Cambodia. bioRxiv. [doi: 10.1101/2021.01.26.428212]

Knowledge of the origin and reservoir of the coronavirus responsible for the ongoing COVID-19 pandemic is still fragmentary. To date, the closest relatives to SARS-CoV-2 have been detected in Rhinolophus bats sampled in the Yunnan province, China. Here we describe the identification of SARS-CoV-2 related coronaviruses in two Rhinolophus shameli bats sampled in Cambodia in 2010. Metagenomic sequencing identified nearly identical viruses sharing 92.6% nucleotide identity with SARS-CoV-2. Most genomic regions are closely related to SARS-CoV-2, with the exception of a small region corresponding to the spike N terminal domain. The discovery of these viruses in a bat species not found in China indicates that SARS-CoV-2 related viruses have a much wider geographic distribution than previously understood, and suggests that Southeast Asia represents a key area to consider in the ongoing search for the origins of SARS-CoV-2, and in future surveillance for coronaviruses.

Ge, X.-Y., Li, J.-L., Yang, X.-L., Chmura, A.A., Zhu, G., Epstein, J.H., Mazet, J.K., Hu, B., Zhang, W. and Peng, C. (2013) Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature 503:535-538. [doi: 10.1038/nature12711]

The 2002–3 pandemic caused by severe acute respiratory syndrome coronavirus (SARS-CoV) was one of the most significant public health events in recent history1. An ongoing outbreak of Middle East respiratory syndrome coronavirus2 suggests that this group of viruses remains a key threat and that their distribution is wider than previously recognized. Although bats have been suggested to be the natural reservoirs of both viruses3,4,5, attempts to isolate the progenitor virus of SARS-CoV from bats have been unsuccessful. Diverse SARS-like coronaviruses (SL-CoVs) have now been reported from bats in China, Europe and Africa5,6,7,8, but none is considered a direct progenitor of SARS-CoV because of their phylogenetic disparity from this virus and the inability of their spike proteins to use the SARS-CoV cellular receptor molecule, the human angiotensin converting enzyme II (ACE2)9,10. Here we report whole-genome sequences of two novel bat coronaviruses from Chinese horseshoe bats (family: Rhinolophidae) in Yunnan, China: RsSHC014 and Rs3367. These viruses are far more closely related to SARS-CoV than any previously identified bat coronaviruses, particularly in the receptor binding domain of the spike protein. Most importantly, we report the first recorded isolation of a live SL-CoV (bat SL-CoV-WIV1) from bat faecal samples in Vero E6 cells, which has typical coronavirus morphology, 99.9% sequence identity to Rs3367 and uses ACE2 from humans, civets and Chinese horseshoe bats for cell entry. Preliminary in vitro testing indicates that WIV1 also has a broad species tropism. Our results provide the strongest evidence to date that Chinese horseshoe bats are natural reservoirs of SARS-CoV, and that intermediate hosts may not be necessary for direct human infection by some bat SL-CoVs. They also highlight the importance of pathogen-discovery programs targeting high-risk wildlife groups in emerging disease hotspots as a strategy for pandemic preparedness.

Ge, X.-Y., Wang, N., Zhang, W., Hu, B., Li, B., Zhang, Y.-Z., Zhou, J.-H., Luo, C.-M., Yang, X.-L. and Wu, L.-J. (2016) Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft. Virologica Sinica 31:31-40. [doi: 10.1007/s12250-016-3713-9]

Since the 2002–2003 severe acute respiratory syndrome (SARS) outbreak prompted a search for the natural reservoir of the SARS coronavirus, numerous alpha- and betacoronaviruses have been discovered in bats around the world. Bats are likely the natural reservoir of alpha- and beta-coronaviruses, and due to the rich diversity and global distribution of bats, the number of bat coronaviruses will likely increase. We conducted a surveillance of coronaviruses in bats in an abandoned mineshaft in Mojiang County, Yunnan Province, China, from 2012–2013. Six bat species were frequently detected in the cave: Rhinolophus sinicus, Rhinolophus affinis, Hipposideros pomona, Miniopterus schreibersii, Miniopterus fuliginosus, and Miniopterus fuscus. By sequencing PCR products of the coronavirus RNA-dependent RNA polymerase gene (RdRp), we found a high frequency of infection by a diverse group of coronaviruses in different bat species in the mineshaft. Sequenced partial RdRp fragments had 80%–99% nucleic acid sequence identity with well-characterized Alphacoronavirus species, including BtCoV HKU2, BtCoV HKU8, and BtCoV1,and unassigned species BtCoV HKU7 and BtCoV HKU10. Additionally, the surveillance identified two unclassified betacoronaviruses, one new strain of SARS-like coronavirus, and one potentially new betacoronavirus species. Furthermore, coronavirus co-infection was detected in all six batspecies, a phenomenon that fosters recombination and promotes the emergence of novel virus strains. Our findings highlight the importance of bats as natural reservoirs of coronaviruses and the potentially zoonotic source of viral pathogens.

Guo, H., Hu, B., Si, H.-r., Zhu, Y., Zhang, W., Li, B., Li, A., Geng, R., Lin, H.-F. and Yang, X.-L. (2021) Identification of a novel lineage bat SARS-related coronaviruses that use bat ACE2 receptor. bioRxiv. [doi: 10.1101/2021.05.21.445091]

Severe respiratory disease coronavirus-2 (SARS-CoV-2) causes the most devastating disease, COVID-19, of the recent century. One of the unsolved scientific questions around SARS-CoV-2 is the animal origin of this virus. Bats and pangolins are recognized as the most probable reservoir hosts that harbor the highly similar SARS-CoV-2 related viruses (SARSr-CoV-2). Here, we report the identification of a novel lineage of SARSr-CoVs, including RaTG15 and seven other viruses, from bats at the same location where we found RaTG13 in 2015. Although RaTG15 and the related viruses share 97.2% amino acid sequence identities to SARS-CoV-2 in the conserved ORF1b region, but only show less than 77.6% to all known SARSr-CoVs in genome level, thus forms a distinct lineage in the Sarbecovirus phylogenetic tree. We then found that RaTG15 receptor binding domain (RBD) can bind to and use Rhinolophus affinis bat ACE2 (RaACE2) but not human ACE2 as entry receptor, although which contains a short deletion and has different key residues responsible for ACE2 binding. In addition, we show that none of the known viruses in bat SARSr-CoV-2 lineage or the novel lineage discovered so far use human ACE2 efficiently compared to SARSr-CoV-2 from pangolin or some of the SARSr-CoV-1 lineage viruses. Collectively, we suggest more systematic and longitudinal work in bats to prevent future spillover events caused by SARSr-CoVs or to better understand the origin of SARS-CoV-2.

MacLean, O.A., Lytras, S., Weaver, S., Singer, J.B., Boni, M.F., Lemey, P., Pond, S.L.K. and Robertson, D.L. (2021) Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen. PLoS Biology 19:e3001115. [doi: 10.1371/journal.pbio.3001115]

Virus host shifts are generally associated with novel adaptations to exploit the cells of the new host species optimally. Surprisingly, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has apparently required little to no significant adaptation to humans since the start of the Coronavirus Disease 2019 (COVID-19) pandemic and to October 2020. Here we assess the types of natural selection taking place in Sarbecoviruses in horseshoe bats versus the early SARS-CoV-2 evolution in humans. While there is moderate evidence of diversifying positive selection in SARS-CoV-2 in humans, it is limited to the early phase of the pandemic, and purifying selection is much weaker in SARS-CoV-2 than in related bat Sarbecoviruses. In contrast, our analysis detects evidence for significant positive episodic diversifying selection acting at the base of the bat virus lineage SARS-CoV-2 emerged from, accompanied by an adaptive depletion in CpG composition presumed to be linked to the action of antiviral mechanisms in these ancestral bat hosts. The closest bat virus to SARS-CoV-2, RmYN02 (sharing an ancestor about 1976), is a recombinant with a structure that includes differential CpG content in Spike; clear evidence of coinfection and evolution in bats without involvement of other species. While an undiscovered “facilitating” intermediate species cannot be discounted, collectively, our results support the progenitor of SARS-CoV-2 being capable of efficient human–human transmission as a consequence of its adaptive evolutionary history in bats, not humans, which created a relatively generalist virus.

Wacharapluesadee, S., Tan, C.W., Maneeorn, P., Duengkae, P., Zhu, F., Joyjinda, Y., Kaewpom, T., Chia, W.N., Ampoot, W. and Lim, B.L. (2021) Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia. Nature communications 12:1-9. doi: [doi: 10.1038/s41467-021-21240-1]

Among the many questions unanswered for the COVID-19 pandemic are the origin of SARS-CoV-2 and the potential role of intermediate animal host(s) in the early animal-to-human transmission. The discovery of RaTG13 bat coronavirus in China suggested a high probability of a bat origin. Here we report molecular and serological evidence of SARS-CoV-2 related coronaviruses (SC2r-CoVs) actively circulating in bats in Southeast Asia. Whole genome sequences were obtained from five independent bats (Rhinolophus acuminatus) in a Thai cave yielding a single isolate (named RacCS203) which is most related to the RmYN02 isolate found in Rhinolophus malayanus in Yunnan, China. SARS-CoV-2 neutralizing antibodies were also detected in bats of the same colony and in a pangolin at a wildlife checkpoint in Southern Thailand. Antisera raised against the receptor binding domain (RBD) of RmYN02 was able to cross-neutralize SARS-CoV-2 despite the fact that the RBD of RacCS203 or RmYN02 failed to bind ACE2. Although the origin of the virus remains unresolved, our study extended the geographic distribution of genetically diverse SC2r-CoVs from Japan and China to Thailand over a 4800-km range. Cross-border surveillance is urgently needed to find the immediate progenitor virus of SARS-CoV-2.

Zhou, P., Yang, X.-L., Wang, X.-G., Hu, B., Zhang, L., Zhang, W., Si, H.-R., Zhu, Y., Li, B. and Huang, C.-L. (2020) A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579:270-273. [doi: 10.1038/s41586-020-2012-7]

Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats1,2,3,4. Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans5,6,7. Here we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of SARSr-CoV. In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor—angiotensin converting enzyme II (ACE2)—as SARS-CoV.

Zhou, P. et al. (2020) Addendum: A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 588:E6-E6. [doi: 10.1038/s41586-020-2951-z]

Zhou, H., Ji, J., Chen, X., Bi, Y., Li, J., Hu, T., Song, H., Chen, Y., Cui, M. and Zhang, Y. (2021) Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses. bioRxiv. doi: [doi: 10.1101/2021.03.08.434390]

Although a variety of SARS-CoV-2 related coronaviruses have been identified, the evolutionary origins of this virus remain elusive. We describe a meta-transcriptomic study of 411 samples collected from 23 bat species in a small (~1100 hectare) region in Yunnan province, China, from May 2019 to November 2020. We identified coronavirus contigs in 40 of 100 sequencing libraries, including seven representing SARS-CoV-2-like contigs. From these data we obtained 24 full-length coronavirus genomes, including four novel SARS-CoV-2 related and three SARS-CoV related genomes. Of these viruses, RpYN06 exhibited 94.5% sequence identity to SARS-CoV-2 across the whole genome and was the closest relative of SARS-CoV-2 in the ORF1ab, ORF7a, ORF8, N, and ORF10 genes. The other three SARS-CoV-2 related coronaviruses were nearly identical in sequence and clustered closely with a virus previously identified in pangolins from Guangxi, China, although with a genetically distinct spike gene sequence. We also identified 17 alphacoronavirus genomes, including those closely related to swine acute diarrhea syndrome virus and porcine epidemic diarrhea virus. Ecological modeling predicted the co-existence of up to 23 Rhinolophus bat species in Southeast Asia and southern China, with the largest contiguous hotspots extending from South Lao and Vietnam to southern China. Our study highlights both the remarkable diversity of bat viruses at the local scale and that relatives of SARS-CoV-2 and SARS-CoV circulate in wildlife species in a broad geographic region of Southeast Asia and southern China. These data will help guide surveillance efforts to determine the origins of SARS-CoV-2 and other pathogenic coronaviruses.


PN said...


steve g said...

That's a bit exhausting to plow through. It is a much more complicated subject than any of the news reports indicate. There does not seem to be any reason to suspect the WHO team or any of the scientists who have been doing this research. I hope they can one day pin it down and lay the subject to rest.

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Faizal Ali said...

How does that info contradict the position that the workers tested negative for SARS-CoV-2?

Faizal Ali said...

I'm still not following the argument that is being made here by proponents of the Lab Leak Conspiracy Theory.

The WIV was investigating a number of viruses between 2012-2015 related to an outbreak of respiratory illnesses among miners. It was suspected that these illnesses could have been viral, hence the research.

None of the viruses investigated are SARS-CoV-2 nor are particularly closely related to it. It is also not practically possible that the SARS-CoV-2 could be derived from any of these viruses.

So how does this support in any way the claim that SARS-CoV-2 was stored in the WIV lab? Could you explain?

Faizal Ali said...

Again, I'm having difficulty following your argument here. Assuming the story you are telling here about the disappearing database is true, you say this happened BEFORE the pandemic. Why hide evidence of the viruses the were investigating before it was known one of those viruses was going to cause a global pandemic?

You mockingly suggest that the hackers would have to have had psychic powers. But it seems you have no difficulty ascribing such powers to WIV scientists.

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Faizal Ali said...

I will repeat my question: How does that contradict the position that the workers tested negative for SARS-CoV-2?

Have you any intention of answering it?

Mikkel Rumraket Rasmussen said...

SARS antibodies is somewhat ambigous. SARS is a symptom of a disease (severe acute respiratory syndrome).

I'm going to need some more clarification on what exactly "SARS-virus IgG antibodies" is and what this indicates. What does the test for this consist of?

Faizal Ali said...

So your claim is that:

1) Even though the first cases of COVID-19 were reported on Dec 31, 2019, it was already spreading in September 2019.

2) Officials of WIV were aware that a virus from their lab was causing an illness that would become a global pandemic in four months, so they deleted the database that listed this virus, then lied about this.

What evidence do you have for any of this? Why is this a more plausible explanation than the one WIV has given: That they took down the database because of hacking attempts?

Are you aware that WHO investigator Peter Daskak has said "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." Or do you think he is in on the conspiracy as well?

Faizal Ali said...

I'm not arguing that SARS-CoV-2 is derived from any of the viruses from the mine. However, Ratg13 is the closest virus to SARS-COV-2, which is very important.

If you are not arguing that SARS-CoV-2 was derived from any of the viruses in that mine, then I fail to see why you think the closeness of RATG-13 is "very important." Could you clarify?

Faizal Ali said...

If I understand correctly, this claim about "SARS antibodies" is based on some English speaking "internet sleuth" using Google Translate to read a thesis written in a Chinese language. Someone can correct me if I am wrong about that.

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Faizal Ali said...

Please present your evidence that WIV workers knew in September 2019 that there was a new virus circulating that had potential to cause a global pandemic, and that this virus was included in their database.

If all you have is that they deleted the database, you surely must admit this does not come even close to justifying your claims.

And perhaps you could also justify your accusation that Peter Daszak is lying.

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Mikkel Rumraket Rasmussen said...

"Considering that they lied about the deaths being caused by a virus"

This phrasing suggests we now know what caused the deaths. We'd have to know that, and know that they knew, to be able to claim that they lied. So, were the deaths caused by a virus and how do we know this?

"The issue is that they lied about the deaths being attributed to a SARS-like virus and they stated that the serum tested negative for SARS-CoV-2 without disclosing that it tested positive for other SARS antibodies."

I think you're playing a little fast and loose with the terms here. Were the deaths actually attributed to a virus, or were they merely initially suspected of being caused by a virus? Big difference.
Also, what's a "SARS-like" virus? SARS is a sort of symptom.

You say the serum tested negative for SARS-Cov2, which is an actual virus, so I assume this is a PCR test that is negative(as in, someone was looking for virus DNA/RNA).

Then you state they tested positive for "other SARS antibodies" - but an antibody test is not a PCR test, so what is meant by "other" SARS antibodies?

This is why I asked for clarification earlier. What actual tests were done?
What were the deaths actually attributed to? Is there some report that states "most likely cause of death" or something to that effect? Were viruses merely suspected initially?

Barbara said...

Dr. Moran, Thank you for this analysis of the Newsweek article! I appreciate your laying out this information clearly.

Faizal Ali said...

I guess you didn't actually read the study you cited. Here is what the authors say themselves:

The thesis was found on the website which is the official website for Master's and Ph.D. thesis in China and therefore considered to be a valid source. The original thesis is in Chinese (7) and we translated it using google translation.

I was unable to find the passage describing the "SARS antibodies" result in what is supposed to be the professional translation. Can you show us where it is?

Faizal Ali said...

I also think you are wrong in saying a "SARS virus" is by definition closely related to the SARS-CoV-2 just by virtue of having "SARS" in its name. So perhaps you could verify your assumption is true?

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Faizal Ali said...

OK, my mistake. However, I do not see how one can access a translation of the PhD thesis, unless I am missing something. I also do not understand the significance of 4 of the the 6 patients developing antibodies. What of the other two? Were they not tested? Or did they test negative? If the latter, then that throws serious doubt on a "SARS virus" being the cause of death.

In any event, I still am not seeing how any of this relates to COVID-19. This seems to be what you are claiming:

In 2012, there was an outbreak of serious respiratory illness resembling SARS among a group of miners, half of whom died.

These miners had been working in a cave and had been exposed to bat feces. WIV was investigating the origins of SARS and suspected it might have originated in bats, therefore they were very interested in investigating this outbreak for obvious reasons.

Then, according to your story, they did in fact identify a new coronavirus that was responsible for the deaths, exactly the sort of thing their research has been trying to uncover.

So what do they do next? Well, the obvious thing would be to publish their findings and announce to the world a potential new viral pathogen that presents a risk to the human population.


Why would anyone do this?

And, the big question, what does any of this have to do with the outbreak of a completely different virus 9 years later that causes a global pandemic?

Your story, even if it was true (and there remains no good evidence that it is) does not make any sense on the face of it. Sorry.

Faizal Ali said...

RATG-13 is NOT closely related, however. It's most recent common ancestor with SARS-CoV-2 most likely existed 50 years ago, and at least 20 years ago. So it is irrelevant.

dean said...

Reading through this is seems that skeletor's intent is not to determine facts here, but merely to smear the reputation of scientists from WHO and China. No real facts from the poster, lots of unsubstantiated assertions.

Faizal Ali said...

I don't think that's his intent. It's just that this sort of sloppy thinking is sadly common. Just find a bunch of stuff that seems suspicious on a superficial reading, and then just assume it all points to something more nefarious lying deeper down. But if you ask such people to such people to actually arrange the pieces of "evidence" into a coherent whole, they can't do it.

Larry Moran said...

I agree with dean. It looks like Skeletor just hates China and that’s why he wants to pin the pandemic on China. Note that his comments concentrate on showing that the Chinese Communist Part (CCP) can’t be trusted and therefore the scientists at WIV must be lying. Facts don’t seem to matter to him because every inconvenient “fact” is just more proof of lying and coverup. It’s classic conspiracy theory thinking.

Faizal Ali said...

I do not deny your good faith. But you have not provided meaningful answers to many of my questions.

What evidence is there that SARS-CoV-2 was ever stored at WIV? Your best "evidence" seems to be that WIV was investigating an outbreak of respiratory illnesses of possible viral origin back in 2012, and concluded they could not demonstrate it was viral. For no apparent reason you think they are lying about this and, for reasons that are also not apparent, you think this somehow means they had samples of SARS-CoV-2 that they hid.

Your argument is bereft of logic and evidence.

Faizal Ali said...

You continue to make false accusations, and incoherent attempts at argument.

They did not lie about deleting the database.

If you are not claiming that they knew SARS-CoV-2 was in the database, then exactly what do you find "suspicious" about its deletion, 3 months before the first cases of COVID-19 were identified? Please spell out your case to me as if I was a rather stupid young child, because I honestly cannot see any logical sequence of events in your scenario.

And your claim that there has been a "multitude of lies, coverups, and non-cooperation" is simply false. No one who has investigated WIV has reported anything other than full cooperation and openness. That will never satisfy people who are hell bent on proving their pet conspiracy theory, however, will it?

Faizal Ali said...

The author of the thesis thought a viral infection was most likely, but did not provide any conclusive evidence for this. This was early in the investigation of the case cluster. The final conclusion was that a viral cause of death could not be demonstrated.

Larry has already explained this in the main article, so I don't know why have I have to repeat this.

Once more I ask: What evidence is there that SARS-CoV-2 was ever stored at WIV? Even if they were wrong about the cause of death of those miners in 2012, what does that have to do with this question? Can you at least try to present a coherent scenario, as opposed to a litany of unrelated and false accusations?

Mikkel Rumraket Rasmussen said...

Hmm all of Skeletor's posts now just say "This comment has been removed by the author."

Did he have a change of heart and remove his posts or what?

Faizal Ali said...

Skeletor's comments have all disappeared. Did he delete them?

Larry Moran said...

He deleted them.

Mark Sturtevant said...

Well, that was a bit of drama!