Talk:RaTG13

New Virus RpYN06 is Closer
New Research published in the Journal cell identified 4 novel coronavisuses and found that the virus, RpYN06 is the closest relative of SARS-CoV-2 in most of the virus genome. RaTG13 still has a higher nucleotide similarity, due to the similarity, in the spike protein. ''Of particular note was that one of the novel bat coronavirus identified here—RpYN06—exhibited 94.5% sequence identity to SARS-CoV-2 across the genome as a whole and in some individual gene regions (ORF1ab, ORF7a, ORF8, N, and ORF10) was the closest relative of SARS-CoV-2 identified to date. However, much lower sequence identity in the spike gene, undoubtedly the product of a past recombination event, made it the second closest relative of SARS-CoV-2, next to RaTG13, at the genomic scale. Hence, aside from the spike gene, RpYN06 possessed a genomic backbone that is arguably the closest to SARS-CoV-2 identified to date''

https://www.cell.com/cell/pdf/S0092-8674(21)00709-1.pdf

The Robertson Lab estimates that RaTG13 shared a common ancestor with SARS-CoV-2 about 50 years ago, but for RpYN06 and two other viruses, it's 40 years ago.

https://www.biorxiv.org/content/10.1101/2021.01.22.427830v3 https://www.youtube.com/watch?v=s3iKF9sblAw&t=563s — Preceding unsigned comment added by 108.29.40.129 (talk) 17:28, 29 June 2021 (UTC)

Collected how?
I know this may seem like a small matter, but both WIV papers (Jiang et al and Zhou et al) sent to Nature indicate that RaTG13 was collected from anal swabs while, RmYN02 was collected from feces samples. ScrupulousScribe (talk) 16:16, 16 January 2021 (UTC)

Please, explain
User:Alexbrn Please, explain, why is unreliable? --Geysirhead (talk) 15:23, 26 February 2021 (UTC)
 * Please see WP:MEDRS: we want review articles or better. This particular source has been discussed to death at various other articles too e.g. Talk:COVID-19 misinformation. Alexbrn (talk) 15:32, 26 February 2021 (UTC)
 * Also WHO says it is "extremly unlikely" instead of "impossible" — Preceding unsigned comment added by Geysirhead (talk • contribs) 19:53, 26 February 2021 (UTC)

Why is there NO real samples of Ratg13, if it smells like a rat it probably is... — Preceding unsigned comment added by 24.4.159.220 (talk) 05:46, 20 March 2021 (UTC)

Lab leak, weak sources
Brand new user is edit-warring a "Controversy" section into this article using weak, non-WP:MEDRS sources including the crappy Segretto/Deigin source which has been so much discussed over several articles. Biomedical sourcing needs to meet WP:MEDRS and this article is not a coat rack for conspiracy theories about COVID-19. Alexbrn (talk) 14:29, 7 March 2021 (UTC)
 * could you assess if this article may be appropriate for ECP protection under the GS? ProcrastinatingReader (talk) 14:57, 7 March 2021 (UTC)
 * , thank you very much for the notification. Please keep me updated and continue to notify me about such cases. This is exactly why the sanctions exist. ~ ToBeFree (talk) 15:57, 7 March 2021 (UTC)

I contributed something that took me a great deal of time to research with credible PubMed.gov peer-reviewed sources. Alexbrn, you've contributed nothing to the page other than to delete topics that you feel are one-sided, when I've clearly documented the two different sides of the controversy. It's as if you don't want people to know that there even is a debate within microbiology circles (the people most likely to be reading this page). This is what RaTG13 is most known for, the initial and lasting controversy around it, and yet, there's no mention of this at all on the page. I'm documenting a part of history, which is the controversy around it. I am not taking any side on the matter. Furthermore, I've used PubMed.gov studies that are linked to Wiley archives. You did not remove contributions from others who used Wiley as a source, and they are stating things as facts, when my contribution is "So and so believes" or "Their argument is". It's clear you are controlling the narrative of shutting down conspiracy theorists and you've misidentified me as one. This is a personal thing for you, has nothing to do with the sources. You're being biased and it's petty and not fair to the community. Edit warring? All I did was contribute something and attempted to keep my contribution up. You came along and deleted my work. I didn't touch yours. — Preceding unsigned comment added by RonnieSays (talk • contribs) 15:15, 7 March 2021 (UTC)
 * Did you read WP:MEDRS? Wikipedia does not base biomedical content on weak sources and generally requires review articles or better. Decorating your contribution with POV editorial phrasing like "Those who argue in favor of a natural origin ... " is likewise unacceptable. Alexbrn (talk) 15:21, 7 March 2021 (UTC)

Yes I did read WP:MEDRS after I noticed you using it as an excuse to take down other people's credible PubMed studies. It seems you use this and don't expect anyone to actually read it and call you out for it. I'd like to know why all the Nature and Wiley articles that you have left above my PubMed (Wiley Archive) articles are valid sources and not mine? You've told others they must cite secondary sources (i.e. Reviews), yet none of those are secondary sources. All primary sources that can also be found on PubMed as well. The only difference between those sources and mine is that those ones don't personally annoy you because your reality is that there aren't two sides to RaTG13 research and everybody must not only agree that it's of natural origin, but that researchers who question this don't exist and their peer-reviewed studies do not exist. As for "Those who argue in favor of a natural origin", I said the same thing about those who argue against it. Why are you only picking and choosing one line to make it look as if I'm a conspiracy theorist? I used the same wording to point out both sides of the controversy. Why is that "unacceptable"? It's clear that what you feel is unacceptable because you're 100% sure that is of natural origin, and you won't accept the fact that there are many microbiologists publishing studies to counter that. You're controlling the narrative, plain and simple. I'm covering both sides, you're only interested in having one side published here. — Preceding unsigned comment added by RonnieSays (talk • contribs) 15:38, 7 March 2021 (UTC)
 * Please see WP:FALSEBALANCE. We do not provide "both sides" when one of the sides is a fringe minority. &mdash;  The Hand That Feeds You :Bite 21:58, 7 March 2021 (UTC)
 * "Those who argue in favor of a natural origin" that's really classic WP:GEVAL indeed, as it's the most plausible origin from a historic perspective but also the scientific consensus. — Paleo  Neonate  – 16:02, 8 March 2021 (UTC)

Lab leak belongs to the conspiracy theory related to COVID-19 and has nothing to do with the theme of this article. The contents of Virology and Phylogenetic should be paid attention to in such SARS‑CoV‑2 related coronavirus articles as RaTG13, RmYN02 and RacCS203.--Htmlzycq (talk) 00:45, 9 March 2021 (UTC)

Culture of RaTG13
Present text: In 2020, Shi and her group retested the serum samples from the miners for SARS-CoV-2. The samples tested negative.[7]

Suggested addition: In 2020, Shi and her group retested the serum samples from the miners for SARS-CoV-2. The samples tested negative.[7] In 2020, Shi stated that her group had neither isolated nor cultured RaTG13. — Preceding unsigned comment added by 137.132.222.179 (talk) 03:35, 13 March 2021 (UTC)
 * X mark.svg Not done And how is that relevant to the topic at hand, which is not the studies done by the team but this particular virus strain? The explicit denial of the conspiracy theories about COVID is not necessary here. RandomCanadian (talk / contribs) 03:46, 13 March 2021 (UTC)

To add to article
Basic information to add to this article: why was this virus, against normal laboratory protocol, renamed from "Bat coronavirus Ra4991" to "RaTG13" by the Wuhan Institute of Virology? 173.88.246.138 (talk) 03:08, 4 April 2021 (UTC)
 * This seems entirely irrelevant. A provisional designation is likely meaningless anyway (hell, Sars-CoV-2 was first 2019-nCoV). RandomCanadian (talk / contribs) 03:49, 4 April 2021 (UTC)


 * I believe this fact is notable because this argument is used in conspiracy theories (just look up "RaBtCoV/4991" in Google Scholar) and hence we should have it covered with a correct explanation. Ain92 (talk) 13:39, 25 May 2021 (UTC)
 * I'm not sure we need to entertain conspiracy theories (in fact, WP:FALSEBALANCE would preclude us doing so). The alternative name can be mentioned (under the format "also designated as ..."), if it is common enough. Cheers, RandomCanadian (talk / contribs) 14:51, 25 May 2021 (UTC)

Still to add to this article (as leaving it unexplained is entirely unencyclopedic and weird): exactly when, by whom, and, most importantly, why, was this virus, against normal laboratory protocol, renamed from "Bat coronavirus Ra4991" to "RaTG13" by the Wuhan Institute of Virology? 173.88.246.138 (talk) 03:06, 10 June 2021 (UTC)
 * The interview given to Science, here; seems to clarify things.


 * Your assertion that this is "against normal laboratory protocol" is, also, still not supported by any reliable source (you have cited none), so it cannot be included. RandomCanadian (talk / contribs) 03:16, 10 June 2021 (UTC)


 * I believe some kind of distillation of this interview excerpt would improve the article while not contributing to "entertain conspiracy theories", what do other colleagues think? Ain92 (talk) 14:49, 25 June 2021 (UTC)
 * The NYtimes refered to the change of name of RaTG13 as a "crucial fact" here, so we have a RS that says it is not irrelevant. I propose we include a brief mention of the name change. Forich (talk) 23:10, 26 June 2021 (UTC)
 * I don't know how you missed (both in the url AND at the top of the page) that this is an opinion piece, by a Turkish sociologist (i.e. someone who has no expertise whatsoever in virology or anything related to that). If this person had some form of relevant qualification (subject matter expert), we might accept the opinion as relevant per WP:SPS - otherwise, the opinion piece is only sufficient to claim what the opinion of its author is. So still not enough to go in the article. The Science interview can be included in some form, ideally summarised, as it is from relevant experts (virologists who sampled this), with care taken to not state controversial matters (q: is there anything controversial there?) as statements of fact. RandomCanadian (talk / contribs) 23:30, 26 June 2021 (UTC)
 * we take the WP:OPINIONs of random Wikipedians seriously for editorial decision making, but we do not take them to exclude careful WP:INTEXT attribution of opinions of writers like Zeynep Tufekci published in WP:RS. She is far from being the only science writer to question the identity and provenance of this virus, but her New York Times article is probably one of the best ones on the subject to date. Let’s be careful not to make any statements of fact in WP:WIKIVOICE, even if some members of DRASTIC suspect it of being only a digital genome, which will come out in RS soon I’m sure. Please note that Tufekci has clashed with Angela Rasmussen a lot on Twitter, so it would be better to find another voice for WP:BALANCE, if there is one. Tagging and . CutePeach (talk) 14:45, 28 June 2021 (UTC)
 * See WP:RSOPINION, and, as pointed out multiple times, WP:FALSEBALANCE. We don't give much weight to people with no relevant expertise (a sociologist? really?) writing opinion pieces (which are primary sources). Nor do we give as much weight to non-experts as to experts (Rasmussen is a bona fide virologist). We prefer WP:BESTSOURCES, and, as described at WP:SOURCETYPES and WP:SCHOLARSHIP, "When available, academic and peer-reviewed publications, scholarly monographs, and textbooks are usually the most reliable sources." "Articles should rely on secondary sources whenever possible." So, and this is the last time I'm bothering to explain this: we give more weight to review papers in relevant journals. If you wish to dispute the current material, the WP:BURDEN is on you to find sources of equivalent quality (reviews or other secondary sources in reputable journals or from reputable organisations). At least for the scientific aspect of this: if there are some aspects of the politics which are not described properly, of course, that's different. RandomCanadian (talk / contribs) 16:25, 28 June 2021 (UTC)
 * Thanks for mentioning Rasmussen, I enjoyed reading her recent timeline. Ain92 (talk) 22:14, 28 June 2021 (UTC)


 * I'ld argue we could also address the poor miners' cause of death, which apparently was a fungus growing on the bat faeces (not a reliable source but that's where I read it). This aspect is likely interesting to the readers of our article, and there's no better place in Wikipedia where to put it. Ain92 (talk) 22:14, 28 June 2021 (UTC)
 * Yknow I searched and searched to try and find a good RS to say COD for the Mojiang miners was Histoplasma capsulatum. I can tell you with extreme certainty that if the official record says "fungal pneumonia," the miners weren't immuncompromised, and they were in a bat cave, that the answer is Histo. That is the only logical conclusion. Seriously there are questions on medical licensing exams (one of which I just took a few weeks ago) which say "a guy was spelunking in caves with bat guano, and then got pneumonia. What does he have?" and the answer is Histoplasma. But if we cannot find a source which specifically says that then we can't include it. We can say it was fungus, because that's what the sources say, but we cannot say Histoplasma. I would bet you very good money that somebody did a fungal smear and culture of the miner's sputum and that grew Histo, and that's how we know it was Histo. These cultures take a while (up to 6 weeks) and that's probably why there was so much disagreement about coronavirus vs fungus for a while before those results came back. But again, that's the downside of WP:V for you. 100% an uncontroversial fact, but it would be WP:OR to include it in this context.-- Shibboleth ink (♔ ♕) 22:20, 28 June 2021 (UTC)
 * Thank you a lot for your research! From what I can read on the wiki, Histoplasma capsulatum appears to be primarily found in the New World, so Asia may in principle have its own species of fungus occupying the same ecological niche. Do you think we may actually get a proper expert on the record? Ain92 (talk) 13:28, 29 June 2021 (UTC)


 * Histoplasmosis is actually also endemic in some parts of China . it's probably bounded by latitude, not by hemisphere. but it is definitely part of an undersiagnosed mycosis trend in China. this is probably due to an east/west divide in the literature versus the actual incidence of the disease. That being said, it would not surprise me if it were a different Histoplasmosis species, not capsulatum. Reminiscent of the borreliosis cluster of diseases in that we label it all as one thing when it's really probably not. if we want to get actual authoritative sources on how this related to the Mojiang miners, though, I bet we will need to use Chinese-language sources. local and national news, coroner's findings, police reports, etc. Stuff like that. That's where I'd look.-- Shibboleth ink (♔ ♕) 16:04, 29 June 2021 (UTC)

In discussing whether a fact is notable for inclusion in Wikipedia, we can perfectly be guided by it being covered in multiple RS. The NYTimes opinion piece saying the RaTG13 name change being crucial can be used for us to consider it notable for inclusion. To RandomCanadian's point, if this opinion is not shared by other RS sources, the notability argument falls down. The actual edit, if merited, can be cited to a more academic source. I would only give it a one-phrase mention at this point, though, in neutral tone. Forich (talk) 18:55, 29 June 2021 (UTC)

Source no. 9
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7995093/

states: " It is highly unlikely that SARS‐CoV‐2 was accidentally released from a laboratory since no direct ancestral virus is identified in the current database."

Really? A database that is maintained by the Wuhan institute and which went offline in Sep 2019*** is the proof against a lab leak? Do you know the old saying: "to put the fox in charge of the henhouse"?

--95.90.218.163 (talk) 02:48, 15 June 2021 (UTC)
 * https://www.researchgate.net/publication/349073738_An_investigation_into_the_WIV_databases_that_were_taken_offline
 * Self-published pieces on research gate are not worth shit as far as Wikipedia is concerned. The only thing that we actually care about is what WP:SCHOLARSHIP says (useful sample here), because all your bias are belong to us. RandomCanadian (talk / contribs) 14:08, 15 June 2021 (UTC)
 * big words, little substance, dear. That the database has been taken offline since Sep 2019 is a matter of public record. The reasoning behind it, is very convincing indeed: "Many scientists are eager to examine the WIV’s once publicly available database of some 22,000 samples and virus sequences, including 15,000 from bats. The database was taken offline in September 2019. Dr. Shi told the WHO-led team in February that the database was taken offline after being subjected to more than 3,000 cyberattacks." https://www.wsj.com/articles/wuhan-lab-leak-question-chinese-mine-covid-pandemic-11621871125 This makes the central conclusion of source no. 9 that "no direct ancestral virus is identified in the current database" invalid. Congratulations. --Felixkrull (talk) 22:51, 15 June 2021 (UTC)
 * That there exists a database doesn't "invalidate" anything - that's your own WP:OR. The only thing which matters regarding scientific information (the origin of a virus, as opposed to political developments related to it) is what the WP:BESTSOURCES say, i.e. if you are able to find peer-reviewed papers published in reputable scientific journals which argue for this. The passive-aggressiveness of your comment is also not helpful. RandomCanadian (talk / contribs) 23:24, 15 June 2021 (UTC)
 * Another confirmation from a reputable source (if you don't fancy WSJ): "For example, the same group of internet sleuths that linked RaTG13 to the mine also uncovered that a genomic database maintained by the Wuhan Institute of Virology, with information about thousands of bat samples and at least 500 recently discovered bat coronaviruses, went offline in September 2019. The official explanation — that it was taken offline because it had been subjected to hacking — doesn’t explain why it was never securely shared some other way with responsible independent researchers." https://www.nytimes.com/2021/06/25/opinion/coronavirus-lab.html . That confirms my initial assesment that source no.9 - besides being overly political, which already raises supicion - can not reasonable conclude that "It is highly unlikely that SARS‐CoV‐2 was accidentally released from a laboratory since no direct ancestral virus is identified in the current database." because the author can not have had access to the respective database since it has been taken offline (with spurious reasoning) by the Wuhan Institute of Virology. I suggest that the source no. 9 not be used. --Felixkrull (talk) 13:36, 25 June 2021 (UTC)
 * Source no. 9 is a peer-reviewed review paper in a credible academic journal. It is one of our WP:BESTSOURCES. Claiming that it is "overly political" is at best dubious, and at worst outright and categorically false. If the source is somehow wrong, then you can try to get your arguments published in similarly credible journals. Until then, and to quote Jimbo, (source: WP:YWAB):


 * So, no, your arguments are still WP:OR - if the source is wrong, find a better one. If you can't find a better one, don't pretend that an opinion piece in the NYT (what you are citing) is somewhat equivalent to it. RandomCanadian (talk / contribs) 03:44, 26 June 2021 (UTC)
 * Thank you for the quote by Jim Wales and the citing of chapter and verse of Wikipedia mnemonics. I am well aware of the sientific method and have read Descartes' Discours de la méthode and Karl Popper's philosophy of science in the original - but you are clearly missing the bigger picture here. It is precisly the stiffling of open scientific discussion and politicized science as source no. 9 that is contrary to the scientific method. (And I am confident that Jimmy Wales would agree here). There have been conspiracy theories abound wrt the covid pandemic, no question about that, but the lab leak was NEVER one and should never have been discredited as such as the infamous and peer-reviewed Lancet article or as source no. 9 did. That's bad science *and* bad politics - because, be rest assured, there will be a fallout from this affaire for the scientific community and will not be a pleasant one. As for "better sources" that do discuss the lab leak theory properly, I will present those here shortly.  --Felixkrull (talk) 23:12, 30 June 2021 (UTC)
 * "It is precisly the stiffling of open scientific discussion and politicized science as source no. 9 that is contrary to the scientific method" Speaking as a scientist, I disagree. Source 9 and the Lancet article are perfectly cromulent sources for how virologists have drawn probabilities in all of this.-- Shibboleth ink (♔ ♕) 23:18, 30 June 2021 (UTC)

rephrase opening paragraph.
"Recent research suggests that BANAL-52, a strain of coronavirus found in bats in Laos is a closer match to SARS-CoV-2 than RaTG13 is" might be better written somethign like: "While RaTG13 was quickly identified as the closest relative to SARS-CoV-2 at the begining of the COVID pandemic, later research found a closer match in Laos named BANAL-52" 2600:8804:6600:83:546C:7184:AE29:3AB2 (talk) 02:42, 22 December 2021 (UTC)

Please edit: Incorrect use of the term "isolate"
The article currently incorrectly states: "between 2012 and 2015, Shi Zhengli and her group isolated 293 different coronaviruses".

They wrote: "From these samples, we detected 293 highly diverse coronaviruses, of which 284 were designated alphacoronaviruses and 9 were designated betacoronaviruses on the basis of partial RdRp sequences." 

In virology, "isolated" suggests that they cultured the virus, which is not what they did. Instead, they amplified a small piece of DNA from the environmental sample. Even using general English, the term "isolated" is not accurate -- they did not separate the virus from the rest of the sample. This mistake could be important, since it suggests that they have hundreds of viable viruses in their collection. Please use the term 'detected'. AdamChrisR (talk) 21:01, 29 December 2023 (UTC)

Clarify : RaTG13 has not been confirmed to exist in nature
i think these two sentences are confusing for folks unfamiliar with laboratory techniques.

First sentence The sequence of RaTG13 was reconstructed from metagenomic sampling (a common practice in environmental virology), and as such, could potentially be an in-silico chimera.

Suggestion Something like

RaTG13 was not captured as a live virus, rather the genetic sequence of RaTG13 was reconstructed from an environmental sample through from process known as metagenomic sampling (a common........

2nd sentence

RaTG13 has not been confirmed to exist in nature, to have been cultured or isolated in any laboratory, or to be a viable human pathogen.

Might be better as

Due to the limitations of metagenomics the exact published sequence of RaTG13 has not been confirmed to exist in nature, to have been cultured or isolated in any laboratory, or to be a viable human pathogen.

I do not know the exact science here. But it's confusing to find out several paragraphs in this might not exist. 108.6.139.251 (talk) 17:09, 11 June 2024 (UTC)