This is an archive of past discussions. Do not edit the contents of this page. If you wish to start a new discussion or revive an old one, please do so on the current talk page. |
Archive 5 | ← | Archive 8 | Archive 9 | Archive 10 | Archive 11 |
The following addition by @ Rotideypoc41352: to the Reservoir and Origin section insinuates a conclusion that is neither supported in nor by the referenced paper:
A phylogenetic network analysis of 160 early coronavirus genomes sampled from December 2019 to February 2020 showed that the virus type most closely related to the bat coronavirus was most abundant in
Guangdong, China, and designated type "A". The predominant type among samples from Wuhan, "B", is more distantly related to the bat coronavirus than the ancestral type "A".
[1]
This implies that Guangdong Province may be considered as an alternative location (to Wuhan) for the initial outbreak, since the "A" cluster is marginally closer to the outgroup, RaTG13. Forster et al., on the other hand, suggest that type "B" exhibits a potential founder effect due to the relative propensity of types "A" and "C" to spread abroad. Note that 17 of the 43 cases of type "A" occur outside of East Asia altogether as opposed to six cases in Guangdong and five cases in Wuhan. All six cases in Guangdong occurred in Shenzhen, as well, which Wikipedia describes as "busiest in China when it comes to border crossings;" one viral lineage traced in the paper even follows a Canadian infected with the type "B" variant who travels to Ottawa from Wuhan via Guangdong Province. Furthermore, only four Guangdong cases make up the ancestral T-allele node that the phylogenetic analysis predicts is equally close to RaTG13 as the ancestral C-allele node made up of three Americans and a Chinese national who was not in Guangdong. Four cases and a median network algorithm do not a substitute for Wuhan make, and Forster et al. never made this claim. This selection should either be rewritten to better represent the source cited or stricken from the article. At the very least, the claims should be qualified and disassociated from Guangdong. Vachaknu ( talk) 10:59, 30 May 2021 (UTC)
References
Continuing discussion here after revert by @ Hemiauchenia:, regarding the following text from the Reservoir and zoonotic origin section, changes emphasized:
All available evidence suggests that SARS‑CoV‑2 has a natural animal origin and is not
genetically engineered. Nevertheless, early in the pandemic, conspiracy theories spread on social media claiming that the virus was
bio-engineered by China at the
Wuhan Institute of Virology. While some scientists, including
David Relman and former CDC director
Robert R. Redfield, believe it is likely that the virus may have been studied by and escaped from the Institute,
[1]
[2] the March 2021 WHO report on the joint WHO-China study stated that such an explanation is "extremely unlikely".
A few topics for discussion:
If a viewpoint is held by a significant minority, then it should be easy to name prominent adherents. I can appreciate that ability to name prominent adherents does not necessarily mean they must be listed by name in the article.
Appreciate your time. Bakkster Man ( talk) 21:17, 29 April 2021 (UTC)
I agree that scientists can be biased, but these scientists are not making biased statements.For clarity, I'm not suggesting these scientists are doing anything wrong. More the 'if all you have is a hammer, every problem looks like a nail' kind of thing. Because of their important work, they may be more likely to lean towards this as the source. It doesn't mean they're wrong, just that they might be more prone to lean this direction. That they
advocate for a transparent and open investigationis exactly what I want as well, and once that new investigation has results we'll cover what it says. Per [[WP:CRYSTALBALL}}: "Although currently accepted scientific paradigms may later be rejected, and hypotheses previously held to be controversial or incorrect sometimes become accepted by the scientific community, it is not the place of Wikipedia to venture such projections." Bakkster Man ( talk) 13:18, 26 May 2021 (UTC)
They state only that the theory should not be dismissed, which I agree with 100%, and have worked to make sure the articles do not do.
In light of social media speculation about possible laboratory manipulation and deliberate and/or accidental release of SARS-CoV-2, Andersen et al. theorize about the virus’ probable origins, emphasizing that the available data argue overwhelmingly against any scientific misconduct or negligence.Bakkster Man ( talk) 13:01, 3 May 2021 (UTC)
Transparency and open scientific investigation will be essential to resolve this issue, noting that forensic evidence of natural escape is currently lacking, and other explanations remain reasonable.. That quote can be paired with what said in his RAI interview:
if you're asking about intent, or whether the virus existed beforehand, it would only be in the records of the Institute of Virology in Wuhan[11], and the more recent open letter which confirms his position [12]. Baric has more papers on coronaviruses published in top-tier journals than any other coronavirolagist, so his expert opinion is very much WP:DUE in this article and related articles. CutePeach ( talk) 00:11, 24 May 2021 (UTC)
I liked the original paragraph posted by Bakkster. An observation to consider is that the premise "some scientists, including David Relman and former CDC director Robert R. Redfield, believe it is likely that the virus may have been studied by and escaped from the Institute" is not negated (not even weakly) by the follow up: "the March 2021 WHO report on the joint WHO-China study stated that such an explanation is extremely unlikely ", because, statistically, having a likely event by expert opinion can coexist with having the same event be extremely unlikely by some other expert opinion. If we wish to illustrate the strength of authority of the experts, then we may like to put less emphasis on the arrived statement of likelihood, and more emphasis on the authority of the source. Or better yet, we could cite a MEDRS that explicitely summarizes the evidence that allowed the WHO to conclude that it was extremely unlikely, so that we are totally transparent. Forich ( talk) 19:56, 30 April 2021 (UTC)
While *minority opinion*, *majority opinion per MEDRS sources*. Bakkster Man ( talk) 20:50, 30 April 2021 (UTC)
Extended content
|
---|
The closest relatives of SARS-CoV-2 from bats and pangolin are evolutionarily distant from SARSCoV-2. There has been speculation regarding the presence of human ACE2 receptor binding and a furin-cleavage site in SARS-CoV-2, but both have been found in animal viruses as well, and elements of the furin-cleavage site are present in RmYN02 and the new Thailand bat SARSr-CoV. There is no record of viruses closely related to SARS-CoV-2 in any laboratory before December 2019, or genomes that in combination could provide a SARS-CoV-2 genome. Regarding accidental culture, prior to December 2019, there is no evidence of circulation of SARS-CoV-2 among people globally and the surveillance programme in place was limited regarding the number of samples processed and therefore the risk of accidental culturing SARS-CoV-2 in the laboratory is extremely low. The three laboratories in Wuhan working with either CoVs diagnostics and/or CoVs isolation and vaccine development all had high quality biosafety level (BSL3 or 4) facilities that were well-managed, with a staff health monitoring programme with no reporting of COVID-19 compatible respiratory illness during the weeks/months prior to December 2019, and no serological evidence of infection in workers through SARS-CoV-2-specific serology-screening. The Wuhan CDC lab which moved on 2nd December 2019 reported no disruptions or incidents caused by the move. They also reported no storage nor laboratory activities on CoVs or other bat viruses preceding the outbreak. |
The difficulty here is the simplest arguments to summarize quickly are the ones based on a lack of relevant data, which is the primary critique of the report. Perhaps I'm just being overly cautious here, but I'd lean towards not trying to summarize. Bakkster Man ( talk) 14:33, 1 May 2021 (UTC)
References
{{
cite journal}}
: |access-date=
requires |url=
(
help); Check |doi=
value (
help); External link in |doi=
(
help)
David Baltimore does not have an MD so it is doubtful that he would be an MD reliable source; however, he could perhaps be used as another proponent, like former CDC director Robert R. Redfield, that SARS-CoV-2 might have a lab origin. Baltimore states: [13]
It is David Baltimore, so I will allow the virology experts on this page to hash out what to make of the article and his quote. -- Guest2625 ( talk) 08:48, 7 May 2021 (UTC)
Remember, ideally we want peer-reciewed published reviews, or certsin types of reports from major medical organizations. Secondary, not primary. Hyperion35 ( talk) 18:55, 8 May 2021 (UTC)
To move the editing along, let's have a straw poll. Which version of the sentence should be included in the article? Either:
Preferences:
I join Forich and Guest2625 in supporting Bakkster Man's proposal to replace the Redfield quote with the Science letter. I agree also to Bakkster Man's four point breakout of the Science letter, but I would add the author's concern that the two predominant theories were not given balanced consideration. Mysticriver1 ( talk) 18:15, 20 May 2021 (UTC)
I propose the following new revised paragraph:
This version of the paragraph adds an extra sentence on the lab thing which is about the right amount of material to include in this article on a non-majority hypothesis. -- Guest2625 ( talk) 08:05, 22 May 2021 (UTC)
Here's another version of the paragraph:
This version includes the statement about the lack of available evidence. With this clause the sentence does have a better transition so perhaps is better. -- Guest2625 ( talk) 09:28, 23 May 2021 (UTC)
The wording of the following paragraph is in dispute:
I think it is fine to live edit the paragraph; however, it might also be beneficial to have a simultaneous conversation here on the talk page. At the moment the paragraph has problems with non-neutral wording, editorializing, and straying from discussing science which is the main theme of this article. Maybe a good way to improve the paragraph is for everyone to provide their ideal version of the paragraph.
I would suggest the following version of the paragraph:
The benefit of this version is that it cuts out most of the politics, the wordiness, and keeps the statement about the lab accident to one sentence and the paragraph very brief. -- Guest2625 ( talk) 09:30, 31 May 2021 (UTC)
Thank you for the feed back. This new version should address the above concerns:
The benefit of this version is that it trims out some more non-science clutter, and then allows the rebuttal sentence of the majority to directly follow. At the moment there is no false equivalence, since the first sentence in the paragraph clearly states that the available evidence indicates a natural origin. And also, the last sentence minimizes the possibility with both the view of the majority of the scientists and the report of the WHO. -- Guest2625 ( talk) 11:34, 31 May 2021 (UTC)
Good point about the statement about geopolitical debate causing confusion. The best thing to do is eliminate it an all non-science commentary and keep that material for the non-science articles on the topic. Here are three new versions. The first with no qualifier as concerns the evidence and the two others making mention:
And
And:
Not quite clear which version is the best. Look forward to hearing other people's feedback and their suggested version of the contested paragraph. -- Guest2625 ( talk) 11:59, 31 May 2021 (UTC)
References
|
---|
References
|
This
edit request to
Severe acute respiratory syndrome coronavirus 2 has been answered. Set the |answered= or |ans= parameter to no to reactivate your request. |
There are currently five list-defined references unused in the article, which is creating an error. 92.24.246.11 ( talk) 12:44, 4 June 2021 (UTC)
The current article strongly supports the zoonotic origin theory, relying on the WHO report to call the lab accident hypothesis "extremely unlikely." Today a new letter came out from 18 scientists published as a letter to the journal of Science calls this evaluation not a "balanced consideration" and that both zoonotic and lab leak remain viable: https://www.reuters.com/business/healthcare-pharmaceuticals/origins-covid-19-need-be-investigated-further-leading-scientists-say-2021-05-14/
Not mentioned in this article, but found elsewhere in places like the Wades article, are serious critiques that the WHO report was tainted by serious conflict of interest.
The article should be updated to reflect a more balanced take and not just rely on the WHO report to call the lab leak "extremely unlikely." When I look at the evidence currently, the lab leak explanation is becoming the more parsimonious explanation. Spudst3r ( talk) 19:42, 14 May 2021 (UTC)
Here's the problem. Saying pmid:33586302 is "from a single scientist from Indonesia" (why does the country matter, hmmm? Does it in some way nullify Hakim's virology expertise? [25]) rather swerves round the facts that:
In short, one of our WP:BESTSOURCES. So implying this is a poor source seems like trying to warp reality to fit an agenda (rather in keeping with the whole lab leak thing). So long as we properly reflect golden sources like this, we are being good editors. Alexbrn ( talk) 12:09, 16 May 2021 (UTC)
long explanation
|
---|
A few years back, my agency decided to make some changes to regulations surrounding opioid (and other substances of abuse) treatment. Now, there is no lack of popular news coverage of the opioid epidemic, but we did not consult that. While it was of great public interest, it simply lacked serious depth, preferring to interview individuals rather than presenting any sort of serious statistical or cost-benefit analyses. What few interviews they had with professionals didn't require them to qualify or quantify their comments or show their work, and they rarely gave any information about whether a given professional's opinions represented a majority view or if they were a lone crank. Individual papers on opioids are a dime a dozen. They range all over the place in quality and findings. I even came across a (non-peer-reviewed) study that purported to show that laws expanding the distribution, possession, and use of naloxone correlated to an increase in opioid deaths (spoiler: it was horribly flawed). You could easily come up with dozens of different and mutually-exclusive proposals based on which individual primary-source paper that you could find. Suboxone? Buprenorphine-only? Methadone? Cold turkey? Do you want to play paper roulette with thousands of lives on the line? We instead looked at reviews published in the relevant journals in the field (ie secondary sources), and had our CMO look over them (which might make it a tertiary source), and this narrowed our approach dramatically, giving us a better idea of what treatment options would lead to the best outcomes, which were first line, second line, contraindications, etc. But that wasn't quite enough, because in a field this complicated you need a better idea of how to translate those findings into clinical practice, and so we consulted with the American Society for Addiction Medicine (ASAM), and consulted with them about their treatment guidelines. They had an excellent scale to allow physicians to classify a patient's addiction level, and recommendations for treatment based on those levels (ie outpatient medication management, short inpatient treatment, intensive inpatient treatment, etc). |
The actual question of a lab leak is not even scientific in nature about the structure/biology of the virus itself, since lab theory proponents primarily point to structural elements of the virus as evidence that its evolution was due to growth in lab culture. And those kinds of claims (for instance, that ACE2 most likely came from culture) absolutely need MEDRS. Bakkster Man ( talk) 20:06, 24 May 2021 (UTC)
BSL-2 lab securitysounds biomedical to me.
Wuhan's lack of proximity to the local bat population or evidence of local infection nearbyboth are biomedical issues.
lack of hospital surveillance logs for the virusThis is literally a claim about a medical facility and medical records.
the timelines for MERS/SARS finding intermediate hosts vs COVIDYou mean virology?
not being able to find the virus after testing 80,000 animalsI mean maybe you could count this as zoology, but seriously now how is viral testing not biomedical?
the article should reflect the fact that the evidence supporting both hypothesis still remain circumstantial -- and let the reader decide by giving an appropriate discussion of the available evidence for the different hypothesisExcept that's not what the sources say. The best sources that we have explicitly say that a lab leak is extremely unlikely, they are clear about a zoonotic spillover event. This is the same special pleading I'd expect to hear from Creationists, the same "teach the controversy" and "let people decide on their own" canards. Hyperion35 ( talk) 01:33, 25 May 2021 (UTC)
"It’s documented that researchers at the Wuhan Institute of Virology were doing gain-of-function experiments designed to make coronaviruses infect human cells and humanized mice. This is exactly the kind of experiment from which a SARS2-like virus could have emerged. The researchers were not vaccinated against the viruses under study, and they were working in the minimal safety conditions of a BSL2 laboratory. So escape of a virus would not be at all surprising. In all of China, the pandemic broke out on the doorstep of the Wuhan institute. The virus was already well adapted to humans, as expected for a virus grown in humanized mice. It possessed an unusual enhancement, a furin cleavage site, which is not possessed by any other known SARS-related beta-coronavirus, and this site included a double arginine codon also unknown among beta-coronaviruses. What more evidence could you want, aside from the presently unobtainable lab records documenting SARS2’s creation?
Proponents of natural emergence have a rather harder story to tell. The plausibility of their case rests on a single surmise, the expected parallel between the emergence of SARS2 and that of SARS1 and MERS. But none of the evidence expected in support of such a parallel history has yet emerged. No one has found the bat population that was the source of SARS2, if indeed it ever infected bats. No intermediate host has presented itself, despite an intensive search by Chinese authorities that included the testing of 80,000 animals. There is no evidence of the virus making multiple independent jumps from its intermediate host to people, as both the SARS1 and MERS viruses did. There is no evidence from hospital surveillance records of the epidemic gathering strength in the population as the virus evolved. There is no explanation of why a natural epidemic should break out in Wuhan and nowhere else. There is no good explanation of how the virus acquired its furin cleavage site, which no other SARS-related beta-coronavirus possesses, nor why the site is composed of human-preferred codons. The natural emergence theory battles a bristling array of implausibilities." [1] Spudst3r ( talk) 20:15, 7 June 2021 (UTC)
The following discussion is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.
There is now considerable evidence beyond right wing bullshit. I would encourage people to read https://thebulletin.org/2021/05/the-origin-of-covid-did-people-or-nature-open-pandoras-box-at-wuhan/ (There are other sources)
The WHO team that investigated had Peter Daszak on it, who was the person that oversaw the US grant that funded the lab. It is the international virology community that is being accused here, not just Wuhan.
The section in this article is extremely POV, saying about five times that they think it had a natural origin. It needs balance.
No natural precursor has been found. The lab was studying gain-of-function Corono viruses. And China has censored the data. This needs to be said.
Look beyond your political biases. Just because Trump is an idiot does not mean he is always wrong -- even a stopped clock is correct twice a day. Tuntable ( talk) 06:39, 2 June 2021 (UTC)
No natural precursor*inhales* Bruh. brUH?? The bat coronaviruses? SARS-CoV-1? Literally the many coronaviruses out there we haven't even found yet? This is not the first time a virus has jumped species, nor will this be the last. It happens all the time! Friend. Friend. A virus does not need a GoF lab to be dangerous. Rotideypoc41352 ( talk · contribs) 12:32, 2 June 2021 (UTC)
That above would certainly lead to strong suspicion about the lab. There are technical bits a well, but that is enough for now.
Maybe Wade is full of shit. But he is widely read and quoted. He deserves to be heard even if only to have his arguments properly debunked.
There are certainly other very credible authors that have doubts https://science.sciencemag.org/content/372/6543/694.1
The anger and censorship above only adds wait to the idea that Wade is correct. The section in the article reads like propaganda, vs Wade's sober writing. I also presume that some (not all) of the editors of this article are Chinese government employees. Tuntable ( talk) 03:18, 3 June 2021 (UTC)
some (not all) of the editors of this article are Chinese government employeesmakes people less likely to believe you are here to build consensus and more likely to just let WP:GS/COVID19 run its course. Not anger (ran out long ago), not "censorship" (this is a private website), just sober writing. Rotideypoc41352 ( talk · contribs) 18:28, 3 June 2021 (UTC)
"My citation is better than your citation" does not cut it. Wade is a respected journalist and he certainly does not read like he is blatantly lying. If he was then that would be of interest. Neither you nor the article have addressed even one of the points Wade made. Maybe Wade is wrong, I came to this article to find out. But there is no real content other than that the some people (including virologists) are passionate about not discussing the Wuhan case, and quick to censor any mention of it, or even to include a citation. That strongly suggests that Wade is correct, and I suspect that this will come out over the next few months. Tuntable ( talk) 03:32, 5 June 2021 (UTC)
I suspect that this will come out over the next few months.Entirely possible, but also not our job to try and predict. WP:CRYSTAL Bakkster Man ( talk) 13:49, 5 June 2021 (UTC)
And thank you for the Gorski paper. However, it does not address Wade's points directly. And it reads like an angry rant while Wade reads like a considered analysis of the facts. I think it is patently obvious that just given the points that I pulled from Wade above that the WIV is definitely a possible source, and it would be very difficult to disprove that given the records are sealed. But I would like more information on the technical arguments, the closeness to RaTG13, the codons used in the Furin cleavage site. But I don't see anything in either this article. The fact that it might have arisen naturally certainly does not prove that the WIV is innocent. Tuntable ( talk) 03:41, 5 June 2021 (UTC)
I might add that the Gorski paper mischaracterizes the Furin argument, which was that it uses human codons. It also mischaracterizes the RaTG13 argument, which is that the SARS-CoV-19 virus is almost identical to RaTG13 for most of it, except for the spike protein, suggesting that that RaTG13 was used as a backbone, and the spike stuff added. If there is a good paper that realistically refutes Wade, I have not seen it.
Tuntable ( talk) 04:14, 5 June 2021 (UTC)
Even Biden suggesting it is plausible enough to require an investigation. It does not matter whether it is true or not. It does not matter who are the most eminent references. It needs to be properly addressed because it is now widespread. People will come to Wikipedia to determine whether it is true.
Having read the article, and the the talk, I still do not have any clear idea why the lab leak hypothesis is considered to be complete nonsense. I understand that many eminent people have said so, and that some of the technical arguments for the lab leak may be dubious. But I have not seen anywhere any proof that it is not possible.
To address it requires summarizing the case for and against. Many people (including myself) are much more interested in rational arguments than authoritative ones. To address the "conspiracy" the arguments put forth by the conspirators need to be stated clearly and succinctly, and then facts provided by eminent sources used to debunk them. Rather than agonizing on about a generic paragraph that gives appropriate weight, provide the facts and let the reader decide.
Personally, it appears obvious that the labs are suspicious because of geography, the lack of animal or human precursors, the fact that the WIV was doing gain-of-function research on coronoviruses at the time, and the fact that the Chinese government has closed access to relevant records, and that nobody has ever said that such a chimera could not, in theory, be created. That seems more than enough to make the conspiracy very plausible.
As @ SSSheridan: points out, this consensus has changed recently, although I think there have always been substantial doubts. As @ Eccekevin: points out, the WHO is a important but not infallible source. As @ Spudst3r: points out, the discussion is not just scientific, but operational, as humanized mice could be the animal intermediatory. Certainly the Ebright concerns raised by @ CutePeach: should be mentioned. The technical details for and against would make a very interesting article, as @ Elle Kpyros: has suggested.
BTW. Do any of the eminent references provide evidence that the intermediatory could not be humanize mice? That would be interesting to know.
Incidentally, the WHO report said "There is no record of viruses closely related to SARS-CoV-2 in any laboratory before December 2019," -- What about RaTG13? Also, did the WHO team actually study the WIV in any detail? And did the team include people closely associated with the WIV (like Peter Daszak)? Tuntable ( talk) 07:16, 6 June 2021 (UTC)
As @ Eccekevin: points out, the WHO is a important but not infallible source.While I agree, you need to provide some kind of reliable, scholarly source making a contrary claim. If the WHO makes one claim, consistent with a bunch of other high quality papers, and the best we can find making a link to humanized mice is a non-MEDLINE article from a single non-virologist, then even if we cite such a paper it would indicate its WP:FRINGE/ALT status by being stuck in a less prestigious journal by a non-expert. If it's a clear issue, it's an easy fix. So provide the links. Though I'll warn, they probably would need to go in the Investigations article (where there's a good argument MEDRS doesn't apply) rather than here (where there's a good argument MEDRS does apply).
Do any of the eminent references provide evidence that the intermediatory could not be humanize mice? That would be interesting to know.To reiterate, unless we have a reliable source that suggests they could be the intermediary, why would we cite a source source saying a thing wasn't possible. We'd have a hella long article if we had to list and cite every possibility that was ruled out that nobody suggested should be considered in the first place. Sure, we ruled out a meteor, but did we rule out a comet? What about Martians? Titans? Alpha Centaurans?
This supports the hypothesis that the PCS/furin cleavage site was gained by a recombination event(s) involving these virus sequences. This notion is important in considering possible zoonotic events, placing laboratory events in the realm of the highly possibleis uncited, making it a primary claim rather than a review of the existing literature. Maybe I've missed it in the citations (if so, please point me to it, this source seems the closest to directly applicable), but the paper doesn't directly cite it.
It is not just "My" original research. It is quite widely quoted, and has prompted an inquiry by the US President. That does not make it correct, but it certainly makes it notable.
I believe that this should be covered here, but I will add a reference to the other article, of which I was unaware. I expect you to instantly revert it for some obscure reason. But the other article does not cover the issues either. So we can continue the discussion there. Tuntable ( talk) 01:16, 7 June 2021 (UTC)
When available, academic and peer-reviewed publications, scholarly monographs, and textbooks are usually the most reliable sources.-- Hob Gadling ( talk) 17:00, 8 June 2021 (UTC)
Ideas that are of borderline or minimal notability may be mentioned in Wikipedia, but should not be given undue weight... Wikipedia is not a place to right great wrongs. Fringe theories may be excluded from articles about scientific topics when the scientific community has ignored the ideas. However, ideas should not be excluded from the encyclopedia simply because they are widely held to be wrong.Bakkster Man ( talk) 17:46, 8 June 2021 (UTC)
The article says: SARS‑CoV‑2 is unique among known betacoronaviruses in its incorporation of a polybasic site cleaved by furin
. Is this correct? I've read that FCS is common among coronaviruses and uncommon on Sarbecoviruses. I don't know how it stands among betacoronaviruses. Can we get this claim fact-checked?
Forich (
talk) 21:02, 31 May 2021 (UTC)
Another specific genomic feature of SARS-CoV-2 is the insertion of four amino acid residues (PRRA) at the junction of subunits S1 and S2 of the S protein26 (Fig. 3a). This insertion generates a polybasic cleavage site (RRAR), which enables effective cleavage by furin and other proteases. Such an S1–S2 cleavage site is not observed in all related viruses belonging to the subgenus Sarbecovirus, except for a similar three amino acid insertion (PAA) in RmYN02, a bat-derived coronavirus newly reported from Rhinolophus malayanus in China.
It contains two subunits S1 and S2 with a polybasic site PRRA at the junction, which enables effective cleavage by furin and other proteases [5]. This multibasic cleavage site appears to be an important virulence factor which may enhance virus replication and multiple tissue tropism as in the case of avian influenza A(H5N1) virus [20, 21]. Mutations in this site can attenuate pathogenicity in animal models and may be an attractive option for designing live attenuated vaccines [21].
Nice work @
RandomCanadian:. This is the current information: A distinguishing feature of SARS‑CoV‑2 is its incorporation of a polybasic site cleaved by furin, which appears to be an important element enhancing its virulence. Although such sites are a common naturally-occurring feature of other viruses, including members of the Beta-CoV genus and other genera of coronaviruses, SARS-Cov-2 is unique among members of its subgenus for such a site.
. Please compare with this phrase from the WHO report (p. 83) in order to assess whether there is room for improvement (i.e. the WHO report says that most Betacoronaviruses do not have the FCS which is more informative than saying that in members of betacoronvairuses FCS sites at the S1/S2 junction occur naturally): This furin-cleavage site is not present in most other betacoronaviruses (for instance, SARS-CoV)
.
Forich (
talk) 22:28, 2 June 2021 (UTC)
Furthermore, SARS-CoV-2 has a unique furin cleavage site insertion (PRRA) not found in any other CoVs in the Sarbecovirus group (fig. S3), although similar motifs are also found in MERS and more divergent bat CoVs. This PRRA motif makes the S1/S2 cleavage in SARS-CoV-2 much more efficient than in SARS-CoV and may expand its tropism and/or enhance its transmissibility. A recent study of bat CoVs in Yunnan, China, identified a three–amino acid insertion (PAA) at the same site. Although it is not known whether this PAA motif can function similar to the PRRA motif, the presence of a similar insertion at the same site indicates that such insertion may already be present in the wild bat CoVs. The more efficient cleavage of S1 and S2 subunits of the S glycoprotein and efficient binding to ACE2 by SARS-CoV-2 may have allowed SARS-CoV-2 to jump to humans, leading to the rapid spread of SARS-CoV-2 in China and the rest of the world.Best not to dive too deeply into details, but I agree we want to get it right. It seems the gap is between 'commonly occurring' and 'present in most'. The former doesn't necessarily imply the latter, but we also don't want to unintentionally suggest that it is implied here. Bakkster Man ( talk) 22:57, 2 June 2021 (UTC)
Re: positive selective pressures on the furin cleavage site, is one of these [3] [4] the paper you were referring to RandomCanadian? The first establishes how crucial the furin site is to pathogenesis, and the second shows via conservation analysis of known sequences that the cleavage sites are all relatively non-mutagenic.-- Shibbolethink ( ♔ ♕) 14:21, 13 June 2021 (UTC)
References
{{
cite journal}}
: Check |doi=
value (
help); External link in |doi=
(
help)
In biology, markov models that describe changes over evolutionary time of the genetic sequence of SARS-CoV-2 are called Substitution models. Its genes are sequence of symbols (RNA has a four nucleotide alphabet) which can used to compute the likelihood of phylogenetic trees using multiple sequence alignment data. When we see the famous estimate of evolutionary distance of SARS-CoV to RatG13 being between 20 and 90 years, that was made by the use of Substitution models. The majority of substitution models used for evolutionary research assume independence among sites (i.e., the probability of observing any specific site pattern is identical regardless of where the site pattern is in the sequence alignment). Wang, Pipes, and Nielsen (2020) observe that the literature has been inconclusive on fully reconstructing the evolutionary history of SARS-CoV-2 because nonsynonimous mutations suggest different conclusion than synonimous mutations. The estimation of synonimous mutations is "complicated" by the skewed distribution of nucleotide frequencies in synonimous sites of SARS-CoV-2. Therefore, I propose we include the fact that SARS-CoV-2 has a skewed distribution of nucleotide frequencies in its synonimous sites. Forich ( talk) 15:40, 6 June 2021 (UTC)
Uh, doesn't § Genome already mention the nucleotide skew? The article text cites Rice et. al. 2021 and Wang et. al. 2020. The sources even discuss host immune targeting of CpG sites and making sure the RNA doesn't form stem loops that stop translation. Rotideypoc41352 ( talk · contribs) 03:36, 8 June 2021 (UTC)
"..some people have recovered from confirmed infections" is quite misleading and might worry some people. Many many people have recovered from confirmed infections especially in developed countries with widespread testing regimes. Galund ( talk) 19:43, 13 June 2021 (UTC)
Talk:Investigations_into_the_origin_of_COVID-19 ( | article | history | links | watch | logs)
Investigations_into_the_origin_of_COVID-19 has an ongoing RFC: "joint WHO-China report" or "WHO-convened report?". A discussion is taking place. If you would like to participate in the discussion, you are invited to add your comments on the discussion page. Thank you. Shibbolethink ( ♔ ♕) 19:25, 25 June 2021 (UTC)
I've advertised this here because the different uses of terms for the report include a section that is transcoded from this article! So please add your input. Thanks! -- Shibbolethink ( ♔ ♕) 19:25, 25 June 2021 (UTC)
FYI, I withdrew this per WP:SNOWBALL. It was overwhelmingly in favor of option B. For more nuance see the withdrawal notice linked above.-- Shibbolethink ( ♔ ♕) 02:06, 30 June 2021 (UTC)
(See Severe_acute_respiratory_syndrome_coronavirus_2#Reservoir_and_origin, starting from "Early in the pandemic, conspiracy theories spread on social media...") In my opinion, conspiracy theories should not even be mentioned here. This conspiracy theory is a social phenomenon and it is irrelevant to the article about a virus (article about pandemic/disease could be a different case). Because it is out of scoupe. Compare it to the article about HIV. AIDS denialism, as well as a theory about AIDS artificial origin (see Operation INFEKTION) are extremely well documented, but still we do not have a word about them in the article about HIV itself. And HIV is a GA, so I suspect that such an approach reflects general consensus. And also "amplified by echo chambers in the American far-right". Who cares about American far-right? There are articles about pandemic in specific countries for it. -- Hwem ( talk) 11:09, 17 June 2021 (UTC)
https://virological.org/t/early-appearance-of-two-distinct-genomic-lineages-of-sars-cov-2-in-different-wuhan-wildlife-markets-suggests-sars-cov-2-has-a-natural-origin/691 Sadly, not yet accepted for publication in a journal, even though a month passed (perhaps more like a working paper than a preprint, IDK). Still being cited however. Ain92 ( talk) 19:27, 18 June 2021 (UTC)
Special:Diff/1029589934 by Coffeeandcrumbs ( talk) leads me to ask if maintaining LDR is worth the effort. Potential transclusion issues aside, people tend to add citation templates inline, as is common, so one of the regulars has to move it into the {{ reflist}}. Also, the template throws an error every time the article stops citing a defined reference. I was just wondering if anything other than precedent stops us from switching to the usual citation style. Rotideypoc41352 ( talk · contribs) 02:24, 21 June 2021 (UTC)
This
edit request to
Severe acute respiratory syndrome coronavirus 2 has been answered. Set the |answered= or |ans= parameter to no to reactivate your request. |
The variants portion should be renamed to "Variants of concern". SARS-CoV-2 has many variants, mostly harmless. Alpha, Beta, Gamma and Delta are variants of concern. 2001:1970:4822:9600:6075:21E8:4598:33B1 ( talk) 05:05, 25 June 2021 (UTC)
{{
edit extended-protected}}
template.
ScottishFinnishRadish (
talk) 10:50, 25 June 2021 (UTC)This
edit request to
Severe acute respiratory syndrome coronavirus 2 has been answered. Set the |answered= or |ans= parameter to no to reactivate your request. |
CHANGE FROM
is not an uncommon occurrence
CHANGE TO
is a common occurrence
BECAUSE
Remove over complex double negative to aid comprehension Missionstatus ( talk) 12:22, 10 July 2021 (UTC)
I'd like to transclude information on this page about virus origins to the new page that's been created, COVID-19 lab leak hypothesis. I don't know if that page will be kept, merged or deleted, but while it exists, we should include what's known in scientific literature about this virus' origins at that page.
Is anyone here willing to help with transclusion of some kind? - Darouet ( talk) 06:17, 19 July 2021 (UTC)
Per my comment above, I've copied text and sources from Severe acute respiratory syndrome coronavirus 2#Reservoir and origin to COVID-19 lab leak hypothesis#Scientific consensus on likely natural zoonosis from bats. I or other editors might copy additional material, and possibly modify it slightly, from this article into that one in order to contextualize the discussion about a possible laboratory origin with strong scientific references. - Darouet ( talk) 11:55, 19 July 2021 (UTC)
You can see the diff of the copying here [27]. - Darouet ( talk) 12:03, 19 July 2021 (UTC)
This
edit request to
Severe acute respiratory syndrome coronavirus 2 has been answered. Set the |answered= or |ans= parameter to no to reactivate your request. |
Dear Colleagues! Please change the outdated image in the Virusbox article for a new, more detailed and scientific one (High quality large image. FP on Commons. Illustrates article well. Published on the N+1 popular science website):
Sources
|
---|
|
Does it have a unique name if we were to have an article just about the spike protein?
There is also a December 2020 paper I would like to see put into context called "The SARS-CoV-2 spike protein disrupts the cooperative function of human cardiac pericytes - endothelial cells through CD147 receptor-mediated signalling: a potential non-infective mechanism of COVID-19 microvascular disease" which can be found at https://www.biorxiv.org/content/10.1101/2020.12.21.423721v1.full
Are there any other concerns about the spike protein besides microvascular disease in cardiac pericytes? WakandaQT ( talk) 09:22, 2 August 2021 (UTC)
I propose to list the cell types that the virus typically infect. So far I was able to find only a couple of sources on that. E.g.: [28] AXONOV (talk) ⚑ 13:36, 3 August 2021 (UTC)
This is an archive of past discussions. Do not edit the contents of this page. If you wish to start a new discussion or revive an old one, please do so on the current talk page. |
Archive 5 | ← | Archive 8 | Archive 9 | Archive 10 | Archive 11 |
The following addition by @ Rotideypoc41352: to the Reservoir and Origin section insinuates a conclusion that is neither supported in nor by the referenced paper:
A phylogenetic network analysis of 160 early coronavirus genomes sampled from December 2019 to February 2020 showed that the virus type most closely related to the bat coronavirus was most abundant in
Guangdong, China, and designated type "A". The predominant type among samples from Wuhan, "B", is more distantly related to the bat coronavirus than the ancestral type "A".
[1]
This implies that Guangdong Province may be considered as an alternative location (to Wuhan) for the initial outbreak, since the "A" cluster is marginally closer to the outgroup, RaTG13. Forster et al., on the other hand, suggest that type "B" exhibits a potential founder effect due to the relative propensity of types "A" and "C" to spread abroad. Note that 17 of the 43 cases of type "A" occur outside of East Asia altogether as opposed to six cases in Guangdong and five cases in Wuhan. All six cases in Guangdong occurred in Shenzhen, as well, which Wikipedia describes as "busiest in China when it comes to border crossings;" one viral lineage traced in the paper even follows a Canadian infected with the type "B" variant who travels to Ottawa from Wuhan via Guangdong Province. Furthermore, only four Guangdong cases make up the ancestral T-allele node that the phylogenetic analysis predicts is equally close to RaTG13 as the ancestral C-allele node made up of three Americans and a Chinese national who was not in Guangdong. Four cases and a median network algorithm do not a substitute for Wuhan make, and Forster et al. never made this claim. This selection should either be rewritten to better represent the source cited or stricken from the article. At the very least, the claims should be qualified and disassociated from Guangdong. Vachaknu ( talk) 10:59, 30 May 2021 (UTC)
References
Continuing discussion here after revert by @ Hemiauchenia:, regarding the following text from the Reservoir and zoonotic origin section, changes emphasized:
All available evidence suggests that SARS‑CoV‑2 has a natural animal origin and is not
genetically engineered. Nevertheless, early in the pandemic, conspiracy theories spread on social media claiming that the virus was
bio-engineered by China at the
Wuhan Institute of Virology. While some scientists, including
David Relman and former CDC director
Robert R. Redfield, believe it is likely that the virus may have been studied by and escaped from the Institute,
[1]
[2] the March 2021 WHO report on the joint WHO-China study stated that such an explanation is "extremely unlikely".
A few topics for discussion:
If a viewpoint is held by a significant minority, then it should be easy to name prominent adherents. I can appreciate that ability to name prominent adherents does not necessarily mean they must be listed by name in the article.
Appreciate your time. Bakkster Man ( talk) 21:17, 29 April 2021 (UTC)
I agree that scientists can be biased, but these scientists are not making biased statements.For clarity, I'm not suggesting these scientists are doing anything wrong. More the 'if all you have is a hammer, every problem looks like a nail' kind of thing. Because of their important work, they may be more likely to lean towards this as the source. It doesn't mean they're wrong, just that they might be more prone to lean this direction. That they
advocate for a transparent and open investigationis exactly what I want as well, and once that new investigation has results we'll cover what it says. Per [[WP:CRYSTALBALL}}: "Although currently accepted scientific paradigms may later be rejected, and hypotheses previously held to be controversial or incorrect sometimes become accepted by the scientific community, it is not the place of Wikipedia to venture such projections." Bakkster Man ( talk) 13:18, 26 May 2021 (UTC)
They state only that the theory should not be dismissed, which I agree with 100%, and have worked to make sure the articles do not do.
In light of social media speculation about possible laboratory manipulation and deliberate and/or accidental release of SARS-CoV-2, Andersen et al. theorize about the virus’ probable origins, emphasizing that the available data argue overwhelmingly against any scientific misconduct or negligence.Bakkster Man ( talk) 13:01, 3 May 2021 (UTC)
Transparency and open scientific investigation will be essential to resolve this issue, noting that forensic evidence of natural escape is currently lacking, and other explanations remain reasonable.. That quote can be paired with what said in his RAI interview:
if you're asking about intent, or whether the virus existed beforehand, it would only be in the records of the Institute of Virology in Wuhan[11], and the more recent open letter which confirms his position [12]. Baric has more papers on coronaviruses published in top-tier journals than any other coronavirolagist, so his expert opinion is very much WP:DUE in this article and related articles. CutePeach ( talk) 00:11, 24 May 2021 (UTC)
I liked the original paragraph posted by Bakkster. An observation to consider is that the premise "some scientists, including David Relman and former CDC director Robert R. Redfield, believe it is likely that the virus may have been studied by and escaped from the Institute" is not negated (not even weakly) by the follow up: "the March 2021 WHO report on the joint WHO-China study stated that such an explanation is extremely unlikely ", because, statistically, having a likely event by expert opinion can coexist with having the same event be extremely unlikely by some other expert opinion. If we wish to illustrate the strength of authority of the experts, then we may like to put less emphasis on the arrived statement of likelihood, and more emphasis on the authority of the source. Or better yet, we could cite a MEDRS that explicitely summarizes the evidence that allowed the WHO to conclude that it was extremely unlikely, so that we are totally transparent. Forich ( talk) 19:56, 30 April 2021 (UTC)
While *minority opinion*, *majority opinion per MEDRS sources*. Bakkster Man ( talk) 20:50, 30 April 2021 (UTC)
Extended content
|
---|
The closest relatives of SARS-CoV-2 from bats and pangolin are evolutionarily distant from SARSCoV-2. There has been speculation regarding the presence of human ACE2 receptor binding and a furin-cleavage site in SARS-CoV-2, but both have been found in animal viruses as well, and elements of the furin-cleavage site are present in RmYN02 and the new Thailand bat SARSr-CoV. There is no record of viruses closely related to SARS-CoV-2 in any laboratory before December 2019, or genomes that in combination could provide a SARS-CoV-2 genome. Regarding accidental culture, prior to December 2019, there is no evidence of circulation of SARS-CoV-2 among people globally and the surveillance programme in place was limited regarding the number of samples processed and therefore the risk of accidental culturing SARS-CoV-2 in the laboratory is extremely low. The three laboratories in Wuhan working with either CoVs diagnostics and/or CoVs isolation and vaccine development all had high quality biosafety level (BSL3 or 4) facilities that were well-managed, with a staff health monitoring programme with no reporting of COVID-19 compatible respiratory illness during the weeks/months prior to December 2019, and no serological evidence of infection in workers through SARS-CoV-2-specific serology-screening. The Wuhan CDC lab which moved on 2nd December 2019 reported no disruptions or incidents caused by the move. They also reported no storage nor laboratory activities on CoVs or other bat viruses preceding the outbreak. |
The difficulty here is the simplest arguments to summarize quickly are the ones based on a lack of relevant data, which is the primary critique of the report. Perhaps I'm just being overly cautious here, but I'd lean towards not trying to summarize. Bakkster Man ( talk) 14:33, 1 May 2021 (UTC)
References
{{
cite journal}}
: |access-date=
requires |url=
(
help); Check |doi=
value (
help); External link in |doi=
(
help)
David Baltimore does not have an MD so it is doubtful that he would be an MD reliable source; however, he could perhaps be used as another proponent, like former CDC director Robert R. Redfield, that SARS-CoV-2 might have a lab origin. Baltimore states: [13]
It is David Baltimore, so I will allow the virology experts on this page to hash out what to make of the article and his quote. -- Guest2625 ( talk) 08:48, 7 May 2021 (UTC)
Remember, ideally we want peer-reciewed published reviews, or certsin types of reports from major medical organizations. Secondary, not primary. Hyperion35 ( talk) 18:55, 8 May 2021 (UTC)
To move the editing along, let's have a straw poll. Which version of the sentence should be included in the article? Either:
Preferences:
I join Forich and Guest2625 in supporting Bakkster Man's proposal to replace the Redfield quote with the Science letter. I agree also to Bakkster Man's four point breakout of the Science letter, but I would add the author's concern that the two predominant theories were not given balanced consideration. Mysticriver1 ( talk) 18:15, 20 May 2021 (UTC)
I propose the following new revised paragraph:
This version of the paragraph adds an extra sentence on the lab thing which is about the right amount of material to include in this article on a non-majority hypothesis. -- Guest2625 ( talk) 08:05, 22 May 2021 (UTC)
Here's another version of the paragraph:
This version includes the statement about the lack of available evidence. With this clause the sentence does have a better transition so perhaps is better. -- Guest2625 ( talk) 09:28, 23 May 2021 (UTC)
The wording of the following paragraph is in dispute:
I think it is fine to live edit the paragraph; however, it might also be beneficial to have a simultaneous conversation here on the talk page. At the moment the paragraph has problems with non-neutral wording, editorializing, and straying from discussing science which is the main theme of this article. Maybe a good way to improve the paragraph is for everyone to provide their ideal version of the paragraph.
I would suggest the following version of the paragraph:
The benefit of this version is that it cuts out most of the politics, the wordiness, and keeps the statement about the lab accident to one sentence and the paragraph very brief. -- Guest2625 ( talk) 09:30, 31 May 2021 (UTC)
Thank you for the feed back. This new version should address the above concerns:
The benefit of this version is that it trims out some more non-science clutter, and then allows the rebuttal sentence of the majority to directly follow. At the moment there is no false equivalence, since the first sentence in the paragraph clearly states that the available evidence indicates a natural origin. And also, the last sentence minimizes the possibility with both the view of the majority of the scientists and the report of the WHO. -- Guest2625 ( talk) 11:34, 31 May 2021 (UTC)
Good point about the statement about geopolitical debate causing confusion. The best thing to do is eliminate it an all non-science commentary and keep that material for the non-science articles on the topic. Here are three new versions. The first with no qualifier as concerns the evidence and the two others making mention:
And
And:
Not quite clear which version is the best. Look forward to hearing other people's feedback and their suggested version of the contested paragraph. -- Guest2625 ( talk) 11:59, 31 May 2021 (UTC)
References
|
---|
References
|
This
edit request to
Severe acute respiratory syndrome coronavirus 2 has been answered. Set the |answered= or |ans= parameter to no to reactivate your request. |
There are currently five list-defined references unused in the article, which is creating an error. 92.24.246.11 ( talk) 12:44, 4 June 2021 (UTC)
The current article strongly supports the zoonotic origin theory, relying on the WHO report to call the lab accident hypothesis "extremely unlikely." Today a new letter came out from 18 scientists published as a letter to the journal of Science calls this evaluation not a "balanced consideration" and that both zoonotic and lab leak remain viable: https://www.reuters.com/business/healthcare-pharmaceuticals/origins-covid-19-need-be-investigated-further-leading-scientists-say-2021-05-14/
Not mentioned in this article, but found elsewhere in places like the Wades article, are serious critiques that the WHO report was tainted by serious conflict of interest.
The article should be updated to reflect a more balanced take and not just rely on the WHO report to call the lab leak "extremely unlikely." When I look at the evidence currently, the lab leak explanation is becoming the more parsimonious explanation. Spudst3r ( talk) 19:42, 14 May 2021 (UTC)
Here's the problem. Saying pmid:33586302 is "from a single scientist from Indonesia" (why does the country matter, hmmm? Does it in some way nullify Hakim's virology expertise? [25]) rather swerves round the facts that:
In short, one of our WP:BESTSOURCES. So implying this is a poor source seems like trying to warp reality to fit an agenda (rather in keeping with the whole lab leak thing). So long as we properly reflect golden sources like this, we are being good editors. Alexbrn ( talk) 12:09, 16 May 2021 (UTC)
long explanation
|
---|
A few years back, my agency decided to make some changes to regulations surrounding opioid (and other substances of abuse) treatment. Now, there is no lack of popular news coverage of the opioid epidemic, but we did not consult that. While it was of great public interest, it simply lacked serious depth, preferring to interview individuals rather than presenting any sort of serious statistical or cost-benefit analyses. What few interviews they had with professionals didn't require them to qualify or quantify their comments or show their work, and they rarely gave any information about whether a given professional's opinions represented a majority view or if they were a lone crank. Individual papers on opioids are a dime a dozen. They range all over the place in quality and findings. I even came across a (non-peer-reviewed) study that purported to show that laws expanding the distribution, possession, and use of naloxone correlated to an increase in opioid deaths (spoiler: it was horribly flawed). You could easily come up with dozens of different and mutually-exclusive proposals based on which individual primary-source paper that you could find. Suboxone? Buprenorphine-only? Methadone? Cold turkey? Do you want to play paper roulette with thousands of lives on the line? We instead looked at reviews published in the relevant journals in the field (ie secondary sources), and had our CMO look over them (which might make it a tertiary source), and this narrowed our approach dramatically, giving us a better idea of what treatment options would lead to the best outcomes, which were first line, second line, contraindications, etc. But that wasn't quite enough, because in a field this complicated you need a better idea of how to translate those findings into clinical practice, and so we consulted with the American Society for Addiction Medicine (ASAM), and consulted with them about their treatment guidelines. They had an excellent scale to allow physicians to classify a patient's addiction level, and recommendations for treatment based on those levels (ie outpatient medication management, short inpatient treatment, intensive inpatient treatment, etc). |
The actual question of a lab leak is not even scientific in nature about the structure/biology of the virus itself, since lab theory proponents primarily point to structural elements of the virus as evidence that its evolution was due to growth in lab culture. And those kinds of claims (for instance, that ACE2 most likely came from culture) absolutely need MEDRS. Bakkster Man ( talk) 20:06, 24 May 2021 (UTC)
BSL-2 lab securitysounds biomedical to me.
Wuhan's lack of proximity to the local bat population or evidence of local infection nearbyboth are biomedical issues.
lack of hospital surveillance logs for the virusThis is literally a claim about a medical facility and medical records.
the timelines for MERS/SARS finding intermediate hosts vs COVIDYou mean virology?
not being able to find the virus after testing 80,000 animalsI mean maybe you could count this as zoology, but seriously now how is viral testing not biomedical?
the article should reflect the fact that the evidence supporting both hypothesis still remain circumstantial -- and let the reader decide by giving an appropriate discussion of the available evidence for the different hypothesisExcept that's not what the sources say. The best sources that we have explicitly say that a lab leak is extremely unlikely, they are clear about a zoonotic spillover event. This is the same special pleading I'd expect to hear from Creationists, the same "teach the controversy" and "let people decide on their own" canards. Hyperion35 ( talk) 01:33, 25 May 2021 (UTC)
"It’s documented that researchers at the Wuhan Institute of Virology were doing gain-of-function experiments designed to make coronaviruses infect human cells and humanized mice. This is exactly the kind of experiment from which a SARS2-like virus could have emerged. The researchers were not vaccinated against the viruses under study, and they were working in the minimal safety conditions of a BSL2 laboratory. So escape of a virus would not be at all surprising. In all of China, the pandemic broke out on the doorstep of the Wuhan institute. The virus was already well adapted to humans, as expected for a virus grown in humanized mice. It possessed an unusual enhancement, a furin cleavage site, which is not possessed by any other known SARS-related beta-coronavirus, and this site included a double arginine codon also unknown among beta-coronaviruses. What more evidence could you want, aside from the presently unobtainable lab records documenting SARS2’s creation?
Proponents of natural emergence have a rather harder story to tell. The plausibility of their case rests on a single surmise, the expected parallel between the emergence of SARS2 and that of SARS1 and MERS. But none of the evidence expected in support of such a parallel history has yet emerged. No one has found the bat population that was the source of SARS2, if indeed it ever infected bats. No intermediate host has presented itself, despite an intensive search by Chinese authorities that included the testing of 80,000 animals. There is no evidence of the virus making multiple independent jumps from its intermediate host to people, as both the SARS1 and MERS viruses did. There is no evidence from hospital surveillance records of the epidemic gathering strength in the population as the virus evolved. There is no explanation of why a natural epidemic should break out in Wuhan and nowhere else. There is no good explanation of how the virus acquired its furin cleavage site, which no other SARS-related beta-coronavirus possesses, nor why the site is composed of human-preferred codons. The natural emergence theory battles a bristling array of implausibilities." [1] Spudst3r ( talk) 20:15, 7 June 2021 (UTC)
The following discussion is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.
There is now considerable evidence beyond right wing bullshit. I would encourage people to read https://thebulletin.org/2021/05/the-origin-of-covid-did-people-or-nature-open-pandoras-box-at-wuhan/ (There are other sources)
The WHO team that investigated had Peter Daszak on it, who was the person that oversaw the US grant that funded the lab. It is the international virology community that is being accused here, not just Wuhan.
The section in this article is extremely POV, saying about five times that they think it had a natural origin. It needs balance.
No natural precursor has been found. The lab was studying gain-of-function Corono viruses. And China has censored the data. This needs to be said.
Look beyond your political biases. Just because Trump is an idiot does not mean he is always wrong -- even a stopped clock is correct twice a day. Tuntable ( talk) 06:39, 2 June 2021 (UTC)
No natural precursor*inhales* Bruh. brUH?? The bat coronaviruses? SARS-CoV-1? Literally the many coronaviruses out there we haven't even found yet? This is not the first time a virus has jumped species, nor will this be the last. It happens all the time! Friend. Friend. A virus does not need a GoF lab to be dangerous. Rotideypoc41352 ( talk · contribs) 12:32, 2 June 2021 (UTC)
That above would certainly lead to strong suspicion about the lab. There are technical bits a well, but that is enough for now.
Maybe Wade is full of shit. But he is widely read and quoted. He deserves to be heard even if only to have his arguments properly debunked.
There are certainly other very credible authors that have doubts https://science.sciencemag.org/content/372/6543/694.1
The anger and censorship above only adds wait to the idea that Wade is correct. The section in the article reads like propaganda, vs Wade's sober writing. I also presume that some (not all) of the editors of this article are Chinese government employees. Tuntable ( talk) 03:18, 3 June 2021 (UTC)
some (not all) of the editors of this article are Chinese government employeesmakes people less likely to believe you are here to build consensus and more likely to just let WP:GS/COVID19 run its course. Not anger (ran out long ago), not "censorship" (this is a private website), just sober writing. Rotideypoc41352 ( talk · contribs) 18:28, 3 June 2021 (UTC)
"My citation is better than your citation" does not cut it. Wade is a respected journalist and he certainly does not read like he is blatantly lying. If he was then that would be of interest. Neither you nor the article have addressed even one of the points Wade made. Maybe Wade is wrong, I came to this article to find out. But there is no real content other than that the some people (including virologists) are passionate about not discussing the Wuhan case, and quick to censor any mention of it, or even to include a citation. That strongly suggests that Wade is correct, and I suspect that this will come out over the next few months. Tuntable ( talk) 03:32, 5 June 2021 (UTC)
I suspect that this will come out over the next few months.Entirely possible, but also not our job to try and predict. WP:CRYSTAL Bakkster Man ( talk) 13:49, 5 June 2021 (UTC)
And thank you for the Gorski paper. However, it does not address Wade's points directly. And it reads like an angry rant while Wade reads like a considered analysis of the facts. I think it is patently obvious that just given the points that I pulled from Wade above that the WIV is definitely a possible source, and it would be very difficult to disprove that given the records are sealed. But I would like more information on the technical arguments, the closeness to RaTG13, the codons used in the Furin cleavage site. But I don't see anything in either this article. The fact that it might have arisen naturally certainly does not prove that the WIV is innocent. Tuntable ( talk) 03:41, 5 June 2021 (UTC)
I might add that the Gorski paper mischaracterizes the Furin argument, which was that it uses human codons. It also mischaracterizes the RaTG13 argument, which is that the SARS-CoV-19 virus is almost identical to RaTG13 for most of it, except for the spike protein, suggesting that that RaTG13 was used as a backbone, and the spike stuff added. If there is a good paper that realistically refutes Wade, I have not seen it.
Tuntable ( talk) 04:14, 5 June 2021 (UTC)
Even Biden suggesting it is plausible enough to require an investigation. It does not matter whether it is true or not. It does not matter who are the most eminent references. It needs to be properly addressed because it is now widespread. People will come to Wikipedia to determine whether it is true.
Having read the article, and the the talk, I still do not have any clear idea why the lab leak hypothesis is considered to be complete nonsense. I understand that many eminent people have said so, and that some of the technical arguments for the lab leak may be dubious. But I have not seen anywhere any proof that it is not possible.
To address it requires summarizing the case for and against. Many people (including myself) are much more interested in rational arguments than authoritative ones. To address the "conspiracy" the arguments put forth by the conspirators need to be stated clearly and succinctly, and then facts provided by eminent sources used to debunk them. Rather than agonizing on about a generic paragraph that gives appropriate weight, provide the facts and let the reader decide.
Personally, it appears obvious that the labs are suspicious because of geography, the lack of animal or human precursors, the fact that the WIV was doing gain-of-function research on coronoviruses at the time, and the fact that the Chinese government has closed access to relevant records, and that nobody has ever said that such a chimera could not, in theory, be created. That seems more than enough to make the conspiracy very plausible.
As @ SSSheridan: points out, this consensus has changed recently, although I think there have always been substantial doubts. As @ Eccekevin: points out, the WHO is a important but not infallible source. As @ Spudst3r: points out, the discussion is not just scientific, but operational, as humanized mice could be the animal intermediatory. Certainly the Ebright concerns raised by @ CutePeach: should be mentioned. The technical details for and against would make a very interesting article, as @ Elle Kpyros: has suggested.
BTW. Do any of the eminent references provide evidence that the intermediatory could not be humanize mice? That would be interesting to know.
Incidentally, the WHO report said "There is no record of viruses closely related to SARS-CoV-2 in any laboratory before December 2019," -- What about RaTG13? Also, did the WHO team actually study the WIV in any detail? And did the team include people closely associated with the WIV (like Peter Daszak)? Tuntable ( talk) 07:16, 6 June 2021 (UTC)
As @ Eccekevin: points out, the WHO is a important but not infallible source.While I agree, you need to provide some kind of reliable, scholarly source making a contrary claim. If the WHO makes one claim, consistent with a bunch of other high quality papers, and the best we can find making a link to humanized mice is a non-MEDLINE article from a single non-virologist, then even if we cite such a paper it would indicate its WP:FRINGE/ALT status by being stuck in a less prestigious journal by a non-expert. If it's a clear issue, it's an easy fix. So provide the links. Though I'll warn, they probably would need to go in the Investigations article (where there's a good argument MEDRS doesn't apply) rather than here (where there's a good argument MEDRS does apply).
Do any of the eminent references provide evidence that the intermediatory could not be humanize mice? That would be interesting to know.To reiterate, unless we have a reliable source that suggests they could be the intermediary, why would we cite a source source saying a thing wasn't possible. We'd have a hella long article if we had to list and cite every possibility that was ruled out that nobody suggested should be considered in the first place. Sure, we ruled out a meteor, but did we rule out a comet? What about Martians? Titans? Alpha Centaurans?
This supports the hypothesis that the PCS/furin cleavage site was gained by a recombination event(s) involving these virus sequences. This notion is important in considering possible zoonotic events, placing laboratory events in the realm of the highly possibleis uncited, making it a primary claim rather than a review of the existing literature. Maybe I've missed it in the citations (if so, please point me to it, this source seems the closest to directly applicable), but the paper doesn't directly cite it.
It is not just "My" original research. It is quite widely quoted, and has prompted an inquiry by the US President. That does not make it correct, but it certainly makes it notable.
I believe that this should be covered here, but I will add a reference to the other article, of which I was unaware. I expect you to instantly revert it for some obscure reason. But the other article does not cover the issues either. So we can continue the discussion there. Tuntable ( talk) 01:16, 7 June 2021 (UTC)
When available, academic and peer-reviewed publications, scholarly monographs, and textbooks are usually the most reliable sources.-- Hob Gadling ( talk) 17:00, 8 June 2021 (UTC)
Ideas that are of borderline or minimal notability may be mentioned in Wikipedia, but should not be given undue weight... Wikipedia is not a place to right great wrongs. Fringe theories may be excluded from articles about scientific topics when the scientific community has ignored the ideas. However, ideas should not be excluded from the encyclopedia simply because they are widely held to be wrong.Bakkster Man ( talk) 17:46, 8 June 2021 (UTC)
The article says: SARS‑CoV‑2 is unique among known betacoronaviruses in its incorporation of a polybasic site cleaved by furin
. Is this correct? I've read that FCS is common among coronaviruses and uncommon on Sarbecoviruses. I don't know how it stands among betacoronaviruses. Can we get this claim fact-checked?
Forich (
talk) 21:02, 31 May 2021 (UTC)
Another specific genomic feature of SARS-CoV-2 is the insertion of four amino acid residues (PRRA) at the junction of subunits S1 and S2 of the S protein26 (Fig. 3a). This insertion generates a polybasic cleavage site (RRAR), which enables effective cleavage by furin and other proteases. Such an S1–S2 cleavage site is not observed in all related viruses belonging to the subgenus Sarbecovirus, except for a similar three amino acid insertion (PAA) in RmYN02, a bat-derived coronavirus newly reported from Rhinolophus malayanus in China.
It contains two subunits S1 and S2 with a polybasic site PRRA at the junction, which enables effective cleavage by furin and other proteases [5]. This multibasic cleavage site appears to be an important virulence factor which may enhance virus replication and multiple tissue tropism as in the case of avian influenza A(H5N1) virus [20, 21]. Mutations in this site can attenuate pathogenicity in animal models and may be an attractive option for designing live attenuated vaccines [21].
Nice work @
RandomCanadian:. This is the current information: A distinguishing feature of SARS‑CoV‑2 is its incorporation of a polybasic site cleaved by furin, which appears to be an important element enhancing its virulence. Although such sites are a common naturally-occurring feature of other viruses, including members of the Beta-CoV genus and other genera of coronaviruses, SARS-Cov-2 is unique among members of its subgenus for such a site.
. Please compare with this phrase from the WHO report (p. 83) in order to assess whether there is room for improvement (i.e. the WHO report says that most Betacoronaviruses do not have the FCS which is more informative than saying that in members of betacoronvairuses FCS sites at the S1/S2 junction occur naturally): This furin-cleavage site is not present in most other betacoronaviruses (for instance, SARS-CoV)
.
Forich (
talk) 22:28, 2 June 2021 (UTC)
Furthermore, SARS-CoV-2 has a unique furin cleavage site insertion (PRRA) not found in any other CoVs in the Sarbecovirus group (fig. S3), although similar motifs are also found in MERS and more divergent bat CoVs. This PRRA motif makes the S1/S2 cleavage in SARS-CoV-2 much more efficient than in SARS-CoV and may expand its tropism and/or enhance its transmissibility. A recent study of bat CoVs in Yunnan, China, identified a three–amino acid insertion (PAA) at the same site. Although it is not known whether this PAA motif can function similar to the PRRA motif, the presence of a similar insertion at the same site indicates that such insertion may already be present in the wild bat CoVs. The more efficient cleavage of S1 and S2 subunits of the S glycoprotein and efficient binding to ACE2 by SARS-CoV-2 may have allowed SARS-CoV-2 to jump to humans, leading to the rapid spread of SARS-CoV-2 in China and the rest of the world.Best not to dive too deeply into details, but I agree we want to get it right. It seems the gap is between 'commonly occurring' and 'present in most'. The former doesn't necessarily imply the latter, but we also don't want to unintentionally suggest that it is implied here. Bakkster Man ( talk) 22:57, 2 June 2021 (UTC)
Re: positive selective pressures on the furin cleavage site, is one of these [3] [4] the paper you were referring to RandomCanadian? The first establishes how crucial the furin site is to pathogenesis, and the second shows via conservation analysis of known sequences that the cleavage sites are all relatively non-mutagenic.-- Shibbolethink ( ♔ ♕) 14:21, 13 June 2021 (UTC)
References
{{
cite journal}}
: Check |doi=
value (
help); External link in |doi=
(
help)
In biology, markov models that describe changes over evolutionary time of the genetic sequence of SARS-CoV-2 are called Substitution models. Its genes are sequence of symbols (RNA has a four nucleotide alphabet) which can used to compute the likelihood of phylogenetic trees using multiple sequence alignment data. When we see the famous estimate of evolutionary distance of SARS-CoV to RatG13 being between 20 and 90 years, that was made by the use of Substitution models. The majority of substitution models used for evolutionary research assume independence among sites (i.e., the probability of observing any specific site pattern is identical regardless of where the site pattern is in the sequence alignment). Wang, Pipes, and Nielsen (2020) observe that the literature has been inconclusive on fully reconstructing the evolutionary history of SARS-CoV-2 because nonsynonimous mutations suggest different conclusion than synonimous mutations. The estimation of synonimous mutations is "complicated" by the skewed distribution of nucleotide frequencies in synonimous sites of SARS-CoV-2. Therefore, I propose we include the fact that SARS-CoV-2 has a skewed distribution of nucleotide frequencies in its synonimous sites. Forich ( talk) 15:40, 6 June 2021 (UTC)
Uh, doesn't § Genome already mention the nucleotide skew? The article text cites Rice et. al. 2021 and Wang et. al. 2020. The sources even discuss host immune targeting of CpG sites and making sure the RNA doesn't form stem loops that stop translation. Rotideypoc41352 ( talk · contribs) 03:36, 8 June 2021 (UTC)
"..some people have recovered from confirmed infections" is quite misleading and might worry some people. Many many people have recovered from confirmed infections especially in developed countries with widespread testing regimes. Galund ( talk) 19:43, 13 June 2021 (UTC)
Talk:Investigations_into_the_origin_of_COVID-19 ( | article | history | links | watch | logs)
Investigations_into_the_origin_of_COVID-19 has an ongoing RFC: "joint WHO-China report" or "WHO-convened report?". A discussion is taking place. If you would like to participate in the discussion, you are invited to add your comments on the discussion page. Thank you. Shibbolethink ( ♔ ♕) 19:25, 25 June 2021 (UTC)
I've advertised this here because the different uses of terms for the report include a section that is transcoded from this article! So please add your input. Thanks! -- Shibbolethink ( ♔ ♕) 19:25, 25 June 2021 (UTC)
FYI, I withdrew this per WP:SNOWBALL. It was overwhelmingly in favor of option B. For more nuance see the withdrawal notice linked above.-- Shibbolethink ( ♔ ♕) 02:06, 30 June 2021 (UTC)
(See Severe_acute_respiratory_syndrome_coronavirus_2#Reservoir_and_origin, starting from "Early in the pandemic, conspiracy theories spread on social media...") In my opinion, conspiracy theories should not even be mentioned here. This conspiracy theory is a social phenomenon and it is irrelevant to the article about a virus (article about pandemic/disease could be a different case). Because it is out of scoupe. Compare it to the article about HIV. AIDS denialism, as well as a theory about AIDS artificial origin (see Operation INFEKTION) are extremely well documented, but still we do not have a word about them in the article about HIV itself. And HIV is a GA, so I suspect that such an approach reflects general consensus. And also "amplified by echo chambers in the American far-right". Who cares about American far-right? There are articles about pandemic in specific countries for it. -- Hwem ( talk) 11:09, 17 June 2021 (UTC)
https://virological.org/t/early-appearance-of-two-distinct-genomic-lineages-of-sars-cov-2-in-different-wuhan-wildlife-markets-suggests-sars-cov-2-has-a-natural-origin/691 Sadly, not yet accepted for publication in a journal, even though a month passed (perhaps more like a working paper than a preprint, IDK). Still being cited however. Ain92 ( talk) 19:27, 18 June 2021 (UTC)
Special:Diff/1029589934 by Coffeeandcrumbs ( talk) leads me to ask if maintaining LDR is worth the effort. Potential transclusion issues aside, people tend to add citation templates inline, as is common, so one of the regulars has to move it into the {{ reflist}}. Also, the template throws an error every time the article stops citing a defined reference. I was just wondering if anything other than precedent stops us from switching to the usual citation style. Rotideypoc41352 ( talk · contribs) 02:24, 21 June 2021 (UTC)
This
edit request to
Severe acute respiratory syndrome coronavirus 2 has been answered. Set the |answered= or |ans= parameter to no to reactivate your request. |
The variants portion should be renamed to "Variants of concern". SARS-CoV-2 has many variants, mostly harmless. Alpha, Beta, Gamma and Delta are variants of concern. 2001:1970:4822:9600:6075:21E8:4598:33B1 ( talk) 05:05, 25 June 2021 (UTC)
{{
edit extended-protected}}
template.
ScottishFinnishRadish (
talk) 10:50, 25 June 2021 (UTC)This
edit request to
Severe acute respiratory syndrome coronavirus 2 has been answered. Set the |answered= or |ans= parameter to no to reactivate your request. |
CHANGE FROM
is not an uncommon occurrence
CHANGE TO
is a common occurrence
BECAUSE
Remove over complex double negative to aid comprehension Missionstatus ( talk) 12:22, 10 July 2021 (UTC)
I'd like to transclude information on this page about virus origins to the new page that's been created, COVID-19 lab leak hypothesis. I don't know if that page will be kept, merged or deleted, but while it exists, we should include what's known in scientific literature about this virus' origins at that page.
Is anyone here willing to help with transclusion of some kind? - Darouet ( talk) 06:17, 19 July 2021 (UTC)
Per my comment above, I've copied text and sources from Severe acute respiratory syndrome coronavirus 2#Reservoir and origin to COVID-19 lab leak hypothesis#Scientific consensus on likely natural zoonosis from bats. I or other editors might copy additional material, and possibly modify it slightly, from this article into that one in order to contextualize the discussion about a possible laboratory origin with strong scientific references. - Darouet ( talk) 11:55, 19 July 2021 (UTC)
You can see the diff of the copying here [27]. - Darouet ( talk) 12:03, 19 July 2021 (UTC)
This
edit request to
Severe acute respiratory syndrome coronavirus 2 has been answered. Set the |answered= or |ans= parameter to no to reactivate your request. |
Dear Colleagues! Please change the outdated image in the Virusbox article for a new, more detailed and scientific one (High quality large image. FP on Commons. Illustrates article well. Published on the N+1 popular science website):
Sources
|
---|
|
Does it have a unique name if we were to have an article just about the spike protein?
There is also a December 2020 paper I would like to see put into context called "The SARS-CoV-2 spike protein disrupts the cooperative function of human cardiac pericytes - endothelial cells through CD147 receptor-mediated signalling: a potential non-infective mechanism of COVID-19 microvascular disease" which can be found at https://www.biorxiv.org/content/10.1101/2020.12.21.423721v1.full
Are there any other concerns about the spike protein besides microvascular disease in cardiac pericytes? WakandaQT ( talk) 09:22, 2 August 2021 (UTC)
I propose to list the cell types that the virus typically infect. So far I was able to find only a couple of sources on that. E.g.: [28] AXONOV (talk) ⚑ 13:36, 3 August 2021 (UTC)