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Thread: The Potential Lab Origin of COVID-19

  1. #41

    Default Re: The Potential Lab Origin of COVID-19

    Quote Originally Posted by Exarch View Post
    The European strains are older than the strains found in Wuhan.
    No, they aren't. They're phylogenetically downstream from the Chinese strains, and anyway, the earliest known patient in China was exposed sometime in November since his symptoms started December 1st. Which if my math is correct, appears to be before December 18th.
    Quote Originally Posted by Enros View Post
    You don't seem to be familiar with how the burden of proof works in when discussing social justice. It's not like science where it lies on the one making the claim. If someone claims to be oppressed, they don't have to prove it.


  2. #42
    Ludicus's Avatar Comes Limitis
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    Default Re: The Potential Lab Origin of COVID-19

    *Sighs*

    As I said before, June 12. Recombination, recombination, high rates of genetic recombination.

    Bat-borne virus diversity, spillover and emergence | Nature ...

    The genetic diversity of many RNA viruses can be attributed to high mutation rates, short generation times and the strong selective pressure of the host environment (during natural infections or after vaccinations); however, positive-stranded RNA viruses, including SARS-CoV and MERS-CoV, have relatively low mutation rates associated with 3′–5′ exoribonuclease proofreading activity 104,105,106,107,108.
    The rapid evolution of coronaviruses to the host environment is largely driven by the high rates of genetic recombination, which facilitate the acquisition of multiple mutations in a single event. Inheriting multiple genetic changes at once can have dramatic effects on viral replication and subsequent adaption to new host environments. Recent phylogenetic analyses have revealed that the variation in MERS-CoV circulating in camel populations is largely driven by recombination 109,110,111,112.
    The entire SARS-CoV genome has now been sequenced across multiple separate but related viruses circulating in bats, strongly suggesting that the human virus is a recombinant form of these ancestral variants 114.
    Outside coronaviruses, recombination in the rabies virus glycoprotein was shown to facilitate cross-species transmission from bats to skunks and raccoons 115. Thus, in addition to the rapid mutation rate characteristic of many RNA viruses, recombination provides an additional mechanism to rapidly overcome barriers in novel host species.
    And again...SARS-CoV-2 carries a history of cross-species recombination, Emergence of SARS-CoV-2 through recombination and strong ...

    ...Thus, it is plausible that RaTG13-like bat-CoV viruses may have obtained the RBM sequence binding to human ACE2 through recombination with Pan_SL-CoV_GD-like viruses. We hypothesize that this, and/or other ancestral recombination events between viruses infecting bats and pangolins, may have played a key role in the evolution of the strain that lead to the introduction of SARS-CoV-2 into humans
    While the SARS and MERS originating strains have been found in civets and dromedary camels respectively (14, 15), so far, efforts to identify a similarly close link in the original pathway of SARS-CoV-2 into humans have failed. If the new SARS-CoV-2 strain did not cause widespread infections in its natural or intermediate hosts, such a strain may never be identified. The close proximity of animals of different species in a wet market setting may increase the potential for cross-species spillover infections, by enabling recombination between more distant coronaviruses and the emergence of recombinants with novel phenotypes. While the direct reservoir of SARS-CoV-2 is still being sought, one thing is clear: reducing or eliminating direct human contact with wild animals is critical to preventing new coronavirus zoonosis in the future.
    Along the findings published here, Dating the emergence of human pathogens | Science Simon Ho and Sebastián Duchêne from the University of Sydney and University of Melbourne have published a complementary Perspective, proposing that similarly refining research about when COVID-19 and other zoonotic diseases emerged will assist in understanding how such pathogens jump from animals to humans. As they say, "although the human COVID-19 SARS-CoV-2 virus split from its closest known relative - another coronavirus from a horseshoe bat, about 30 to 40 years ago, the jump to humans most likely happened more recently".

    And that's it. Everything else is wishful thinking coupled with right wing speculative BS.
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  3. #43
    Aexodus's Avatar Persuasion>Coercion
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    Default Re: The Potential Lab Origin of COVID-19

    Now that politics have been raised, what are the right wing implications of suggesting a virus escaped from a lab.
    Patronised by Pontifex Maximus
    Quote Originally Posted by Himster View Post
    The trick is to never be honest. That's what this social phenomenon is engineering: publicly conform, or else.

  4. #44
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    Default Re: The Potential Lab Origin of COVID-19

    Quote Originally Posted by sumskilz View Post
    No, they aren't. They're phylogenetically downstream from the Chinese strains, .
    Are you talking about the recent strain in Beijing or the strains discovered in Italy?

    and anyway, the earliest known patient in China was exposed sometime in November since his symptoms started December 1st. Which if my math is correct, appears to be before December 18th
    Yeah, gonna have to dig a little deeper, the earliest european cases were French and discovered to have had the virus back in November 2019

    The first case of coronavirus in France dates back to December 2. The head of the medical imaging department of the Albert-Schweitzer hospital in Colmar (Haut-Rhin) told franceinfo, Thursday, May 7, that a man hospitalized on that date for a "respiratory infection" was found to have Covid-19, through subsequent reviews. So far, a resident of Seine-Saint-Denis, who fell ill at the end of December, was considered the first person affected by Covid-19 in France.The medical imaging department headed by Michel Schmitt "took over all the scanners" of the last six months, made "for trauma, tumors, heart and infectious pathologies", in order to check if they did not contain the "typical anomalies" of the Covid-19. The disease in fact causes "several lesions in both lungs", with an "appearance of lesions and disseminations that do not correspond to another pathology", he specifies to franceinfo.
    Fifteen suspected cases between November and December
    This new study of scanners has identified two cases of suspected coronavirus, on November 16 and 17. "We have one case on November 29, three cases on December 2, one case on December 10, one case on December 13, one case on December 27, two cases on January 3 and after, it gradually increases ...", details Michel Schmitt.
    One of the suspected cases of December 2 was later confirmed by a test for Covid-19 and is now "certain all data combined". The 57-year-old man, hospitalized "about a week", is now in good health. To date, it is unknown how he contracted the virus.
    For the two suspected cases in November, the scanners have yet to be confirmed by other elements. "You have to contact the patients, see what has become of them, know their history and, if history justifies it, do a blood test and an antibody test," explains Michel Schmitt. In total, the study of scanners started "ten days ago" revealed "338 typical Covid-19 scanners between November 1 and April 30, 2020". The hospital is currently "cross-referencing" these data with screening tests, in order to confirm the suspected cases.
    Source: https://www.francetvinfo.fr/sante/ma...e_3952985.html

    QAnon is fun but like "9/11 was an inside job" back in the 2000s, conspiracy theories lack basis in scientific objectivity let alone scientific rigour.

  5. #45

    Default Re: The Potential Lab Origin of COVID-19

    Quote Originally Posted by Ludicus View Post
    *Sighs*

    As I said before, June 12. Recombination, recombination, high rates of genetic recombination.
    You didn't actually answer the question Aexodus asked, nor did you add anything new to the discussion. You just reposted the same speculation that has been circulating in the scientific literature. Speculation which if correct, wouldn't fully account for all the mysterious aspects of of SARS-CoV-2's emergence. Neither SARS-CoV nor MERS-CoV emerged fully adapted to infecting humans far away from their hosts and/or intermediate hosts, yet right next to one of the few labs in the world that holds samples of such viruses.

    Let's recall exactly who it was who first had this thought:

    Shi, a virologist who is often called China’s “bat woman” by her colleagues because of her virus-hunting expeditions in bat caves over the past 16 years, walked out of the conference she was attending in Shanghai and hopped on the next train back to Wuhan. “I wondered if [the municipal health authority] got it wrong,” she says. “I had never expected this kind of thing to happen in Wuhan, in central China.” Her studies had shown that the southern, subtropical provinces of Guangdong, Guangxi and Yunnan have the greatest risk of coronaviruses jumping to humans from animals—particularly bats, a known reservoir. If coronaviruses were the culprit, she remembers thinking, “Could they have come from our lab?”
    Shi no longer speaks this way. In January of 2020, the Wuhan lab published the RNA BatCoV RaTG13, without mentioning that they had previously published part of the sequence before under a different name (BtCoV/4991), at odds with standard scientific practice. It took various internet "conspiracy theorists" to uncover this fact. The two are now listed as the same in some databases (for example) including some Chinese databases. Allegedly the two are the same, the partial previously published sequence is identical but it's not a full sequence, and the Wuhan lab supposedly is no longer in possession of the actual virus. Which is probably true because they were forced by the Chinese government to destroy their samples, as noted in the previously referenced NPR report. What's confusing is that the Wuhan lab (supposedly) only bothered to sequence the entire strain in January of 2020, which is confusing because it was found in a 2013 investigation of a mineshaft where six miners became ill with SARS-like pneumonia, two of them died. So you would think the researchers at the Wuhan lab would have found this virus interesting enough to really look into seven years ago when this all happened, rather than waiting until January of 2020. After all, finding CoVs with the potential to infect humans was their primary mission.

    Quote Originally Posted by Ludicus View Post
    And that's it. Everything else is wishful thinking coupled with right wing speculative BS.
    You are arguing that the Bulletin of Atomic Scientists and Independent Science News are right wing (not to mention the authors of all the studies I quoted)? Both are scientist run public advocacy publications aimed at general audiences. I suspect their readership and supporters are largely left wing.

    Quote Originally Posted by Aexodus View Post
    Now that politics have been raised, what are the right wing implications of suggesting a virus escaped from a lab.
    I suppose he's referring to that which is ranted about in the preamble of the notoriously "right wing" Bulletin of Atomic Scientists' article I linked:

    On May 15, the Bulletin of the Atomic Scientists published a short commentary titled, “Let evidence, not talk radio, determine whether the outbreak started in a lab,” by Ali Nouri, a biologist and president of the Federation of American Scientists. “The outbreak” referred to the pandemic of SARS-CoV-2 now circling the globe. It is a thin commentary, and it is puzzling why the Bulletin thought it desirable to publish it at all. Only two weeks earlier the journal had published a reasoned and competent appraisal by Kings College London biosecurity expert Filippa Lentzos titled, “Natural spillover or research lab leak? Why a credible investigation is needed to determine the origin of the coronavirus pandemic.”

    The Nouri article very correctly pilloried the statements by President Donald Trump, Secretary of State Mike Pompeo, presidential legal advisor Rudy Giuliani, and radio personality Rush Limbaugh. These are as notorious a gang of four fabricators as will ever likely be recorded in American history. They were ably assisted by Fox News, which the Nouri critique also mentions. Nouri ended his commentary with these lines: “Our leaders ought to … take steps to prevent the next pandemic, instead of diverting our attention to unsupported sensationalist theories spread by cable TV and talk radio.”

    Perhaps the most damaging blows to efforts to obtain a certain answer as to the origin of the SARS-CoV-2 “outbreak” have been the pronouncements by Trump, Pompeo, and their echo chambers. But they and their remarks are not the measure by which the question of the possibility that a laboratory escape began the pandemic should be examined. Trump’s diversionary ranting comes from a president who did nothing for two months in the face of an oncoming lethal pandemic, actively denied and denigrated intelligence warnings of the imminent danger, and said that SARS-CoV-2 would “just go away … like a miracle” and that “within a couple of days is going to be down close to zero.” All this has been widely and thoroughly chronicled.1

    But long before Trump, Pompeo and Co. sought a Chinese scapegoat for the president’s gross and willful incompetence, researchers understood that the possibility of laboratory escape of the pathogen was a plausible, if unproven, possibility. It is most definitely not “a conspiracy theory.”
    Take a look at this behavior:

    Spoiler Alert, click show to read: 
    Chan was right, Andersen was wrong, presumably that's why he stopped talking when he did. The two Pangolin papers were not independent. Which should have been obvious to Andersen since the same author is on both, and they studied the exact same captive pangolins which had been smuggled in from outside China. It seems like Andersen is spending a lot of his time trying to discourage other scientists who are looking into it. If your primary concern is scientific truth, I would think the more investigation from multiple angles the better. There is literally zero solid evidence either way, yet he claims the mystery is solved.

    Quote Originally Posted by Exarch View Post
    Are you talking about the recent strain in Beijing or the strains discovered in Italy?
    No strains have been discovered in Italy that are upstream from the earliest ones sampled in Wuhan, at least nothing has been published that makes such a claim. I would think it would be big news if the RNA pulled from the Italian water system was from an earlier strain.

    Quote Originally Posted by Exarch View Post
    Yeah, gonna have to dig a little deeper, the earliest european cases were French and discovered to have had the virus back in November 2019
    As I said before, two lung scan compatible with having been COVID-19 aren't enough evidence on their own to draw any conclusions. It's possible that they were, but the RNA from China is still upstream from any that has been found in Europe.
    Quote Originally Posted by Enros View Post
    You don't seem to be familiar with how the burden of proof works in when discussing social justice. It's not like science where it lies on the one making the claim. If someone claims to be oppressed, they don't have to prove it.


  6. #46
    Ludicus's Avatar Comes Limitis
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    Default Re: The Potential Lab Origin of COVID-19

    Quote Originally Posted by sumskilz View Post
    One of the reasons SARS-CoV-2 took the world by storm was that when it first appeared in humans it was already highly adapted to infecting our species, one could say almost fine-tuned by the fact that it appears not to have become anymore efficient thus far, despite the massive number of transmissions. That's the big mystery...all the mysterious aspects of of SARS-CoV-2's emergence... If your primary concern is scientific truth, I would think the more investigation from multiple angles the better.
    According to the broader scientific community, there is no big mystery, and there is no evidence for lab release theory. The time SARS-CoV-2 was first detected in late 2019, it was already pre-adapted to human transmission to an extent similar to late epidemic SARS-CoV. The MERS-CoV has jumped multiple times from camels to humans, with the correct RBD, but efficient human to human transmission was not established until the acquisition of the furin cleavage site.
    SARS-CoV and SARS-CoV-2 ( SARS-CoV-2 intermediate host remains unknown) are closely related and originated in bats. During the 2002–2004 SARS outbreak, over 8,000 people from 29 different countries and territories were infected, and at least 774 died worldwide.
    In fact,I quote, "SARS-CoV-2 resembles SARS-CoV in the late phase of the 2003 epidemic after SARS-CoV had developed several advantageous adaptations for human transmission"- as the bat-women Alina Chan put it, in the paper, "SARS-CoV-2 is well adapted for humans. What does this mean for re-emergence?" (not peer-reviewed, I think). Which simply means that there may be lingering populations of progenitor SARS-CoV-2 adept for human transmission and disease, why is she surprised...

    Once again, for the third time-reared the posts 31 and 33- in addition to the furin cleavage site, an extra-proline is also present, and we know that the addition of such glycans typically occurs under immune selection. Unless this can his can be easily done in a lab,it is just not possible for CoV-2's O-linked glycan to have developed under a typical cell-culture setting. The evolutionary pressure is essential for the selection process. Developing the glycan shield requires evolutionary pressure from an intact immune system, which cultures cell lack.

    Excluding Trump/Pompeo's enormous evidence, no-one has any evidence that the outbreak came from a Chinese lab. It occurred to me that Gavin Menzies has no smoking gun that proves his theory, because the xenophobic Confucian officials destroyed all records of Zheng He voyages.

    So, I'm starting to think that China discovered America before Columbus.
    Last edited by Ludicus; June 20, 2020 at 11:24 AM.
    Il y a quelque chose de pire que d'avoir une âme perverse. C’est d'avoir une âme habituée
    Charles Péguy

    Every human society must justify its inequalities: reasons must be found because, without them, the whole political and social edifice is in danger of collapsing”.
    Thomas Piketty

  7. #47

    Default Re: The Potential Lab Origin of COVID-19

    Quote Originally Posted by Ludicus View Post
    According to the broader scientific community, there is no big mystery, and there is no evidence for lab release theory.
    No, according to a small number of virologists who have conflicts of interests, and everyone who hasn't bothered to look carefully at their arguments. I've quoted plenty of scientists skeptical of their arguments, as well as those who doubt lab origin, but nevertheless recognize it to be a possibility. In the latter case, you can't get more mainstream than Nature.

    Quote Originally Posted by Ludicus View Post
    Once again, for the third time-reared the posts 31 and 33- in addition to the furin cleavage site, an extra-proline is also present, and we know that the addition of such glycans typically occurs under immune selection. Unless this can his can be easily done in a lab,it is just not possible for CoV-2's O-linked glycan to have developed under a typical cell-culture setting. The evolutionary pressure is essential for the selection process. Developing the glycan shield requires evolutionary pressure from an intact immune system, which cultures cell lack.
    There isn't a lack of evolutionary pressure during passaging, creating evolutionary pressure is the entire point of the experiment. In any case, I've already responded to what you're referring to, and added this:

    Andersen and colleagues49 also state that “The acquisition of both the polybasic cleavage site and predicted O-linked glycans also argues against culture-based scenarios”. Methods for insertion of apolybasic cleavage site in infectious bronchitis CoV are given in Cheng and colleagues54 and resulted in increased pathogenicity. Concerning the predicted O-linked glycans around the newly inserted polybasic site, it should be noted that this prediction was not confirmed by Cryo-EM inquiry into the SARS-CoV-2 spike glycoprotein.55 Nevertheless, while it is true that O-linked glycans are much more likely to arise under immune selection, they could be added in the lab through site-directed mutagenesis56 or arise in the course of in vivo experiments, for example, in BLT-L mice that have human lung implants and autologous human immune system57 or in mice expressing human ACE2 receptor.58 To overcome problems of bat CoV isolation, experiments based on direct inoculation of bat CoV in suckling rats have been carried out.59 Pangolins or other animals with similar ACE2 conformation could have been used as experimental animals as well.
    Andersen et al predicted that there would be O-linked glycans around the furin cleavage site, and then claimed their own unverified predication as evidence. Well, their prediction was wrong. There aren't O-linked glycans around the furin cleavage site, not that it would matter anyway for the reasons quoted above.

    Could be the fact that his interlocutor has proven to be more knowledgeable on the topic than he is, but it seems Andersen has become less skeptical than you Ludicus (for the moment anyway):

    Spoiler Alert, click show to read: 
    He has stopped talking out his ass at least, admitting (in so many words) that he doesn't really know enough to be as certain as he was presenting himself to be.

    From another recent general audience article:

    Last year, Yuan Zhiming published an article in the Journal of Biosafety and Biosecurity confessing to concerns about high security laboratories in China. He admitted maintenance costs were “generally neglected” and several of their top-level research centres lacked sufficient funds for “routine yet vital processes”. He said openly that “part-time researchers” performed the work of skilled staff, which “makes it difficult to identify and mitigate potential safety hazards”.

    In a second article co-authored with four colleagues, he wrote that their biosafety systems needed to be “further improved and strengthened”.

    Today, his words carry greater significance. For Professor Yuan is head of biosafety at Wuhan Institute of Virology (WiV), the first lab in China with top-level biosecurity status. It carries out cutting-edge research into bat viruses and has been named by the US President as the possible source of the coronavirus behind the global pandemic. But Yuan now denies there is any chance this disease could have leaked from his laboratory, insisting they followed strict safety procedures to protect staff and the environment from contamination. “There is no way this virus came from us,” he told state media — and like other Chinese officials, even hinted it might have emerged in the United States rather than his city.

    Given the stakes, it is not surprising Prof Yuan has suddenly become so convinced about his laboratory’s security...

    Donald Trump’s public condemnation of the Wuhan lab, saying he had seen “strong evidence” to back his case, only makes these matters more complex. His allegations, lacking any data, served to inflame a contentious and toxic issue. Some prominent scientists and journalists have been quick to dismiss the idea as a conspiracy theory. “We do not believe that any type of laboratory-based scenario is plausible,” concluded one influential paper in Nature Medicine (although it failed to mention one author is a guest professor at a body running one of the suspect units while another has just been honoured by Beijing for his work in China).

    Another tireless figure insisting “scientists know Covid-19 wasn’t created in a lab” is former Kingston University parasitologist Peter Daszak, $402,000-a-year head of a charity that investigates spillovers of disease from animals. Daszak is understandably furious after his 15-year collaboration on bat diseases with Wuhan was disrupted by the National Institutes of Health’s decision to stop funding their research due to biosecurity concerns. This was widely seen as typical Trump, lashing out at his enemies. Yet the health body’s director is Francis Collins, a well-respected geneticist appointed by Barack Obama. “Whether [the coronavirus] could have been in some way isolated and studied in this laboratory in Wuhan, we have no way of knowing,” he said later.

    He is right. For scientists, like journalists, should deal in facts — and at this stage we have no clear idea about the origins of this nasty disease. It may be a natural zoonotic virus, crossing over from animals like several previous epidemics including Ebola and the Sars outbreak at the start of this century. Few experts would be surprised if this turned out to be the case, although any intermediate host species has yet to be found. Meanwhile there are some wild conspiracy theories swirling around about bio-weapons and deliberate release by the Communist regime. Yet anyone who denies with certainty that Sars-Cov-2 — the new strain of coronavirus — might have leaked accidentally from one of Wuhan’s high-security laboratories is talking tosh...

    Last month, I revealed in the Mail on Sunday the results of an important study by two scientists at the Broad Institute, a top genetic research unit set up by Harvard University and Massachusetts Institute of Technology, with a colleague from the University of British Columbia. It disproved the market source idea based on available genetic data. But the scientists also expressed surprise that Sars-Cov-2 was “already pre-adapted to human transmission”, contrasting its genetic stability as it rampaged around the planet with the coronavirus that evolved rapidly during the global Sars epidemic between 2002 and 2004.

    Such stability is good news for finding a vaccine. Yet if this coronavirus can be traced back ultimately to bats, as seems near-certain, some scientists are puzzled that it emerged in such well-honed shape to wreak havoc on humans. As Collins has noted, and diseases such as Ebola have proved, nature can be the most lethal bio-terrorist. Yet that fascinating study implied single introduction of a human-adapted form of the virus into the population — and as the authors said, this means all routes for zoonotic transmission must remain in contention unless otherwise proven. “The possibility that a non-genetically engineered precursor could have adapted to humans while being studied in a laboratory should be considered,” they concluded.

    Then came another significant pre-print paper by an Australian team of vaccine researchers, which found the virus was “not typical of a normal zoonotic infection” since it was “uniquely adapted to infect humans”. Nikolai Petrovsky, the professor of medicine at Flinders University who led the study, echoed Gao when telling me he had never seen a zoonotic virus behave in such a way. He dared point in public to something being muttered privately by some other scientists: the coincidence of the most closely-related known viruses to Sars-Cov-2 being studied in Wuhan in conjunction with collaborating US laboratories. “There is currently no evidence of a leak but enough circumstantial data to concern us,” he said. “It remains a possibility until it is ruled out.”...

    Shi’s lab was not the only one in Wuhan working on bat-borne diseases. There was another one with lower level biosecurity run by the CDC just 500 yards from the animal market. A paper posted by two Chinese scientists in February on a site for sharing research — then pulled two days later — claimed that 605 bats were kept at this laboratory, describing how the creatures had attacked, bled and urinated on a researcher. “It is plausible that the virus leaked,” the mysterious study concluded...

    We also know that WiV — the biggest repository of bat coronaviruses in Asia — had been carrying out ‘gain-of-function’ experiments on bat coronaviruses since 2015. It had been playing around with the Sars virus, inserting snippets from other bat diseases and constructing new chimeric coronaviruses. Barack Obama’s administration stopped funding such work in 2013 on grounds it was too dangerous, although ironically this ban was lifted under Trump after scientists argued that it aids understanding of how pandemic viruses evolve. But critics such as Richard Ebright, a biosafety expert and professor of chemical biology at Rutgers University, insist that the only impact of such work is creation of “a new, non-natural risk”. He points out WiV was creating chimeric coronaviruses using “seamless, unidirectional ligation” procedures that leave no signatures of human manipulation in the resulting genome sequences.

    Ebright is an outlier on these issues. Another microbiologist who works with viruses in high-security labs told me she could never “design a virus that is this diabolical”. But others have expressed alarm over China’s rush to develop a network of high-security research centres to win primacy in biosciences. The BSL-4 level laboratory in Wuhan, for instance, was built with French help against advice of its intelligence services, while the Washington Post found that, two years ago, US experts warned the State Department of safety concerns after visiting the site. Now other leading figures insist we should not discount the idea of an accident. “It’s important to be upfront that we do not have sufficient evidence to exclude entirely the possibility that it escaped from a research lab doing gain of function experiments,” tweeted Carl Bergstrom, professor of biology at Washington University.

    Clearly we must be cautious when there is so much at stake — unlike former spy chief Sir Richard Dearlove when he blamed a lab leak based on a weak new Norwegian-British study. But, equally, we cannot simply dismiss the idea as conspiracy theory. Not least when the Chinese government engaged in a cover-up over the initial outbreak of the disease, even silencing doctors trying to warn people in Wuhan — and then moved fast to tighten laboratory safety, especially for handling of viruses, in February...

    There is no firm evidence of an accident or leak beyond a set of strange biological quirks and suspicious coincidences. But nor does the alternative hypothesis — that this is a freak event of nature and humans were the perfect host for a new zoonotic virus — have indisputable supporting evidence at this stage. No one has discovered an intermediate host, nor offered credible explanation of how a coronavirus moved from some bats in dank Yunnan caves to infect people hundreds of miles away in the bustling city of Wuhan.
    Last edited by sumskilz; June 20, 2020 at 03:18 PM.
    Quote Originally Posted by Enros View Post
    You don't seem to be familiar with how the burden of proof works in when discussing social justice. It's not like science where it lies on the one making the claim. If someone claims to be oppressed, they don't have to prove it.


  8. #48
    Ludicus's Avatar Comes Limitis
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    Default Re: The Potential Lab Origin of COVID-19

    Quote Originally Posted by sumskilz View Post
    No, according to a small number of virologists who have conflicts of interests, ... you can't get more mainstream than Nature.
    OK. So, where should I look? A regular update from the Nature Index. COVID-19 research update: Where are the gaps in coronavirus research.
    Nothing here.
    Here? 5 June The biggest mystery: what it will take to trace the coronavirus Nature
    Since the pandemic began, the question of where the coronavirus came from has been one of the biggest puzzles. It almost certainly originated in bats, and a new study out this week — the most comprehensive analysis of coronaviruses in China — adds further weight to that theory.
    But the lack of clarity around how the virus passed to people has meant that unsubstantiated theories — promoted by US President Donald Trump — that it escaped from a laboratory in China persist.
    By contrast, most researchers (1) say the more likely explanation, given what is known so far about this virus and others like it, is that bats passed it to an intermediate animal, which then spread it to people.
    (1) "according to a small number of virologists who have conflicts of interests", did you say?

    Let's go straight to your last, long quote, the general audience article:
    Last year, Yuan Zhiming... today, his words carry greater significance. For Professor Yuan is head of biosafety at Wuhan Institute of Virology (WiV)
    OK, let's hear Yuan Zhiming, remember, "today his words carry greater significance"



    Well? what do you have to say?

    Quote Originally Posted by sumskilz View Post
    I've already responded ..and added this.. .
    As I said before, I've already read Rosanna's paper, and she recognizes," it is true that O-linked glycans are much more likely to arise under immune selection"

    Quote Originally Posted by sumskilz View Post
    Well, their prediction was wrong. There aren't O-linked glycans around the furin cleavage site,
    Given the defensive function these O-linked glycans perform, does it really matter? SARS-CoV-2 S gene encodes 22 N-linked glycan sequons per protomer, which likely play a role in protein folding and immune evasion. From your link,
    Deducing the N- and O-glycosylation profile of the spike ...
    Even though O-glycosylation has been predicted on the spike protein of SARS-CoV-2, this is the first report of experimental data for both the site of O-glycosylation and identity of the O-glycans attached on the subunit S1.
    Although it is unclear what function these predicted O-linked glycans perform, they have been suggested to create a ‘mucin-like domain’, which could shield SARS-CoV-2 spike protein epitopes or key residues (Bagdonaite 2018).
    Published exactly on the same day, 4 May , Site-specific glycan analysis of the SARS-CoV-2 spike - NCBI
    Although unoccupied glycosylation sites were detected on SARS-CoV-2 S, when quantified they were revealed to form a very minor component of the total peptide pool...This combined mass spectrometric and cryo-EM analysis reveals how the N-linked glycans occlude distinct regions across the surface of the SARS-CoV-2 spike...The site-specific glycosylation analysis reported here suggests that the glycan shield of SARS-CoV-2 S is consistent with other coronaviruses
    ----
    I was being ironic when I said "why is she surprised", but in fact, why is she surprised? Alina correctly said,

    -It is plausible for SARS-CoV-2 spike to have evolved its broad species tropism (ability to bind to the ACE2 receptor across diverse species) naturally in bats or a wide range of intermediate species.
    - Ultimately, these observations suggest that by the time SARS-CoV-2 (COVID-19) was first detected in late 2019, it was already pre-adapted for human transmission
    - to an extent more similar to late epidemic SARS-CoV rather than early-to-mid epidemic SARS-CoV.
    - I think the issue here is finding the precursor and the origin of SARS-CoV-2.

    She correctly added,

    -The response to the first SARS-CoV outbreak deployed the following strategies that were key to detecting SARS-CoV adaptation to humans and cross-species transmission, and could be re-applied in today’s outbreak to swiftly eliminate progenitor pools.
    (i) Sampling animals from markets, farms, and wild populations for SARS-CoV-2-like viruses.
    (ii) Checking human samples banked in early/mid 2019 for SARS2-like viruses or SARS2-reactive antibodies to detect precursors circulating in humans. SARS2 isolates from Wuhan, particularly early isolates, could identify branches originating from a less human-adapted progenitor.
    iii) Evaluating the over- or underrepresentation of food handlers and animal traders among the index cases to determine if SARS-CoV-2 precursors may have been circulating in the animal trading community. Meanwhile, it would be safer to more extensively limit human activity that leads to frequent or prolonged contact with wild animals and their habitats.

    Then she rightly asks,

    -"Did SARS-CoV-2 transmit across species into humans and circulate undetected for months prior to late 2019 while accumulating adaptive mutations?"
    -Or was SARS-CoV-2 already well adapted for humans while in bats or an intermediate species?"

    All she said sounds good, until she have exhausted these plausible explanations, and then she adds, "Even the possibility that a non-genetically-engineered precursor could have adapted to humans while being studied in a laboratory should be considered, regardless of how likely or unlikely", and cites The Washington Post (ref.39) https://www.washingtonpost.com/opini...coronaviruses/
    Really, is that necessary? the Washington Post? may I quote the Guardian? Five Eyes network contradicts theory Covid-19 leaked from lab

    The authors of "Emergence of SARS-CoV-2 through recombination and strong purifying selection" postulate that CoV-2 likely emerged from evolutionary selection and frequent recombination of viral genes from different species, leading to the introduction of CoV-2 in humans.
    ---
    In this study (version posted June 17, 2020), the authors measured how all amino-acid mutations to the SARScoV2 spike RBD affect ACE2 binding and expression in a deep mutational study. Deep mutational scanning of SARS-CoV-2 receptor ... - bioRxiv

    "...our data also indicate that global RBD stability contributes to ACE2-binding affinity... Our discovery of multiple strong affinity-enhancing mutations to the SARS-CoV-2 RBD raises the question of whether positive selection will favor such mutations, since the relationship between receptor affinity and fitness can be complex for viruses that are well-adapted to their hosts (Callaway et al., 2018; Hensley et al., 2009; Lang et al., 2020).Strong affinity-enhancing mutations are accessible via single-nucleotide mutation from SARS-CoV-2 (Figure S8C), but none are observed among circulating viral sequences in GISAID (Figure 8A), and there is no significant trend for actual observed mutations to enhance ACE2 affinity more than randomly drawn samples of all single nucleotide mutations (see permutation tests in Figure S8D).
    Taken together, we see no clear evidence of selection for stronger ACE2 binding, consistent with SARS-CoV-2 already possessing adequate ACE2 affinity at the beginning of the pandemic"
    In fact, phylogenetics estimates consistently point to a host jump around 6 October/11 December - and a rapid global spread.
    ----
    The reason why I mention this article is very simple. In this paper, there is not a single mention suggesting a man-made virus. The author's conclusion, based on evidence, is "Our sequence-phenotype maps can directly inform efforts to engineer vaccines in several ways".

    However, after reading this paper, Alina couldn't resist to quote the underlined lines, trying to insinuate that this is one more circumstantial evidence that the CoV-2 came from a Chinese lab. One guess "supported" by another guess does not create a fact.
    I'm not calling into question her professional competence, but the scientist-turned-detective (that's what she calls herself) seems suspiciously biased toward a lab origin, overemphasizing these unlikely scenarios.
    Bertrand Russell insisted that the philosophical burden of proof lies upon a person making unfalsifiable (not capable of being proved false) claims.
    Last edited by Ludicus; June 21, 2020 at 02:30 PM.
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  9. #49

    Default Re: The Potential Lab Origin of COVID-19

    Quote Originally Posted by Ludicus View Post
    Given the defensive function these O-linked glycans perform, does it really matter?
    No, it doesn't matter in determining whether or not SARS-CoV-2 was the result of gain-of-function experiments, and if you've read the relevant part of Rossana Segreto's paper which I've quoted several times, you should understand why. Hint: Andersen et al's argument was a strawman, and they were wrong anyway.

    Quote Originally Posted by Ludicus View Post
    So? As you can plainly see, the O-linked glycans Andersen et al predicated at S673, T678 and S686 are not present.

    Linking that other paper makes me think you didn't understand the argument in the first place. No one believes that SARS-CoV-2 was created in a lab from nothing. Everyone recognizes that it has constituent parts each of which has an evolutionary history.

    The fact that Yuan Zhiming now speaks quite differently on Chinese state television post-pandemic than he did prior to the pandemic is pretty much expected. The same is true of Shi Zhengli. I don't see why anyone would consider that as counter evidence to the lab escape hypothesis.

    Beyond that, I don't want to have to keep addressing the same issues I've already thoroughly addressed.
    Quote Originally Posted by Enros View Post
    You don't seem to be familiar with how the burden of proof works in when discussing social justice. It's not like science where it lies on the one making the claim. If someone claims to be oppressed, they don't have to prove it.


  10. #50
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    Quote Originally Posted by sumskilz View Post
    Linking that other paper makes me think you didn't understand the argument in the first place.
    Don't be arrogant. Not at all.The second paper, complementary with the first one, simply called my attention.It is quite interesting because it shows how the CoV-2 lacks a dense glycan shield, despite extensive glycosylation, showing vulnerabilities the glycan shield,as well as it happens in the extensive N-linked glycan modifications of SARS and MERS CoV S proteins that do not constitute an effective shield,also.

    Quote Originally Posted by sumskilz View Post
    The fact that Yuan Zhiming now speaks quite differently on Chinese state television post-pandemic than he did prior to the pandemic is pretty much expected
    You can simply pick which one suits you best "yesterday, his words carry greater significance".Today "he is a liar".

    Quote Originally Posted by sumskilz View Post
    There aren't O-linked glycans around the furin cleavage site... and then claimed their own unverified predication as evidence....Andersen et al's argument was a strawman..."
    Stop calumniating Anderson, sumskilz...

    Anderson, "the ignorant", prudently wrote, The proximal origin of SARS-CoV-2 | Nature Medicine - 17 March
    "Several viruses utilize mucin-like domains as glycan shields involved immune evasion. Although prediction of O-linked glycosylation is robust, experimental studies are needed to determine if these sites are used in SARS-CoV-2"
    Anderson, the "ignorant", is cited more than once in the paper "Deducing the N-and-O- glycolization profile of the spike protein of novel coronavirus SARS-CoV-2", published May 4. (previous post)

    "O-glycans, which are involved in protein stability and function, have been observed on some viral proteins and have been suggested to play roles in the biological activity of viral proteins (Bagdonaite 2018; Andersen et al. 2020)."

    "Remarkably, we have unambiguously identified two unexpected O-glycosylation sites at the receptor-binding domain (RBD) of subunit S1. O-glycosylation on the spike protein of SARS-CoV-2 is predicted in some recent reports and most of these predictions are for sites in proximity to furin cleavage site (S1/S2) as similar sites are O-glycosylated in SARS-CoV-1 (Andersen et al. 2020; Uslupehlivan 2020). However, we observed O-glycosylation at two sites on the RBD of spike protein subunit S1, and this is the first report on the evidence for such glycan modification at a crucial binding location of the spike protein".

    So in conclusion: Anderson talks too much and knows too little.
    ---
    It's fair to say that without knowing the origin of the virus, there is a likelihood it could strike again. But we already know that the CCP has an intention to cover up "the truth".
    Given the fact that a lab-origin is absolutely impossible to rule out (...or God's existence), rumors and conspiracy theories will never stop, although virus samples in labs are almost never still infectious, after being frozen in nitrogen during the collection process and then inactivated in the lab to preserve their genetic sequence. Let's keep the hope, there is already a League of the "Scientists-Turned-Detectives".

    Like it or not, the first and most widely accepted hypothesis posits that the CoV-2 evolved naturally, jumping from bats to humans, probably via an intermediate species.

    The NATURE revisited - without comments,
    Engineered bat virus stirs debate over risky research : Nature
    Editors’ note, March 2020: We are aware that this story is being used as the basis for unverified theories that the novel coronavirus causing COVID-19 was engineered. There is no evidence that this is true; scientists believe that an animal is the most likely source of the coronavirus
    Anderson has been having a lot of fun. He writes, "I should mention that I had a fun time diving into many of the @reddit threads. It appears we might not have convinced all the theorists out there"




    Dr. Hume Field diagnosing an old problem, "It's puzzling to me, there is a perfectly natural or scientific explanation staring you in the face. But there seems to be a need from some people to say "that's too simple"
    Home -who sold his soul to the CCP-has played a has played a key role in the identification of various species of bats as the natural reservoir of Hendra virus and Australian bat lyssavirus (Australia), Nipah virus (Malaysia and Indonesia), SARS coronavirus (China), and Reston Ebolavirus (Philippines).

    --------
    Conspiracy theorists are having a bad day. This paper was withdrawn: Uncanny similarity of unique inserts in the 2019 ... - bioRxiv

    Btw, remember Montaignier? the man who said the CoV-2 was made in a lab, the man behind the Hydroxychloroquine BS, the man who said CoV-2 has elements of Plasmodium falciparum (malaria), the man who said there was manipulation around this virus - "someone added sequences, in particular of HIV"(sic) ?
    ------
    The purge has begun, Fifty-four scientists have lost their jobs as a result of NIH probe
    For 93% of the 189 scientists whom NIH has investigated to date, China was the source of their undisclosed support... There are 399 scientists “of possible concern” to NIH
    ----
    60 Minutes report critical of Gaetz' role in cutting grant for coronavirus research

    Gantz is the idiot who claimed China's Wuhan Institute had "birthed a monster", and now claims " Members of the Democratic caucus are raising money for an organization that wants to destroy the United States of America" (BLM?)

    Matt Gaetz wears a gas mask on the floor of the House in early March.




    Democrats are infinitely more dangerous than the "yellow peril".
    Last edited by Ludicus; June 22, 2020 at 06:19 PM.
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  11. #51

    Default Re: The Potential Lab Origin of COVID-19

    Quote Originally Posted by Ludicus View Post
    Anderson, "the ignorant", prudently wrote, The proximal origin of SARS-CoV-2 | Nature Medicine - 17 March

    "Several viruses utilize mucin-like domains as glycan shields involved immune evasion. Although prediction of O-linked glycosylation is robust, experimental studies are needed to determine if these sites are used in SARS-CoV-2"
    Correct, and experimental studies have indicated that the O-linked glycans they predicted do not exist.

    Let’s review:

    While not peer-reviewed, Andersen et al is the only serious paper that directly argues against the lab escape hypothesis. According to Andersen et al, the inserted furin cleavage site was unlikely to have arisen during passage in a lab due to the O-linked glycans they predicted, which as it turns out, do not exit.

    However, this was a strawman on their part in the first place.

    Quote Originally Posted by Ludicus View Post
    The NATURE revisited - without comments,
    Engineered bat virus stirs debate over risky research : Nature

    Editors’ note, March 2020: We are aware that this story is being used as the basis for unverified theories that the novel coronavirus causing COVID-19 was engineered. There is no evidence that this is true; scientists believe that an animal is the most likely source of the coronavirus
    Yes, I recommend anyone interested to read that article. Unlike the editor's note, it is uncolored by the polarization of recent events.

    Regarding the editor's note, another term for an "unverified theory" is a "hypothesis". Counter to the editor's silly implication, scientists don't unanimously agree on much of anything, but what the vast majority believe is that the virus is chimeric having passed through multiple species of animals. This is true of those who find the lab escape hypothesis quite plausible and those who find it implausible, and everyone in between, as such, saying so is irrelevant.

    Note that they interviewed Richard Ebright as one of their experts. What do you think his opinion on the origin of COVID-19 might be?



    Moving on...

    Evidently, BioRxiv are doing their part to promote open scientific inquiry and discussion by deleting questions and comments:



    That screenshot is from Rossana Segreto's account. Google Scholar results for Rossana Segreto. What would be the rationale for this deletion?

    A preprint posted a few weeks back:

    Abstract: A recent manuscript (Zhou, P. et al. “A pneumonia outbreak associated with a new coronavirus of probable bat origin”, Nature 579, 270–273 (2020). https://doi.org/10.1038/s41586-020-2012-7) from Wuhan Institute of Virology claimed the identification of a bat coronavirus, RaTG13, which showed 96.2% genome homology with SARS-CoV-2. In this paper, we raise the puzzling observations surrounding the identification, characterization, unique genome features of this RaTG13 strain, as well as its 100% nucleotide identity in partial RdRp gene with another bat coronavirus strain BtCoV/4991. And the paper presented premature hypothesis of potential bat origin of SARS-CoV-2 while RaTG13 strain was not successfully isolated. We also present the concerns on the methodology, data quality and experiment procedures described in this paper. We call for the authors to provide additional data, to share related samples to be verified and further characterized by other scientists.
    Major Concerns on the Identification of Bat Coronavirus Strain RaTG13 and Quality of Related Nature Paper

    I haven't really dug into it, so I can't speak to its quality, but regarding the last sentence, it should be remembered that everything we know about the closest bat coronaviruses to SARS-CoV-2 comes from the Wuhan Institute of Virology, and no one else can take a look at their evidence, because they say they don't have it anymore.
    Last edited by sumskilz; June 23, 2020 at 03:01 AM.
    Quote Originally Posted by Enros View Post
    You don't seem to be familiar with how the burden of proof works in when discussing social justice. It's not like science where it lies on the one making the claim. If someone claims to be oppressed, they don't have to prove it.


  12. #52

    Default Re: The Potential Lab Origin of COVID-19

    Nice, informative OP, but I don't really see the point of the thread. Whether the virus escaped from a lab or the populace contracted it from pangolins is immaterial; the salient fact in this pandemic is that China is a biological hazard for humanity.
    "Blessed is he who learns how to engage in inquiry, with no impulse to hurt his countrymen or to pursue wrongful actions, but perceives the order of the immortal and ageless nature, how it is structured."
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  13. #53
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    Default Re: The Potential Lab Origin of COVID-19

    Quote Originally Posted by Timoleon of Korinthos View Post
    Nice, informative OP, but I don't really see the point of the thread...the salient fact in this pandemic is that China is a biological hazard for humanity.
    Well said, Timoleon,in fact, wild animal markets must be banned worldwide, once and for all. In China, Illegal wildlife trade goes online as China shuts down markets
    Ending the trade won't be easy.

    But I clearly see the point of this thread.Mother Jones summarizes it well.

    The Non-Paranoid Person's Guide to Viruses Escaping From Labs

    Which left no firm explanation for how a virus that had originated in bats in remote caves in southern China had suddenly appeared in downtown Wuhan.
    Even the most common theories—that it had jumped from the bat to a person or another animal that served as an intermediate host as it traveled to Wuhan—would require a remarkable confluence of events.

    No wonder then that to some it was like a black hole suddenly opening in the Swiss countryside outside the CERN particle-collider.

    It was all perfect fodder for conspiracy-minded bigots like Rush Limbaugh.

    ARS-CoV-2’s genome showed no signs of being anything but natural, and five of the world’s top scientists criticized the lab-escape hypothesis in the pages of Nature Medicine. “Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus,” they wrote.

    Jonna Mazet, the director of PREDICT, made the case for the WIV’s safety practices, pointing out all the reasons why an accident involving researchers from the WIV was incredibly unlikely. “I’m a scientist,” Mazet said. “I would never say a lab accident was not possible. I’m just saying it’s a lot less likely than a lot of other explanations.

    ” Researchers in the field wear full Tyvek suits and masks, and freeze samples in liquid nitrogen. In the lab, they break viruses into pieces before studying it and do all their work inside biosafety cabinets designed to prevent any escapes.

    For all those reasons, most mainstream scientists doubt the lab connection.
    “We have not found evidence to support any theory that the origins of SARS-CoV-2 among humans occurred in a laboratory either intentionally or by accident,” Daniel Lucey recently wrote on the blog of the Infectious Diseases Society of America.
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    Default Re: The Potential Lab Origin of COVID-19

    Mother Jones hahahaha

    Sorry but seriously that’s like going ‘and now let’s see what Breitbart says’.
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    Default Re: The Potential Lab Origin of COVID-19

    @Ludicus

    Although to be fair the contra argument in many cases has been that there is no obvious sign of a blunt direct manipulation. The kind of thing say Monsanto does in round up ready plants. The argument against pass through generations with or without mutagenic intervention is not as secure.
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    Default Re: The Potential Lab Origin of COVID-19

    Quote Originally Posted by conon394 View Post
    @Ludicus

    Although to be fair the contra argument in many cases has been that there is no obvious sign of a blunt direct manipulation.
    Moreover this an argument impossible to win. There are so many pathways possible in a laboratory, it is always possible to hypothesize a pathway that can mimic any natural origins. This a guaranteed unbeatable argument when the burden of proof is reversed.

    I stay on my position of parsimony. This is the third outbreak of a novel coronavirus in 20 years.
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  17. #57

    Default Re: The Potential Lab Origin of COVID-19

    Quote Originally Posted by Timoleon of Korinthos View Post
    Nice, informative OP, but I don't really see the point of the thread. Whether the virus escaped from a lab or the populace contracted it from pangolins is immaterial; the salient fact in this pandemic is that China is a biological hazard for humanity.
    SARS-CoV-2 has unique characteristics among coronaviruses that make it a particular problem, such as its ability to infect a variety of organ systems and its ability to cause (potentially long term) damage in even asymptomatic cases. If these characteristics are the result of gain-of-function research rather than chance recombination of multiple viruses, then it matters for the prevention of future (similar or potentially worse) pandemics.

    Although to your point, if it was the result of chance recombination of multiple coronaviruses, it is almost certainly connected to China's wildlife trade. There is however no evidence connecting it to the Wuhan wet market and no evidence of coronaviruses turned up in a survey of the pangolins source population.

    Quote Originally Posted by Genava View Post
    I stay on my position of parsimony. This is the third outbreak of a novel coronavirus in 20 years.
    I consider your position reasonable, but assessing parsimony is somewhat a matter of personal intuition in this case. It could likewise be the seventh time in the past 20 years that workers were accidentally infected with a betacoronavirus in a lab, and the second global pandemic that was caused by a lab leak (which virologists were reluctant to accept until quietly decades later).

    Since it is well-documented that WIV was creating novel chimeric coronaviruses and passaging them, since it is well-documented that the WIV had a history of safety concerns, since by their own admission WIV had the closest related virus in their possession, since the pandemic began in Wuhan, and since SARS-CoV-2 was already highly adapted to infecting humans when it was first identified, in my opinion, the lab escape hypothesis requires very few assumptions.
    Last edited by sumskilz; June 30, 2020 at 09:57 AM.
    Quote Originally Posted by Enros View Post
    You don't seem to be familiar with how the burden of proof works in when discussing social justice. It's not like science where it lies on the one making the claim. If someone claims to be oppressed, they don't have to prove it.


  18. #58
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    Default Re: The Potential Lab Origin of COVID-19

    Quote Originally Posted by Genava View Post
    This is the third outbreak of a novel coronavirus in 20 years.
    Right. Epidemiologists have been warning of a coronavirus outbreak for years. For example, Ralph Baric, University of North Carolina, among others.This was not the first, and this is not the last pandemic.Even Bill Gates has warned about a pandemic like the coronavirus.



    The "enormous evidence" coronavirus came from Chinese lab is a by product of the U.S.-China Cold War. Blaming China for "mass worldwide killing" is a political distraction from Trump's miserable, almost criminal mishandling of the outbreak that has already cost countless lives.
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    Default Re: The Potential Lab Origin of COVID-19

    Update.
    Recently published.
    Wong YC, Lau SY, Wang KK, et al. Natural transmission of bat-like SARS-CoV-2ΔPRRA variants in COVID-19 patients. Clin Infect Dis July 10, 2020. Full-text: https://doi.org/10.1093/cid/ciaa953

    Conclusions
    Our findings demonstrate that bat-like SARS-CoV-2ΔPRRA not only naturally exists but remains transmissible in COVID-19 patients, which have significant implications to zoonotic origin and natural evolution of SARS-CoV-2.
    SARS-CoV-2 contains the furin cleavage PRRA motif in the S1/S2 region, which enhances viral pathogenicity but is absent in closely related bat and pangolin coronaviruses. It remains unknown if bat-like coronaviral variants without PRRA (ΔPRRA) can establish natural infection in humans.
    In this study, these variants were readily detected among acute patients, including a family cluster showing that these variants exist naturally and are currently transmitting in COVID-19 patients
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    Default Re: The Potential Lab Origin of COVID-19

    Quote Originally Posted by Ludicus View Post
    In this study, these variants were readily detected among acute patients, including a family cluster showing that these variants exist naturally and are currently transmitting in COVID-19 patients
    They are finding variants of SARS-CoV-2 at very low levels in individual COVID-19 patients. Since they recognize this and the fact that these variants would be selected against, then it should have been logical for them to assume that SARS-CoV-2 was the source of variants (as others have already noticed) rather than coming up with the rather flimsy hypothesis that the variants were the source of SARS-CoV-2. Find the variants in someone who isn't already infected with SARS-CoV-2, or find them in an animal, or find them in an old blood sample, or find them anywhere where they aren't most likely mutations of SARS-CoV-2 soon to be eliminated by purifying selection, then such a hypothesis will have some weight.

    Moving on...

    From a somewhat recent interview with virologist Birger Sørensen:

    Asked about what significance his approached has had when he has analyzed the coronavirus, Sørensen explains:

    “We have examined which components of the virus are especially well suited to attach themselves to cells in humans. And we have done this by comparing the properties of the virus with human genetics. What we found was that this virus was exceptionally well adjusted to infect humans.”

    He pauses for a second.

    “So well that it was suspicious,” he adds.

    It is already known that the novel coronavirus, like the virus that caused the SARS epidemic in Southeast Asia in 2002-2003, could attach itself to the ACE-2 receptors in the lower respiratory tract.

    “But what we have discovered is that there are properties in this new virus which enables it to use an additional receptor, and create a binding to human cells in the upper respiratory tract and the intestines which is strong enough to produce an infection,” Sørensen elaborates.

    Sørensen says that it is the use of this additional receptor that most likely results in a different illness in Covid-19 patients than the one resulting from SARS.

    “This is what enables the virus to transmit to a greater degree between humans, without the virus having attached itself to the ACE-2 receptors in the lower respiratory tract, where it causes deep pneumonia.

    “That is also why so many of the Covid-19 patients have mild symptoms at the start of the illness, and are contagious before they develop severe symptoms,” he adds.

    It might also explain why some people are ‘super spreaders’ without being ill themselves, Sørensen says.

    In the already published article Sørensen and his colleagues Angus Dalgleish and Andres Susrud describe what they claim is curious about the spike protein of the coronavirus, which makes it especially well suited to infect humans. These findings are the foundation for the hypothesis Sørensen and his colleagues develop in the new article, where they claim that the virus is not natural in origin.

    “There are several factors that point towards this,” says Sørensen. “Firstly, this part of the virus is very stable; it mutates very little. That points to this virus as a fully developed, almost perfected virus for infecting humans.

    “Secondly, this indicates that the structure of the virus cannot have evolved naturally. When we compare the novel coronavirus with the one that caused SARS, we see that there are altogether six inserts in this virus that stand out compared to other known SARS viruses,” he goes on explaining.

    Sørensen says that several of these changes in the virus are unique, and that they do not exist in other known SARS coronaviruses.

    “Four of these six changes have the property that they are suited to infect humans. This kind of aggregation of a type of property can be done simply in a laboratory, and helps to substantiate such an origin,” Sørensen points out.

    Asked about whether this implies that the virus is not natural, Sørensen goes on to explain the laboratory process that leads to the creation of new viruses.

    “In a sense it is natural. But the natural processes have most likely been accelerated in a laboratory,” he explains. “It’s also possible for a virus to attain these properties in nature, but it’s not likely. If the mutations had happened in nature, we would have most likely seen that the virus had attracted other properties through mutations, not just properties that help the virus to attach itself to human cells.”

    Sørensen vividly explains this argument:

    “Imagine that you have cultivated a billion coronaviruses you have gathered from nature, then you take this mass of viruses and inject them into a human cell culture from for example the upper respiratory tract. As a result, a few of these viruses will change in order to better attach themselves to this type of cell in the nose and throat region and therefore to infect humans more easily. You end up with a virus with a spike protein which is perfect for attaching to and penetrating human cells.” Sørensen explains.

    Asked about the particular mutations in the virus that lead to this conclusion, Sørensens says:

    “What we see is that an area that you could observe in the first SARS coronavirus has been moved, so that the parts of the virus that are particularly well suited to attach to humans, have become part of the spike protein that the virus uses to penetrate human cells. And it is this moving of the area of the virus which makes the virus, together with the injected areas explained above, able to utilise an additional receptor to infect humans.”

    On a board in the meeting room where Sørensen is hosting our meeting, he illustrates what he is trying to explain, and how a component of the virus which previously was situated on another part of the shell of the virus, now has become a part of the spike protein of the virus.

    Sørensen is therefore quite confident that the virus has originated in a laboratory.

    “I think it’s more than 90 percent certain. It’s at least a far more probable explanation than it having developed this way in nature”, Sørensen responds.

    Sørensen also highlights other data than those related to the virus’ properties:

    “The properties that we now see in the virus, we have yet to discover anywhere in nature. We know that these properties make the virus very infectious, so if it came from nature, there should also be many animals infected with this, but we have still not been able to trace the virus in nature.

    “The only place we are aware of where an equivalent virus to that which causes Covid-19 exists, is in a laboratory. So the simplest and most logical explanation is that it comes from a laboratory. Those who claim otherwise, have the burden of proof,” Sørensen says.

    There are indeed earlier known experiments where changes to the corona virus have been engineered. An interesting example of this kind of research is a collaborative effort between Wuhan Institute of Virology and University of North Carolina at Chapel Hill. In a 2015 article, Menachery et al. describe experiments with laboratory created corona viruses – so called gain-of-function-studies. The purpose of this research is partly to be better prepared for new pathogenic variants of the virus. But the researchers also write: «the potential to prepare for and mitigate future outbreaks must be weighed against the risk of creating more dangerous pathogens». This risk must also be evaluated in light of previous known accidents where corona viruses have escaped from laboratories in China.

    But several researchers have already pointed out that artificially created viruses would be easy to identify. We therefore ask Sørensen why this has not been identified earlier.

    Sørensen believes there are several reasons for this.

    “The first is that this is a very uncomfortable finding, and the production of new scientific articles that can be used to prove such findings has all but ground to a halt. Chinese scientists no longer publish articles that can be used to support such a hypothesis”, he says.

    “And newer articles that are published about the virus must be thoroughly investigated, especially in relation to the basic material that is being used,” Sørensen expands, and points to a new x-ray article published in Nature by Shang et al., which Sørensen also earlier has criticised for being misleading.

    “To do my analysis, I have therefore had to go back to the source material, and look at those articles that were published before the Covid-19 outbreak, where we have chosen to assume that the data that have been used is okay and reflects the actual conditions,” Sørensen says.

    Asked about why there has not been more debate on this topic Sørensen has several explanations.

    “This quickly becomes a discussion on politics, rather than science, Sørensen responds.

    “Nobody wants to put forward the inconvenient truth, many scientists are also concerned about their own funding and position if they were to put forward such a controversial hypothesis, Sørensen elaborates. It is nevertheless a fact that many people on the web have engaged in such a debate. But so far, those who participate in such forums are characterized as conspiratorial. It is also the case that a debate about this type of viral research and the technologies used may damage reputation and lead to new restrictions on how to conduct molecular genetic research. With this in mind, it is not difficult to see that it must be difficult to get accepted papers in peer reviewed journals that focus on such research.
    Quote Originally Posted by Enros View Post
    You don't seem to be familiar with how the burden of proof works in when discussing social justice. It's not like science where it lies on the one making the claim. If someone claims to be oppressed, they don't have to prove it.


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