Talk:SARS-CoV-2

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01. There is consensus that the terms "Wuhan virus" or "China virus" should not be used in the Lead of the article. The terms and their history can be discussed in the body of the article. (April 2020)

Erroneous statement of similarity to feline coronavirus

In the "Phylogenetics and taxonomy" section, the claim is made: "The furin cleavage site PRRAR↓ is identical to that of the feline coronavirus, an alphacoronavirus 1 strain." However, the source cited for this statement contradicts this claim. According to the source, there are two variants of feline coronavirus. FECV, which is milder, and FIPV which can be fatal, and that the mild variant has an optimized furin cleavage site, whereas the severe variant has a mutated or even missing furin cleavage site:

For example, the feline enteric coronavirus (FECV), responsible for a milder and localized form of enteric infection in the infected cat, carried a highly optimized furin cleavage site at S1/S2. In contrast, in the spike protein of the feline infectious peritonitis virus (FIPV), that caused systemic infection and death of the infected cat, the polybasic insert was either completely lost or found mutated.

It goes on to state that the mild form (FECV) has a furin cleavage site with the sequence RRARR↓ (note that this does not match the sequence PRRAR↓ which the Wikipedia article claims is identical):

The presence of a furin cleavage site RRARR↓S in the feline spike protein of the less infectious strain FECV and the presence of PRRAR↓S in the SARS-CoV-2 prompted us to analyse the sequences more carefully.

It also states that of the two feline coronavirus variants, SARS-CoV-2's cleavage site is more similar to the mild variant's site (which as shown above does not have an identical furin cleavage site):

Thus the polybasic insert of CoV-2 spike protein is closer to that of the spike protein of the milder feline coronavirus but carries crucial substitutions that are either uncommon or are disfavored in classical Furin substrates.

This clearly shows that the cited paper does not support the claim made in this article that the PRRAR↓ furin cleavage site present in SARS-CoV-2 is identical to the furin cleavage site in the feline coronavirus. It even appears that not only is the claim not supported by that source, but that the claim may even be incorrect (according to the statements from the source). Moulding (talk) 21:11, 31 January 2023 (UTC)

Why don't we just say "nearly identical" since it's only one proline off? And other source say they're very similar: [1] [2]

Indeed, the second source there says: For instance, a similar P-R-R-A-R motif in the spike of a feline CoV has been observed to be encoded with a CGG-CGA for the double Arginine (Bank-Wolf et al. 2014). In this case, a single mutation could change the CGG-CGA to a CGG-CGG. — Shibbolethink ^{(♔ ♕)} 21:54, 31 January 2023 (UTC)

The second source refers only to the general PRRAR motif found in some FIPV sequences, not the entire cleavage sequece. As can be seen in the original source graphic, the entire cleavage sequence that matched that motif in FIPV was PRRARM↓S, which still is not identical to PRRAR↓S. It also shows that the consensus sequence appears to be SRRSRR↓S (which is not at all similar to SARS-CoV-2's sequence, and it may be misleading for this Wikipedia article to suggest otherwise).

Original source graphic: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3713968/figure/F2/ Moulding (talk) 23:06, 31 January 2023 (UTC)

I'm just gonna change the text to be "highly similar" to, since they are quite similar in the sense of BLOSUM similarity. — Shibbolethink ^{(♔ ♕)} 01:57, 1 February 2023 (UTC)

Airborne

I changed the lead to clarify that SARS-CoV-2 is airborne. Sparkie82 (t•c) 23:46, 22 February 2023 (UTC)

Origin update?...

From the article's intro: "Available evidence indicates that it is most likely of zoonotic origin and has close genetic similarity to bat coronaviruses, suggesting it emerged from a bat-borne virus."

The citation provided there though (#18) is dated 2020, when the pandemic was still quite new, and our understanding of the virus and its origins were much more limited. We now have US government agencies, like the Energy Dept in the recent report, saying that a lab leak origin is more likely. So I would suggest that this part of the intro be updated, rewritten, and much newer citations used. -2003:CA:871C:D28:77AA:E11E:9B4:E4E6 (talk) 11:32, 28 February 2023 (UTC)

See: COVID-19 lab leak theory and Investigations into the origin of COVID-19 where this discussion is more appropriately placed. I'll bring the consensus wording from those pages. — Shibbolethink ^{(♔ ♕)} 13:28, 28 February 2023 (UTC)

In close to 50 years, the origin of Ebola still haven't been found. And note that DOE seems to have low confidence in their claim. Not to mention to 200 million farms in China. Gah4 (talk) 04:02, 1 March 2023 (UTC)

Early origin

Found a review of early detections, including viral DNA from a skin sample in Italy November 12, 2019. https://gh.bmj.com/content/7/3/e008386.long Sennalen (talk) 21:27, 5 March 2023 (UTC)

The authors themselves describe how much false positives likely impacted these results:

laboratory evidence for early circulation is often dismissed and labelled as a result of false-positive testing. Antibody detection results can indeed be affected by the presence in sera of antibodies which, although able to recognise SARS-CoV-2 antigens, were induced by other agents.12 However, the presence of SARS-CoV-2 neutralising activity in these sera and the fact that several patients presented more than one class of antibodies recognising SARS-CoV-2 suggest that, although some cross-reactivity should be taken into account, at least some of the sera could contain antibodies induced by a prior SARS-CoV-2 infection... PCR-based methods are highly sensitive and, therefore, more prone to false-positive results.

So yes, it's certainly possible these are real, but they are also very far from proven. The sequencing data does also predict an emergence into humans in late October/early November based on mutation rates: [3][4][5] — Shibbolethink ^{(♔ ♕)} 22:38, 5 March 2023 (UTC)

That's one mode of testing. Evidence was found in sera antibodies and RNA skin samples from November and sewage two weeks later. There were no positives in June-August. It's not an isolated false positive, but a body of evidence consistent with the same timeline. Sennalen (talk) 23:28, 5 March 2023 (UTC)

@Shibbolethink: No real harm in reastating it, but the part you added wasn't missing. Sennalen (talk) 20:50, 10 March 2023 (UTC)

I think wikipedia policy makes it clear that we should always put mainstream criticisms of things next to their mention whenever possible, and not separate them so as to de-emphasize or isolate criticism. That's why I made the edit I did, even if I do think the addition is a good one to the article. I think it should probably be integrated more with that paragraph, though, as it currently reads weird wrt the later sentences about December of 2019... Given that most sources place the beginning of the pandemic in late November, early December. I am happy to help fix it but I also think you are well-equipped to do so — Shibbolethink ^{(♔ ♕)} 20:55, 10 March 2023 (UTC)

Not sure what you're asking for Sennalen (talk) 00:12, 11 March 2023 (UTC)

small correction

Pardon the newb comment but I’m used to making small edits as I read Wikipedia articles, but it looks like this article isn’t editable to me.

In Origins it says “… published on Nature …”, should be “in”. Hambolger (talk) 14:57, 9 March 2023 (UTC)

 Done thanks for the help — Shibbolethink ^{(♔ ♕)} 15:07, 9 March 2023 (UTC)

Edit request: Addition of {{Update section}} template to variants section

Please add "{{Update section|date=April 2023}}" after "{{Main|Variants of SARS-CoV-2}}"

Why? The variants section is very much out of date. The statement "Nextstrain divides the variants into five clades (19A, 19B, 20A, 20B, and 20C), while GISAID divides them into seven (L, O, V, S, G, GH, and GR)." is out of date since at least March 2021 when there were already new GISAID clades GV and GRV, see https://gisaid.org/resources/statements-clarifications/clade-and-lineage-nomenclature-aids-in-genomic-epidemiology-of-active-hcov-19-viruses/ AncientWalrus (talk) 20:14, 24 April 2023 (UTC)

 Done Actualcpscm (talk) 20:39, 24 April 2023 (UTC)

Lab leak theory

The fact that this page doesn’t even mention the possibility that the virus originated in a lab is baffling, given that there are a number of credible experts who have stated it is plausible, not to mention the U.S. intelligence agencies who’ve concluded it’s probable. The complete omission of this viewpoint calls into question the neutrality and objectivity of the entire article. 68.12.22.29 (talk) 04:11, 26 April 2023 (UTC)