Talk:Zoonotic origins of COVID-19

Page created

A page dedicated to zoonotic theories seemed neccessary to give attention to the full breadth and depth of the subject. This aims at a deeper level of detail, which more general articles like SARS-CoV-2 and Origin of Covid-19 can refer to in WP:SUMMARY style. This should especially be an improvement on the situation where the COVID-19 lab leak theory is the only article with scope to discuss the evidence for zoonosis in detail. This article is carried almost entirely by scientific peer-reviewed journals. Significant non-scientific viewpoints have been raised in a brief addendum. This contrasts with most other articles in the topic area, where WP:MEDPOP and even less qualified sources have been relied on for core facts and framing. I hope that this article will serve as a positive example for good practices around WP:NPOV, WP:MEDASSESS, and WP:DESCF throughout the COVID-19 topic area and open scientific questions in general. Sennalen (talk) 18:24, 26 November 2023 (UTC)

CFORK or POVFORK?

This article does not look to me to be a properly executed WP:CFORK and instead seems to be closer to a WP:POVFORK. I encourage discussion of the issues outlined here and at the relevant thread on WP:FTN to address this matter. I will refrain from posting AfD until this is worked out, but that is another option, of course. jps (talk) 16:07, 27 November 2023 (UTC)

This is a WP:DETAIL companion to Origin of Covid-19. There is long-standing precedent for this kind of treatment, in the form of the parallel page: COVID-19 lab leak theory. It is not appropriate for a minority view to have a detailed treatment and the majority view not to. A link and summary should be integrated into the parent page, following WP:SUMMARY style. Per WP:SYNC it is appropriate to add material at child articles before parent articles. It is not a POV fork, because it is written from a neutral point of view and does not deviate in any significant way from the views described in the parent page. The parent article text should be updated in due course with extracts from this, more detailed and up-to-date, treatment. Sennalen (talk) 18:46, 27 November 2023 (UTC)

If you think that COVID-19 lab leak theory is a "parallel" page, I think you need to clarify. That page is one that talks about a set of distinct minority reports and conspiracy theories about the origin of COVID-19. This page is about how COVID-19 formed in animals. There is not a strong comparison to be made between the two, in my estimation.

I think what you are missing is the WP:SPINOUT approach. In the instance where information is not present in higher-level articles, it is often better to start there lest you run into POV-fork situations. Given some of the rhetorical approaches you are proposing here, I would argue that you are minimally at risk of running into this problem which is why merging back may be better. We can always spin-out later.

jps (talk) 19:26, 27 November 2023 (UTC)

That's a method for dealing with an existing article with a length or due weight problem, but it's not a mandatory process for article creation. We could bulk copy this article into the middle of a different article to create the problems that necessitate SPINOUT, but it would be less trouble to address your concerns about rhetorical approach in situ. Sennalen (talk) 19:41, 27 November 2023 (UTC)

Nothing is mandatory at Wikipedia. I'm not saying that your approach is wrong. I'm saying it may run into problems. You are free to do with that information what you will. jps (talk) 20:07, 27 November 2023 (UTC)

I support a merge. Origins of COVID-19 has a weight issue, because it gives more space to lab theories, and mainly focuses on a side issue (investigations). And in terms of WP:FRINGE, even a CFORK should be avoided; the majority view (zoonosis) belongs in the main article, not its own article. A merge would fix both of these. DFlhb (talk) 13:53, 28 November 2023 (UTC)

Merge. A blatant WP:POVFORK, even in its title which implies zoonotic origin is a fact. That alone needs to be changed to something like 'Zoonotic origin of COVID-19 theory', given that both zoonotic and lab leak currently remain propositions, with high-level scientific support on both sides – as the instigator would well know. Gold stamp for sheer rhinoceros brazenness and investment of energy though! MisterWizzy (talk) 04:13, 29 November 2023 (UTC)

@MisterWizzy: As a point of fact, the original title was "COVID-19 zoonosis theories". It was changed unilaterally by jps, who was also the one who requested the merge. Sennalen (talk) 05:49, 29 November 2023 (UTC)

• Merge as an obvious WP:POVFORK of Origin of COVID-19; no credible reason has been presented why this would require a separate article. --Aquillion (talk) 07:07, 29 November 2023 (UTC)

  The heart of the article is the molecular details in "processes of host adaptation". That would be overweighted in the parent and need to be spun out again. Going through the motions would be a waste of everyone's time, but not the worst thing that could happen I guess. Merging would give an opportunity to replace a lot of outdated and news RS sources in the parent with up-to-date journal articles given here. Sennalen (talk) 07:12, 29 November 2023 (UTC)

  Once the primary research has been filleted-out, there might not be much left. But I'm leaning merge for what is. Bon courage (talk) 07:34, 29 November 2023 (UTC)

• Since mass deletions have fatally compromised the coherency of the article, and it is clear that no relief from disruption is coming, the best fate for this is merging into the parent. Maybe in the future a repaired version can be spun out again. Sennalen (talk) 15:59, 30 November 2023 (UTC)

• Merge per the above and Wikipedia:Fringe theories/Noticeboard#COVID origin again. I see no reason not to proceed with the merge since we're clearly looking at a WP:POVFORK here. Generalrelative (talk) 05:59, 19 December 2023 (UTC)
• If a merge is executed, what section(s) will be salvaged, and who will do the merging? If there are not good answers to these questions, perhaps a WP:BLAR should be considered. –Novem Linguae (talk) 07:04, 19 December 2023 (UTC)

  I think some further fettling of the content is needed here (stripping improper primary sources, mainly), and then what's left can form the basis for the merge. A complication is the different ref formats, which will be tedious to reconcile. I might try and write a script ... Bon courage (talk) 07:09, 19 December 2023 (UTC)

Articles for Deletion

This article has been nominated at Articles for Deletion. Interested editors may participate at Wikipedia:Articles for deletion/Zoonotic origins of COVID-19. TarnishedPath^talk 09:20, 9 March 2024 (UTC)

First sentences

I'm open to revisions, but there are two considerations that should take overriding priority:

1. MOS:FIRST should be followed.
2. The origin of Covid-19 is unknown. A scientific consensus about what is likely, plausible, or parsimonious is not sufficient to say that something is the origin in wikivoice without qualifiers.

Sennalen (talk) 20:03, 27 November 2023 (UTC)

A blanket declaration like (2) is essentially an antiscience, post-modernist POV that, like, nothing can really ever be known, dude. That more-or-less matches a WP:PROFRINGE POV. Is that your intention? Because, for example, we know a lot of facts about the origin of COVID-19, so it is manifestly false to say its "origin" (inasmuch as one can identify "origin" as a precise term) is "unknown". jps (talk) 20:06, 27 November 2023 (UTC)

This is not an abstract debate about the philosophy of science. WP:STICKTOSOURCE There is particular evidence that most people would accept as conclusive proof - namely, an ancestral sequence and/or an infected animal. To date those have not been found, and they may never be found. It is not mandatory that the answer to any question becomes known after a certain amount of effort has been expended on answering it. The language of best sources - like those cited here - is that the origin is believed, suspected, likely, etc., but many of them also say explicity, "unknown." Sennalen (talk) 20:16, 27 November 2023 (UTC)

Footnotes with direct quotes from sources saying precisely these things were on the version prior to your edits in anticipation of precisely this argument.[1] Sennalen (talk) 20:20, 27 November 2023 (UTC)

The arguments you are making categorically do not even comport with the reliable sources you are pretending to represent. There is no source which says anything like (2). jps (talk) 23:59, 27 November 2023 (UTC)

Just looking at the first source that was removed, the quote is: "the proximal phylogenetic origin of SARS-CoV-2 and its mode of introduction into human circulation remain unclear".

Surely that supports "(2) The origin of Covid-19 is unknown".

I haven't looked at the other sources. - Palpable (talk) 01:35, 28 November 2023 (UTC)

"Unclear proximal phylogenetic origin" is not a synonym for "unknown origin". Specificity matters. We aren't here to play creationist-like games of complaining about missing links. We have the general outline of the origin story for this virus. We may not know patient zero and whether there were intermediaries, but we do know a lot about the origin of this virus. To pretend otherwise is fairly close to farcical at this point. jps (talk) 17:02, 28 November 2023 (UTC)

I went back through the papers cited here and looked for anything that looked like a summary statement about the origin of the virus. Several did not, particularly those with a molecular focus. News sources were not included.

There are four sources that describe it as flat out unknown. Five say it "likely" came from animals, or with similar qualifiers. Seven give no indication they considered a non-animal origin but stressed the uncertainty about what animal it could have been. Two seemed very sure it was bats. In general, caution and circumspection go hand in hand with scientific integrity rather than opposing it. I believe this review strongly supports using appropriate qualifiers on summary claims. Sennalen (talk) 02:08, 28 November 2023 (UTC)

A review of sources.

(Bolding is mine) Unknown The origin of SARS-CoV-2, as well as its mode of introduction into the human population, is currently unknown. [2] SARS-CoV-2, the causative agent of COVID-19, emerged in December 2019. Its origins remain uncertain. [3] The natural or accidental origin of SARS-CoV2 remains an unsolved conundrum. [4] The initial outbreak of human cases of the virus was connected to the Huanan Seafood Wholesale Market in Wuhan, and while related viruses have been found in horseshoe bats and pangolins, their divergence represents decades of evolution leaving the direct origin of the pandemic unknown. [5] Probably animals The origin of SARS-CoV-2 is still hotly debated and there is no dispositive proof of whether the virus started its spread after a single or multiple zoonotic events or if the virus ‘escaped’ from a research laboratory through accidental exposure or breach of safety protocols. So far, zoonotic emergence is considered the most likely option by some scientists [6] Great efforts have been undertaken worldwide to trace the origin of SARS-CoV-2, but it remains elusive when and where SARS-CoV-2 originated. The current consensus is that it is extremely unlikely that a lab leak was the source of the pandemic virus [25]. Instead, many studies have supported the view that SARS-CoV-2 had a zoonotic origin and evolved in nature (...) Despite the zoonotic signatures observed in the SARS-CoV-2 genome, it remains unclear how this virus was transmitted from animals to human populations. (...) Bats are common natural hosts for CoVs, supporting that SARS-CoV-2 likely had a bat origin. [7] SARS-CoV-2 is closely related to SARS-CoV, which caused a more limited outbreak in several countries in 2003 (Peiris et al., 2003; Rota et al., 2003); however, several bat- and pangolin-derived viruses are even more closely related to SARS-CoV-2, indicative of a zoonotic origin [8] All previous human coronaviruses have zoonotic origins, as have the vast majority of human viruses. The emergence of SARS-CoV-2 bears several signatures of these prior zoonotic events. (...) As for the vast majority of human viruses, the most parsimonious explanation for the origin of SARS-CoV-2 is a zoonotic event. (...) We contend that although the animal reservoir for SARS-CoV-2 has not been identified and the key species may not have been tested, in contrast to other scenarios there is substantial body of scientific evidence supporting a zoonotic origin. Although the possibility of a laboratory accident cannot be entirely dismissed, and may be near impossible to falsify, this conduit for emergence is highly unlikely relative to the numerous and repeated human-animal contacts that occur routinely in the wildlife trade. [9] Furin cleavage sites in spike proteins naturally occurred independently for multiple times in coronaviruses. Such feature of SARS-CoV-2 spike protein is not necessarily a product of manual intervention, though our observation does not rule out the lab-engineered scenario.[10] Animal but not sure which SARS-CoV-2 was speculated to have originated in bats and then jump to the human population via an intermediate animal host [1,2,3]. Although viruses similar to SARS-CoV-2, such as BANAL-20-52 derived from the Malayan horseshoe bat (Rhinolophus malayanus), RaTG13 derived from the intermediate horseshoe bat (Rhinolophus affinis), and Pangolin‐CoV present in Malayan pangolins (Manis avania) [4,5,6] have been identified, at present the exact animal origin of SARS-CoV-2 remains unclear.[11] Because the question of the original host or animal reservoir of SARS-CoV-2 is unresolved, identifying other animals that are highly susceptible to this virus infection is an important task for pandemic control and prevention. [12] The animal reservoir of SARS-CoV-2 is unknown despite reports of SARS-CoV-2-related viruses in Asian Rhinolophus bats1,2,3,4, including the closest virus from R. affinis, RaTG13 (refs. 5,6), and pangolins7,8,9. The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that recently emerged in China is thought to have a bat origin, as its closest known relative (BatCoV RaTG13) was described previously in horseshoe bats. [13] The most probable explanation for the introduction of SARS-CoV-2 into humans involves zoonotic jumps from as-yet-undetermined, intermediate host animals at the Huanan market [14] Bats are considered as the likely source of SARS-CoV and SARS-CoV-2 viruses, as a rich diversity of SARS-related (or SARS-like) viruses have been identified in several bat species. Notably, a bat coronavirus named BatCoV-RaTG13 has been identified as being most closely related to SARS-CoV-2 on a genomic level with a remarkable 96% sequence identity (Zhou et al., 2020b). To date, the direct precursor of SARS-CoV-2 and the involvement of an intermediate host in the emergence of the human virus remain to be identified, and there has been much attention drawn to the origin of the virus. [15] As such, it may be argued that the progenitor of SARS-CoV-1 has never been identified. Although in contrast to the situation for SARS-CoV-2, viral strains with near-perfect whole-genome sequence identity have been isolated from captive Himalayan palm civets (Paguma larvata) and a raccoon dog (Nyctereutes procyonoides) [64]. These observations led to the hypothesis that a carnivore may have acted as an intermediate host in the jump of SARS-CoV-1 into humans [65]. Early in the COVID-19 pandemic, there were suggestions that pangolins (Manis javanica) could have acted as an intermediate host for SARS-CoV-2 [66]. However, current evidence does not indicate that an established reservoir outside of bats may have been required for the host jump into humans [67] (Fig. 2). Certain it's bats The origin of SARS-CoV-2 can be unambiguously traced to horseshoe bats [16] Our analyses, based on public data, provide compelling evidence that during this time window SARS-CoV-2 evolved in a host environment highly similar, if not identical, to other five bat coronaviruses Honorable mention There is no “origin” to SARS-CoV-2 [17] Sennalen (talk) 02:08, 28 November 2023 (UTC)

• The precise origin may be unknown but it's accepted that it's zoonotic, and it is also accepted that some other notions (e.g. bioweaponry, bioengineering, asteroid debris, 5G masts) are conspiracy theories or just nonsense. Content on zoonotic origin should be on just that, and not start sidling up to the FRINGE stuff which is already covered elsewhere on Wikipedia. Bon courage (talk) 06:55, 28 November 2023 (UTC)

What is concerning about the categorical statements made above as attempted "principles" for editing this content is the way they can be immediately repurposed to allow for WP:PROFRINGE WP:ADVOCACY. This is not the only time this account has engaged in this kind of rhetoric. Since this is a WP:CTOP, we need to be vigilant about this and if that sort of advocacy continues, we need to ask for help from WP:AE. jps (talk) 12:08, 28 November 2023 (UTC)

If you think this and that are "accepted", add the sources that agree with you rather than removing sources that you disagree with. If you do not want to stick to sources because you don't like the points of view contained, that is WP:NOTHERE. Sennalen (talk) 14:54, 28 November 2023 (UTC)

Again, you have been warned. Continue down this path at your own risk. Your snow job above demonstrates nothing vis-a-vis the attempted railroading of discussion by posting an "uncertainty monster" principle. We're cleaning up the article now. You're welcome to offer higher-quality sources or work with what we've got. jps (talk) 15:10, 28 November 2023 (UTC)

We need to zero in more on Palpable's points on clarifying exactly what we mean by zoonosis, both in article and talk space. There's no disagreement that Covid-19 had a zoonotic progenitor in bats circa 50 years ago. The proximal origin however - exactly where it was before the first human infection, is indeed unknown. There is no scientific consensus or Wikipedia consensus that every proposed laboratory origin is a fringe theory, so we should not write as if there is. It may be time for a new RfC if people think that (non)consensus is out of date. Sennalen (talk) 14:56, 29 November 2023 (UTC)

This is a highly skewed and blinkered summary of the state of knowledge currently. 50 years is an arbitrary and absurd number of years to pick out of thin air, for example. And the obsession with lab leaks is fairly disconfirming. Notice the rhetorical sleight of hand with phrasing like "no scientific consensus or Wikipedia consensus that every proposed laboratory origin is a fringe theory". This is not an article about laboratory origin ideas. This is an article about the zoonotic origins of COVID-19. jps (talk) 15:00, 29 November 2023 (UTC)

I think we can safely say that any "lab origin" idea that doesn't involve zoonosis is firmly in the crank-o-sphere (i.e. it's "man-made virus" time). All lab leak stuff is (perhaps more mildly) covered by FRINGE in any case. I'm sure I've read something about how the zoonosis-in-the-lab became a fallback position for the LL proponents as their position crumbled. I'll see if I can dig it out ... But in the meantime this is not meant to be an article about "lab leaks". Bon courage (talk) 15:08, 29 November 2023 (UTC)

50 years is not out of thin air, it's from Lytras (2022) used in the article. I'm not interested in lab ideas that don't involve zoonosis. The ones that do involve zoonosis are related to zoonosis, clearly. Many respected sources about zoonotic origin, such as Holmes (2021), devote a lot of their attention to it. It's not observing due weight to completely leave it out. Sennalen (talk) 16:00, 29 November 2023 (UTC)

A 50-year time frame for a LCA analysis for a bat virus and the COVID-19 virus is manifestly not the same as "zoonotic progenitor". That you are pretending it is makes me fairly amazed. WP:CIR is a standard we require for writing. This is not evident from your argument. jps (talk) 18:41, 29 November 2023 (UTC)

Can you please tone it down already? 40-50 years is the estimated date for the most recent known evidence for a zoonotic progenitor. Evidence should take a central role in the scientific process. We are trying to draw the proper distinction between the known zoonotic phylogenetic origin and the unknown proximal origin. This aligns with your desire to assert more clarity where it's justified. Sennalen (talk) 18:50, 29 November 2023 (UTC)

It is all I can to extend good faith when you are insisting that 40-50 years is a relevant timeframe for zoonotic progenitor. Are you proposing that this timeframe is when human crossover happened? If not, then what point are you trying to make? jps (talk) 18:53, 29 November 2023 (UTC)

Absolutely not. Crossover happened in Q4 2019. The timeframe is for the latest date that we know (rather than reasonably surmise) a bat was infected with a direct progenitor of SARS-CoV-2. Sennalen (talk) 19:22, 29 November 2023 (UTC)

No... the difference between these two timescales has nothing to do with what we "know" versus what we "surmise". LCA uses accurate genetic clock techniques to identify the divergence time. It has nothing to do with "knowing" something versus "surmising" something. jps (talk) 20:00, 29 November 2023 (UTC)

I'm not sure what you're getting at now. What and when do you consider the LCA? Sennalen (talk) 20:09, 29 November 2023 (UTC)

I don't know how to be any more clear. You can ask at the Reference Desk, I suppose, if you are still confused. jps (talk) 20:37, 29 November 2023 (UTC)

That's really unhelpful. The reference desk can not answer what your interpretation is. I have told you my interpretation, and you don't like it. You're entitled to that. But you should be able to say what your interpretation is. Sennalen (talk) 20:41, 29 November 2023 (UTC)

We're in WP:IDIDNTHEARTHAT territory at this point. Your options are either to re-read this thread, ask for third-party explanation, or WP:DROPTHESTICK. I don't have anything more for you because I've already jumped through your hoops as many times as I am willing. jps (talk) 22:20, 29 November 2023 (UTC)

Bon courage, Palpable: Can you tell what jps' position is on the proximal origin or the timing of a lowest common ancestor? Sennalen (talk) 22:24, 29 November 2023 (UTC)

So the first part of the first sentence is SARS-CoV-2, the causative agent of COVID-19, was first introduced to humans through zoonosis. But when I read, for example, this editorial published March 2023 in the Journal of Virology, it says stuff like this:

Two major hypotheses regarding the origin of SARS-CoV-2 have been debated: a direct zoonotic origin and the introduction of the virus into humans from a laboratory

unequivocally ruling in or out the zoonotic explanation is not possible since the evidence will always depend on certain probabilities, and certainty is impossible without knowledge of the initial events.

the lab leak- and zoonotic-origin explanations are not equally probable, and the available evidence favors the latter.

The best existing scientific evidence supports a direct zoonotic origin.

At no point does it say anything with anywhere near the level of certainty implied by SARS-CoV-2, the causative agent of COVID-19, was first introduced to humans through zoonosis, and I would be very surprised if it did, given the current state of knowledge. Finally, I would like to assert, for the record, that neither myself nor the Journal of Virology hold an antiscience, post-modernist POV that, like, nothing can really ever be known, dude.  Tewdar  14:52, 10 March 2024 (UTC)

If it wasn't zoonosis, what was it? We have solid sourcing for zoonosis. Bon courage (talk) 15:27, 10 March 2024 (UTC)

That's not what I said, or implied. If you have solid sourcing (MEDRS, presumably) that we can summarize into Wikivoice as saying, without equivocation or qualification (for such is the lead), that SARS-CoV-2, the causative agent of COVID-19, was first introduced to humans through zoonosis, then present them, please.  Tewdar  15:38, 10 March 2024 (UTC)

That's well-established. PMID:33116300 is what's cited in the SARS-CoV-2 article for example. Bon courage (talk) 15:42, 10 March 2024 (UTC)

Okay, well, that's fine, but I can immediately find (slightly) more recent and (arguably) more relevant reviews like this that use more nuanced language: As for the vast majority of human viruses, the most parsimonious explanation for the origin of SARS-CoV-2 is a zoonotic event. Note that no such nuance is used for human coronavirus-OC43 (HCoV-OC43), human coronavirus-HKU1 (HCoV-HKU1), human coronavirus-229E (HCoV-229E), and human coronavirus NL63 (HCoV-NL63) which have zoonotic origins, according to the same review.  Tewdar  16:12, 10 March 2024 (UTC)

Would you consider the Journal of Virology editorial to be MEDRS?  Tewdar  16:13, 10 March 2024 (UTC)

An (outlier) editorial is a weak source to undercut a review. As for PMID:34480864 you'll find the authors have evolved their views since 2021. Here, for example, is the lead author one year later.[18] Bon courage (talk) 16:26, 10 March 2024 (UTC)

It looks to me like more recent review articles are needed. And, despite the victorious headline 'lab leak theory is dead' in the Conversation article, the second linked paper (obviously a primary source) is still not as certain as our Wikipedia lede: these lineages were most probably the result of at least two separate cross-species transmission events into humans [...] The most probable explanation for the introduction of SARS-CoV-2 into humans involves zoonotic jumps from as-yet-undetermined, intermediate host animals at the Huanan market. I mean, I don't really give a toss and probably won't be making any more comments on this subject. But if it were down to me, I don't think I would be summarising the current state of knowledge quite like the first sentence of this article does.  Tewdar  16:44, 10 March 2024 (UTC)

So far as I'm aware even the LL fans have segued into a 'zoonosis in the lab' accident type of event. The alternative (human-made virus) is firmly in the conspiracy theory realm. Bon courage (talk) 16:54, 10 March 2024 (UTC)

Erm... I suppose this was a reply to me? Anyway... see ya 😁  Tewdar  16:58, 10 March 2024 (UTC)

So, to be clear, when the lede of the Origin of COVID-19 article says that SARS-CoV-2 most likely was transmitted to humans via another animal in nature or during wildlife trade such as that in food markets, that is actually incorrect in your view, and should be changed to say that SARS-CoV-2 was transmitted to humans via another animal in nature or during wildlife trade such as that in food markets?  Tewdar  09:10, 11 March 2024 (UTC)

From the sources, the prevailing view seems to be that the zoonosis was most likely at the market. So I'm not seeing the issue. Bon courage (talk) 09:23, 11 March 2024 (UTC)

The 'issue' is that Zoonotic origins of COVID-19 says that SARS-CoV-2 [...] was first introduced to humans through zoonosis, whereas the parent Origin of COVID-19 article says SARS-CoV-2 most likely was transmitted to humans via another animal in nature or during wildlife trade such as that in food markets (emphasis added). Do you see how those two statements differ? One says 'was'. The other says 'most likely was'. My suspicion is that if you changed 'most likely was' to 'was' in that other article, one of the 163 page watchers would revert the change.  Tewdar  09:44, 11 March 2024 (UTC)

There is no contradiction. The consensus appears to be it was zoonosis but the precise time/place hasn't been pinpointed with certitude. Some LL proponents think it was during scientific field work, or in a lab, for example (the point you brushed off above). Bon courage (talk) 09:50, 11 March 2024 (UTC)

'Was' and 'most likely was' are most certainly not equivalent. This is my only point here. I have no idea what you are talking about in your second sentence (- oh, I ignored that comment because it seemed to be irrelevant to the discussion and was unsupported by sources). If anybody is brushing off points, it is you - do you think the Origin of COVID-19 article should be changed to say SARS-CoV-2 was transmitted to humans via another animal in nature or during wildlife trade such as that in food markets, in line with the Zoonotic origins article, or not? Alternatively, since according to you there is no contradiction, this article could be changed to SARS-CoV-2 [...] was most likely first introduced to humans through zoonosis, and would apparently have the same meaning as the current lede.  Tewdar  10:01, 11 March 2024 (UTC)

it (a) was zoonosis and (b) most likely "in nature" or at the market. These are not contradictory statements. If you want to move "most likely" to just before "in nature" to make it less ambiguous, I'd support that. Bon courage (talk) 10:29, 11 March 2024 (UTC)

Why don't you change it. I'll watch from a safe distance.  Tewdar  10:52, 11 March 2024 (UTC)

Of course, even if we accept that this interpretation is due to ambiguity, there are other articles like COVID-19 pandemic that say The scientific consensus is that the virus is most likely of a zoonotic origin, from bats or another closely related mammal, without any possible ambiguity that the 'most likely' might here refer to the actual animal source, unless you want to say that the comma should be removed.  Tewdar  11:08, 11 March 2024 (UTC)

No that's not right. The virus is zoonotic, as we say. When the merge is done we can tidy it all up to be consistent on that point. Bon courage (talk) 12:36, 11 March 2024 (UTC)

So, you will make this very quick and simple change to the COVID-19 pandemic and Origin of COVID-19 articles 'when the merge is done'? Why not just change it now? I'd change it myself, but I suspect that it would be insta-reverted.  Tewdar  12:48, 11 March 2024 (UTC)

For the former article, even changing to The scientific consensus is that the virus is of a zoonotic origin would be quite enough qualification to shut me up.  Tewdar  12:52, 11 March 2024 (UTC)

If you have strong feelings about how things should be, go ahead and be WP:BOLD. I'm not seeing anything that worries me particularly and there is plenty higher up my worry list. Bon courage (talk) 12:59, 11 March 2024 (UTC)

Definition of zoonosis

Zoonosis is an ambiguous term. In colloquial usage, zoonosis is the opposite of lab-leak. But in more technical sources, zoonosis just refers to having a natural ancestor. For example, the SAGO report asserts a zoonotic origin while acknowledging the possibility of a research-related spillover.

This matters because everybody agrees that SARS-CoV-2 originated with a bat virus and therefore had a zoonotic origin at some point. Yet the proximal origin is highly controversial. Confusion around the definition of zoonosis muddies the waters.

It would be best if Wikipedia divided the possible origins by spillover location: natural, market, or research-related. But if this article is named for zoonosis, the ambiguous meaning of zoonosis should be clarified in the lede. - Palpable (talk) 21:22, 27 November 2023 (UTC)

I am in favor of precision and welcome suggestions of better titles. Sennalen (talk) 22:52, 27 November 2023 (UTC)

We are left with the article topic as presented. Thus, I have changed the title of this article to reflect that. jps (talk) 00:02, 28 November 2023 (UTC)

Tobias chop

[19] Yikes. Focusing this much on one source is absurd. Tobias is a self-admitted FOIA advocate, but it seems to me that his bias is apparent from his various arguments. While better than some of the more rabid Lab Leak conspiracy theorists in terms of care of analysis, there is still something reminiscent of Climategate going on here where people are deliberately misinterpreting e-mails between scientists as somehow indicative of a conspiracy. Basically the origin point of a conspiracy theory. The early concerns over certain genomic features have been conclusively put to bed, and this entire thing is a distraction from the subject of this article anyway. Yikes! jps (talk) 12:45, 28 November 2023 (UTC)

Yes, it a terrible source for an article apparently about a serious scientific topic. Bon courage (talk) 12:48, 28 November 2023 (UTC)

It is the least biased source I could find on a news event with widespread media attention. Moreover, the event is just a recent capstone on sustained attention to the FOIA release spanning over two years. It is not itself scientific research, but it is significant information contextualizing the research. All of this makes it appropriate for inclusion in the "Views" section, which by its position and framing weights it far less than the scientific record. Sennalen (talk) 15:20, 28 November 2023 (UTC)

It's just WP:FRINGE commentary being used to undercut high-quality science, and off-topic to boot. Bon courage (talk) 15:37, 28 November 2023 (UTC)

If that's the least biased source on the news event, then I submit that this news event may not be worthy of inclusion here. jps (talk) 16:24, 28 November 2023 (UTC)

I'm sure I've read something on how these emails have been cherry-picked and misunderstood to create more grist to the lableak mill (i.e. They changed their mind! That's not science!). But it's all just side-show froth as far as the main topic of this article is concerned (zoonosis). In general, using a reporter's hot takes to undercut gold-standard MEDRS is not a good look for any Wikipedia article. Bon courage (talk) 16:29, 28 November 2023 (UTC)

Yeah, I have a hard time imagining why it may be at all relevant. Nothing in the removed text or the source itself seems to add any new information to the zoonotic origins of COVID-19. jps (talk) 16:59, 28 November 2023 (UTC)

Arbitration Enforcement Request

There is a request for enforcement regarding editor behavior concerning this page and COVID-19 origins at Wikipedia:Arbitration/Requests/Enforcement#ජපස Sennalen (talk) 22:11, 28 November 2023 (UTC)

Cite review articles, don't write them

The more I look at this article, the more it appears to be an attempt to write a journal-esque review article based on selected primary literature. Articles should be based on secondary sources and WP:BMI in particular should normally rely on WP:MEDRS. A heavy trim is in order (and is ongoing). Bon courage (talk) 08:28, 29 November 2023 (UTC)

That's a fair assessment. Thanks for sharing your concerns. It was absolutely meant to give the kind of understanding of the topic that a review article would. (The stipulation in WP:NOTJOURNAL is only about avoiding inaccessible jargon.)

A mix of sources was used, including primary, secondary, and reviews. Neither WP:PRIMARY nor WP:MEDPRI is a prohibition on primary sources. Rather, they should be used with caution - e.g., not using them to contextualize other material. Primary sources can provide a deeper layer of verifiability than brief elliptical mentions that are common in secondaries.

The article as originally written mostly conforms to the guidelines. I don't doubt there are things to improve, but the productive way to approach that would have been to WP:PRESERVE, tag, and discuss. A lot of what's there could actually be supported with other existing sources too. Sennalen (talk) 14:44, 29 November 2023 (UTC)

I disagree that the article as-was "mostly conforms to the guidelines". Controversies or uncertainties in medicine should be supported by reliable secondary sources describing the varying viewpoints. Large swathes of this article are/were completely dependent on unreliable sources. The ONUS would be on you to establish consensus for dubiously-sourced content. Bon courage (talk) 14:52, 29 November 2023 (UTC)

I take our charge seriously when there is problematic content to remove it from public view. WP:ONUS is the relevant principle. If something needs to be restored, there is article history but it is far better to be overly cautious an exclude medical-related material in public-facing articles that is even a little bit questionable. There is WP:NODEADLINE and the upsides far outweigh the downsides when it comes to irresponsibly sourced content. jps (talk) 14:56, 29 November 2023 (UTC)

I totally agree with your sentiment when it comes to core medical content. Whether there's no deadline for addition or no deadline for deletion turns on whether there's risk of harm. There is real risk of harm in bad information about diagnosis and treatment. No one is going to read a statement here about zinc finger protein and then go stick a bat up their nose. Sennalen (talk) 15:24, 29 November 2023 (UTC)

Letting badly-sourced content hang around is how the encyclopedia deteriorates. And there is more then enough of that sort of thing on COVID topics already. When there's so much decent sourcing on pretty much all things COVID, there's really no need to scrape around for primaries. Bon courage (talk) 15:28, 29 November 2023 (UTC)

I can respect that, but if that's where you're coming from, you should turn the same scathing view on the WP:MEDPOP all over the Covid topics. Sennalen (talk) 16:03, 29 November 2023 (UTC)

For sure. (Except in the case where for reasons of WP:PARITY it's useful for debunking misinformation, like turbo cancer e.g.) Bon courage (talk) 16:07, 29 November 2023 (UTC)

Okay, yeah. That is a case where I think Gorski is appropriate. Sennalen (talk) 16:21, 29 November 2023 (UTC)

Commonly heard on Wikipedia: "Yes of course SBM is good for debunking all these other things which are obviously bunk, but it's not suitable for ${my pet topic}". Bon courage (talk) 16:29, 29 November 2023 (UTC)

Not for anything with good coverage in peer-reviewed journals. Sennalen (talk) 16:30, 29 November 2023 (UTC)

Views removed

[20] I think this section was serving mostly as a WP:COATrack for ongoing questions and controversies surrounding the politicization of scientific studies regarding COVID-19 origins. But, crucially, none of the sources really had anything to say about the investigation of zoonotic origins directly. The "anywhere but here" editorial from Science is interesting and relevant to other articles, but not this one. Our focus needs to be on zoonotic origins, not on how geopolitics filters out certain discourse.

Just about the only two points which were even vaguely related were the questions about close relatives of the virus found in wildlife (poorly cited paper criticized in the "anywhere but here" editorial as an object lesson) and the point that the wet market provenance has contributed to certain racist/racialized backlash. I think those points might be integrated in other sections of the article, but they are still somewhat tangential so I think there is no great loss if they are not discussed, necessarily.

Anyway, that's that.

jps (talk) 13:40, 29 November 2023 (UTC)

It's right not to weight societal views too much in comparison to scientific research. Going to zero is certainly not the right answer, though.

There's also some mixed signals here - is the article being pruned of context to just focus on zoonosis, or is it being prepped to merge with the parent? If it's to merge, this stuff about Chinese politics becomes even more important. Origin of Covid-19 currently gives too much credence to the WHO report and the frozen food idea and could use this material. Sennalen (talk) 15:30, 29 November 2023 (UTC)

The removed text with the two narrow exceptions I outlined had nothing to do with "societal views on zoonotic origins". It had to do with societal views on other matters. jps (talk) 18:43, 29 November 2023 (UTC)

"Preparing for a merge" does not mean adding material that does not belong here but, if at all, in the other article. --Hob Gadling (talk) 18:58, 29 November 2023 (UTC)

Pekar

ජපස, you seem to have misunderstood some aspects of Pekar (2022). As the "Selection" section of the undecimated version of the article explains, lineages S and L are defined by particular SNVs. They were well-known before Pekar (2022). There is not a scientific consensus, but the more prevalent view is that these SNVs are host adaptations acquired in humans. Pekar (2022) makes the novel claim that they were acquired before crossing the species barrier, and that it was crossed twice separately. Pekar is primary for those claims, and as they say in the paper, their methods were Phylodynamic rooting methods, coupled with epidemic simulations. None of it has any bearing on whether a spillover happened or whether SARS-CoV-2 was ever in an animal - all of that is assumed. Sennalen (talk) 15:27, 30 November 2023 (UTC)

This revert reintroduces the wording "Based on epidemiological simulations, the most recent common ancestor of circulating human strains was in a non-human animal prior to spillover." This wording implies that Pekar et al. (2022) simulated the most recent common ancestor of all circulating human strains to be in a non-human animal. This is not what the paper does. If you want to talk about evidence for multiple spillover events from Pekar et al. (2022), then do so (provided you find third-party commentary on such), but this wording is highly misleading. jps (talk) 16:45, 30 November 2023 (UTC)

Here is the key part of article text I was summarizing. Answering these questions requires determining the ancestral haplotype, the genomic sequence characteristics of the most recent common ancestor (MRCA) at the root of the SARS-CoV-2 phylogeny. In this study, we combined genomic and epidemiological data from early in the COVID-19 pandemic with phylodynamic models and epidemic simulations. We eliminated many of the haplotypes previously suggested as the MRCA of SARS-CoV-2 and show that the pandemic most likely began with at least two separate zoonotic transmissions starting in November 2019.[21]

This confirms they were calculating a MRCA using methods including simulation, and that they say it supports multiple spillover.

The simulation more specifically was a nonreversible, random-effects substitution process model in a Bayesian phylodynamic framework that simultaneously reconstructs the underlying coalescent processes and the sequence of the MRCA of the SARS-CoV-2 phylogeny

This supports that they say the MRCA was not in humans: If lineages A and B arose from separate introductions, then the MRCA of SARS-CoV-2 was not in humans

The input data was We queried the GISAID database (56), GenBank, and National Genomics Data Center of the China National Center for Bioinformatics (CNCB) for complete high-coverage SARS-CoV-2 genomes collected by 14 February 2020, resulting in a dataset of 787 taxa belonging to lineages A and B and 20 taxa with C/C or T/T haplotypes.. I think it's fair to gloss that as "circulating human strains".

Let me know if any of these don't seem like adequate support. Sennalen (talk) 16:57, 30 November 2023 (UTC)

• Are we talking here about PMID:35881005? If so, I think the Gordian Knot may be cut by excising it from the article, as it's not WP:MEDRS. Bon courage (talk) 17:14, 30 November 2023 (UTC)

  That is the one. It's one of the most cited articles in the area, so it needs to be represented. There are several review articles that could buttress the citations. Sennalen (talk) 17:19, 30 November 2023 (UTC)

  Great, if it's much cited there should be some WP:SECONDARY sourcing which is usable here! Bon courage (talk) 17:21, 30 November 2023 (UTC)

  It would take some time to figure out what the perfect wingman would be, but I know it's discussed in [22] and [23] that are already used in the article. Sennalen (talk) 17:30, 30 November 2023 (UTC)

  That article uses Pekar et al. as an example of speculation that there were intermediate animal hosts. No mention is made of two spillovers. jps (talk) 17:43, 30 November 2023 (UTC)

  Agreed. Secondary sourcing would be much better than what is currently at work. jps (talk) 17:39, 30 November 2023 (UTC)

  Part of the angst stems from trying to turn an article written to be about a WP:SUBPOV into a main topic article. Pekar was here to represent the view of Pekar per se. Square peg, round hole. Sennalen (talk) 17:53, 30 November 2023 (UTC)

  You intended this article to be about a point of view and not facts? Scientific papers are not opinion pieces and treating them as such is a practice much better left for venues like Conservapedia. jps (talk) 18:24, 30 November 2023 (UTC)

  A point of view and evidence that supports it, yes. WP:YESPOV - State facts as facts, opinions as opinions, and seriously contested assertions as attributed. Is that not what you would do with a serious but unproven hypothesis like double spillover? Or the identity of an intermediate host? Sennalen (talk) 19:04, 30 November 2023 (UTC)

You seem to be under the misapprehension that there is a spectrum of opinion to fact when it comes to empirical claims. I submit that this is a mistake in consideration of genre. A paper in Nature (and, to a lesser extent, Science) is speculative by nature (ha!) and will couch its conclusions as such. The authors aren't arguing that it is their opinion that there were two spillover events. The authors are arguing that there is evidence that there were two spillover events. They may be mistaken in that analysis which is why WP:MEDRS is so very allergic to primary sources. But what they are not doing is writing an op-ed about what they think is going on in the world. I understand that this topic has fallen victim from time-to-time to this kind of game playing (c.f. Great Barrington declaration), but peer-reviewed published papers are either worthy of inclusion and citation with their points plainly asserted or they are worthy of exclusion. There is no middle ground. I fear that you may have adopted an editorial bent from political and cultural topics where opinions are the currency of a lot of the sources. That is not the case here. jps (talk) 19:44, 30 November 2023 (UTC)

I don't disagree. (Well I disagree that I adopted an editorial bent, but I don't disagree with the rest.) That's why the op-ed kind of opinion was confined to a "Views" basement. Sennalen (talk) 19:49, 30 November 2023 (UTC)

If you don't disagree, then why did you make blanket categorical statements that run afoul of such principles? It would have been fine to say "We don't know the identity of patient zero." It would have been fine to say "We know that bats were hosts for SARS-CoV-2 progenitors." It's not really okay to say "The origin of Covid-19 is unknown." as an editorial principle. Do you really not understand that? jps (talk) 20:02, 30 November 2023 (UTC)

Between case Wuhan-1 and a bat 50 years ago, there is a missing gap. This gets us back to Palpable's comment that we need to be careful about what we mean when we say "origin". When I said the origin is unknown, I meant is that we can't be certain what happened during the period of time that lacks evidence. Nothing could be more in accordance with the scientific process.

Some scientists such as Pekar has inferred that certain things happened, but other scientists have reached other conclusions, and I don't just mean lab leaks, but also differents kinds of hosts and spillovers. But yes, lab leaks too. The last RfC in 2021 did not find a consensus that lab leaks are all conspiracy theories. You're not the only one who acts like that's a self-evident consensus though. It urgently needs a new RfC, regardless of what answer it comes back with, having one would be better than an open wound in the community that exists now.

That's fine that you don't like lab leak ideas, but I'm not responsible for the state of the evidence that allows for them. It is what it is. It doesn't do any good to project all kinds of agendas on me. Sennalen (talk) 20:19, 30 November 2023 (UTC)

Between case Wuhan-1 and a bat 50 years ago, there is a missing gap. Saying that there was a MRCA between RaTG13 and SARS-CoV-2 40 or 50 years ago is not the same thing as identifying a bat 50 years ago. What source talks about a missing gap? jps (talk) 20:27, 30 November 2023 (UTC)

Okay, I assume the MRCA was in a bat. If there's a reason to think otherwise, I'm genuinely curious. Likewise if there's anything that would fill in that time period, please say what it is. I'm sure of the sources made some general remarks about the gap in the evidence by way of introduction to whatever it was the paper was really about, but it might take me awhile to find an example. It's not something I tried to put a claim about in the article. Sennalen (talk) 20:37, 30 November 2023 (UTC)

No. That's not how this works. You made a statement: Between case Wuhan-1 and a bat 50 years ago, there is a missing gap.. You must provide the sources to back it up. jps (talk) 21:29, 30 November 2023 (UTC)

I didn't expect the Spanish Inquisition! Is it better to say, "To my knowledge, between case Wuhan-1 and a bat 50 years ago, there is a missing gap."?

If you want to target that 50 year estimate specifically, the best source is probably the one it came from[24]

There's also some talk on that theme in the abstract of this[25], and there's the one from Frutos that is all about unknowns.[26] Hope this helps. Sennalen (talk) 22:33, 30 November 2023 (UTC)

This response indicates your predilections towards this topic, and I find them disconfirming. None of those sources should be used as organizational principles to preference a kind of uncertainty about the origin of COVID-19. There is a linear model: This coronavirus, like other coronaviruses, is zoonotic in origin. It was first detected in Hubei, its closest relatives are in bats. That is the primary focus. That is what the vast majority of WP:MEDRS sources are going to lead us to writing. Details beyond this with guesses about how many years progenitors were circulating undetected are secondary to the main points. And yet you have consistently tried to push the details as the main point. I don't think this is workable in a collaborative sense. You have either been pushed into a bizarre editorial outlook by your overinvolvement in Lab Leak Theory discussions or there is some other agenda, but what I do not see is a fealty to the best sources and basic discourse on this topic. This is a common problem in areas where we see WP:PROFRINGE advocacy and whether you are doing it intentionally or not, that is what I am seeing here. jps (talk) 12:30, 1 December 2023 (UTC)

Details beyond this with guesses about how many years progenitors were circulating undetected are secondary to the main points. That would be true in the setting of a main Covid-19 Origin article, which is not the article I set out to write. This article was supposed to be a detail article, where the primary focus is the state of knowledge about what happened prior to December, 2019. Just because it's not an article you would have written doesn't mean I have nefarious motives. Sennalen (talk) 13:20, 1 December 2023 (UTC)

Not to put too fine a point on it, but it looks to me like you set out to write a WP:GEVAL WP:POVFORK as a complement to COVID-19 lab leak theory. jps (talk) 13:51, 1 December 2023 (UTC)

People have already said as much, but the truth is I set out to write a WP:DETAIL WP:SUBPOV companion to Origin of Covid-19. You could say it's a complement to the lab leak page too, not in that the acceptance of the theories has parity, but in that the lab leak page is also a DETAIL SUBPOV. Sennalen (talk) 14:33, 1 December 2023 (UTC)

Action plan

I think everyone agrees Origin of Covid-19 should be better. I didn't write this to fulfill that mission. I thought that would have been too bold - but it seems like no one is going to trust any attempt at a spinout anyway unless it's a package deal with the parent. I could remix this material into something built from the start to be a draft for the parent. I trust that if I do that, we can talk about any concerns people have with weight or secondary sources without going ham deleting everything? Sennalen (talk) 03:50, 2 December 2023 (UTC)

All non-WP:MEDRS (used for WP:BMI) needs to be removed as a initial cleanup. This action is ogoing. Bon courage (talk) 03:58, 2 December 2023 (UTC)

I'm talking about deleting things on the future draft. If there is a problem in draft space it should be tagged for fixing, not deleted. Sennalen (talk) 04:02, 2 December 2023 (UTC)

Given its current state, I do not have a strong opinion about what to do with this article during work on the parent. Delete, draftify, leave it alone - all acceptable. I have my original saved to disk. Sennalen (talk) 03:59, 2 December 2023 (UTC)

If the article had been a nice summary of the relevant MEDRS that would have been great. I still think there's potential for something like that (after merge) to be part of a nice restructuring across the COVID 'origin' articles which will improve things. Bon courage (talk) 09:39, 3 December 2023 (UTC)

Selective pressure on the nsp1 gene needs a review article in your opinion,[27] but a phase III trial saying juice cures covid "seems fine"?[28] Sennalen (talk) 15:13, 3 December 2023 (UTC)

As an example of an unproven method, but yikes! on closer inspection that was not clear there. Tidied-up ... thanks! Bon courage (talk) 15:59, 3 December 2023 (UTC)

So you can see the sausage being made, it's at User:Sennalen/sandbox/CovidOrigin starting with a bibliography. This would be a good time to look them over and see if any seem fatally unusable for any possible claim. As a reminder, the scope is expanding to be larger than this articles', and as a consequence the space for lab leak will be larger than it is here in an article specifically about zoonosis. That is not evidence of any secret agenda. Sennalen (talk) 17:36, 2 December 2023 (UTC)

Have you considered instead that it might be more informative and useful for the reader to discuss virology, epidemiology, evolution and emergence without such an emphasis on the proximal origin? SARS-CoV-2 puts "Reservoir and origin" ahead of "Virology" and seems to jump right to proximal origins. COVID-19 looks pretty unorganized and the "History" section dives right into proximal origin. COVID-19 pandemic#Epidemiology jumps right from proximal origin to case counts. There are of course many papers that directly address proximal origin, but many of the papers and sources cited for the scattered "lab leak vs zoonosis" content do not. They give as background or introduction some content related to coronavirus emergence, zoonosis and proximal origin of COVID-19 but then move on to the purpose of the paper. Editors then pick and choose from these some wording or point they want to make about the proximal origin and seemingly ignore the rest. For instance i found "The past, current and future epidemiological dynamic of SARS-CoV-2" useful and informative (it's only cited 23 times so i don't know how important it is.) Likewise i thought some of the content here could be useful for a more generic introduction to the epidemiology which could put the proximal origin within its proper perspective.

Of the now three articles dealing with origins and lab leak, and the other scattered content, all seem to mangle the use and concept of 'zoonosis', never tell me why it was important to identify reservoirs and i think really lack the background required for the reader to understand the content. It would be nice if at least one began with and focused on epidemiology rather than the politics. I think some of the content here could have been useful for doing that. fiveby(zero) 17:11, 4 December 2023 (UTC)