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Accidental leakage hypothesis

BBC has reported on a new hypothesis on the origin of the virus: a possible accidental leakage. In the article they deny a couple of times the plausibility of the hypothesis, but oddly enough, their title was posted with an interrogation mark: "Coronavirus: Is there any evidence for lab release theory?". Also odd is the ending paragraph, which seems to me to indicate that the story is not over. Check it out: "Amid this war of words between the countries, the painstaking - and largely unseen - scientific work to trace the origin of the virus will continue." If other reputable sources mention this hypothesis I propose to include it in this Wiki entry --Forich (talk) 01:31, 19 April 2020 (UTC)

And then what? How many more lunatic fringe theories should go in? It is just flu? (Bolsanaro); it is all caused by 5G transmissions (Icke et al), fluoride/contraception in the water? cocaine on banknotes? Yes, like dictionaries, Wikipedia should report what actually exists rather than what should (or should not) exist but per wp:FALSEBALANCE, we really have to be very careful about how much airtime we give to this kind of fake news. As I wrote a few weeks ago, careless talk costs lives. --John Maynard Friedman (talk) 13:08, 19 April 2020 (UTC)
  • Yes, sure I checked your article [1]. There are many other articles which say exactly the same. But what is their argument, exactly? Author asks: "How do we know the virus didn’t escape from a lab?" and answers: "Indeed, accidental laboratory exposures and escapes have occurred in the past, including the influenza virus and SARS-CoV. However, this week the chairman of the joint chiefs of staff echoed that the weight of evidence continued to suggest natural rather than accidental emergence for SARS-CoV-2." It then cites this article which provides precisely zero evidence that "the virus didn’t escape from a lab". This is a hearsay by an administrator that has nothing to do with any science or any actual investigation. Please see quotation of Dr. Alex Greninger cited in one of the sources (my comment above). My very best wishes (talk) 15:39, 28 April 2020 (UTC)
I disagree in your assesment of the accidental-leakage hyphotesis as a fringe one. You are making a straw-man argument by mixing the hypothesis together with others that are well-known to be easily-disregarded. My original post had nothing to do with those, and is not my problem whether those are included in this entry. Now that we are clear on the subject discussed, my point stands: reputable news agencies are reporting on the accidental-leakage hypothesis and I propose that we discuss here how to mention it in this entry --Forich (talk) 14:17, 20 April 2020 (UTC)

Please, see Talk:2019–20 coronavirus pandemic § Leaked from lab. There is extensive discussion about the topics and sources there. --MarioGom (talk) 08:19, 21 April 2020 (UTC)

Indeed, anyone interested in discussing how to include a mention of the accidental-leakage hypothesis should direct their efforts at the pandemic page, linked above by MarioGom, since that's the appropiate place for it. Patient zero remains undisputably unknown and speculation about sources of earliest contagion add little to this entry. --Forich (talk) 05:02, 22 April 2020 (UTC)
And the consensus there is this is a wild conspiracy theory, minimally different from the 5G conspiracy. WP:DUCK. --John Maynard Friedman (talk) 09:55, 21 April 2020 (UTC)

There is at least one plausible hypothesis for lab release. "... a researcher at Flinders University in South Australia lays out another scenario that involves human intervention. Bat coronaviruses can be cultured in lab dishes with cells that have the human ACE2 receptor; over time, the virus will gain adaptations that let it efficiently bind to those receptors. Along the way, that virus would pick up random genetic mutations that pop up but don't do anything noticeable, said Nikolai Petrovsky, in the College of Medicine and Public Health at Flinders." (https://www.livescience.com/coronavirus-wuhan-lab-complicated-origins.html) (Asifwhale (talk) 00:25, 24 April 2020 (UTC))

The Chinese govt has also responded to this claim. As well as the WHO. I think this deserves inclusion with NPOV. But I think we can merge this concept into the leakage from the wuhan weapons lab theory, whether or not it is accidental. I dont see how we would need two sections or subsections on these highly related speculations. Jtbobwaysf (talk) 19:22, 21 April 2020 (UTC)

I came to this article looking for a neutral description of this issue based on reputable sources. Because it is so often spoken of, I'd welcome such content. -Reagle (talk) 19:32, 21 April 2020 (UTC)
  • This depends on notability, not science. If a hypothesis, a conspiracy theory, whatever has been widely covered in media, it should be included. But it should be properly included, i.e. we should say this is an unproven view, a hypothesis, etc., however it was described in RS. But I am holding off on that one. My very best wishes (talk) 16:36, 23 April 2020 (UTC)
  • "Fringe theory" is not a scientific term, for the record. In science, there are testable hypotheses based on a proposed mechanism (which the researcher elaborated on), and then there are theories that are well-supported hypotheses based on scientific consensus (what most people refer to as "fact"). There was no pseudoscientific element of the researcher's proposition; it was all defined with proper vocabulary. (Asifwhale (talk) 00:25, 24 April 2020 (UTC))
I commented here - even before all these publications appear. Sure, it came from bats, but how exactly it came from the bats is a mystery. Looks suspicious. One can not exclude it pass through a lab. My very best wishes (talk) 20:01, 23 April 2020 (UTC)
  • Also, Nikolai Petrovsky is a world-renowned scientist who has developed countless vaccines. (Asifwhale (talk) 15:37, 25 April 2020 (UTC))
  • There is nothing extraordinary with laboratory-based outbreaks. This had happen with Marburg virus in 1998 [2], and again in 1990 [3]. There were other similar cases. Now, I am looking at the publication about "coronavirus hunters". One should realize that such research activities can potentially lead to a leakage of the most deadly viruses. They wear hazmat suits. Yes, sure, that is exactly what researchers from "Vektor" did, but the leakage had happen. I am reading (link above) that "The new coronavirus matched a sample taken from a horseshoe bat in a cave in Yunnan in 2013," says Daszak. "It was 96.2% identical.". OK, 96% is not really the same, but who took this sample in 2013 and what they did with it? This is a legitimate question. Not so much related, but bats, while harboring a lot of deadly viruses (merely because they form enormously dense populations where everything is transmitted very quickly), are not invincible - see White-nose syndrome. Was it such a bad thing? My very best wishes (talk) 15:47, 27 April 2020 (UTC)
P.S. The "virus hunting" [4] was justified by the argument that the transmission to human population would happen any way. But this argument will not hold if COVID-19 in fact resulted from an accident leaking or worse. That's why the complete clarity on the emergence of this virus is so important. My very best wishes (talk) 16:20, 27 April 2020 (UTC)

I find it astonishing that this conspiracy theory is still running anywhere outside the National Enquirer/Daily Mail/Oval Office where it belongs. Please read this article: Kindrachuk J, Coronavirus Frontlines (17 April 2020). "A Virologist Explains Why It Is Unlikely COVID-19 Escaped From A Lab". Forbes. Retrieved 22 April 2020. and then read Occam's Razor. — Preceding unsigned comment added by John Maynard Friedman (talk • contribs) 17:39, 27 April 2020 (UTC)

  • I was the one who wrote that info on the main page. I even had to remove one of your "citation needed" comments because you were so poorly read on the topic. Please do not direct scientists on this talk page to read Forbes articles. While lab release is possible, it is nearly impossible to scientifically find evidence to support it; there can only be speculation, which is valid. To confirm anything, actual detective work or transparency on all bat experiments would have to be released. (Asifwhale (talk) 22:27, 27 April 2020 (UTC))
  • OK, here is the story. This is a publication in Nature in 2016 entitled A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence. They created a genetically modified strain of SARS that was capable of invading humans by using human angiotensin converting enzyme II (ACE2) as a receptor. That is exactly what COVID-19 does. In terms of protein structure, we are talking about this protein complex between the spike protein and receptor. Here is another paper about it in PNAS. Now, if I understand correctly, that kind of dangerous research has been shutdown by the NIH under Obama administration: [5], [6]. However, the Chinese researchers in Wuhan did continue these studies and discovered numerous SARS-like coronaviruses which used the same ACE2 receptor to infect cells and could "replicate efficiently in primary human airway cells,", as they published in PLOS. Add the fact that SARS had escaped from the lab in Wuhan several times, and it seems pretty obvious that the COVID-19 could indeed be leaked from the lab after being an object of experiments in this lab. My very best wishes (talk) 00:15, 28 April 2020 (UTC)
This idea of "lab leak" was allegedly "disproved" by the sequence analysis. But this is nonsense. The sequence analysis can not disprove it at all. Yes, it came from bats, but this could happen through the lab. As cited here [7], "Although researchers will likely continue to sample and sequence coronaviruses in bats to determine the origin of SARS-CoV-2, "you can't answer this question through genomics alone," said Dr. Alex Greninger, an assistant professor in the Department of Laboratory Medicine and an assistant director of the Clinical Virology Laboratory at the University of Washington Medical Center. That's because it's impossible to definitively tell whether SARS-CoV-2 emerged from a lab or from nature based on genetics alone. For this reason, it's really important to know which coronaviruses were being studied at WIV. "It really comes down to what was in the lab," Greninger told Live Science." My very best wishes (talk) 00:15, 28 April 2020 (UTC)
  • Thank you. I think it would be appropriate to include this information, especially since it is commentary from credible scientists. The part about coronaviruses being genetically modified to bind to the ACE2 receptor is a little off. They are all capable of that naturally. The Nature paper just mentions that humans as species have many subtlety different gene sequences for ACE2 (orthologs), and the spike protein can bind to any of them; so despite our diversity, the virus can effectively infect across many individuals and populations. In a lab, however, one can mutate the spike protein (enhance or gene knockdown) to see the effects. Or grow the virus on human cell cultures where the spike protein gene would then be placed under high selective pressure (which is also why it cannot be used for phylogenetics purposes; there has to be neutral selection on the gene for it to be selected for phylogenetics analysis). (Asifwhale (talk) 01:03, 28 April 2020 (UTC))

We stand together to strongly condemn conspiracy theories suggesting that COVID-19 does not have a natural origin.
— Calisher C, Carroll D, Colwell R, Corley RB, Daszak P, Drosten C, et al. (19 February 2020). "Statement in support of the scientists, public health professionals, and medical professionals of China combatting COVID-19". The Lancet. 395 (10226). doi:10.1016/S0140-6736(20)30418-9.

Misinformation related to the 2019–20 coronavirus pandemic § Accidental leakage covers this.

Have the peer-reviewed scientific journals published anything new since early April? Is this article all up-to-date on those? You've read up on them, added the info in, and have plenty of time left to kill? A round of applause for you! Pat yourself on the back. Take a break. What're you still doing here? Go on, now. Log out, power off the device, relax. You deserve some well-earned rest. Rotideypoc41352 (talk · contribs) 08:31, 28 April 2020 (UTC)

This source tells: "We stand together to strongly condemn conspiracy theories suggesting that COVID-19 does not have a natural origin. Scientists from multiple countries have published and analysed genomes of the causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and they overwhelmingly conclude that this coronavirus originated in wildlife, as have so many other emerging pathogens".
  • Yes, sure, this is true. No one disputes that the virus originated from bats. But it appears that a number of similar viruses (we do not know if any one of them was COVID-19) were collected, brought to the lab in Wuhan and studied by the Chinese researchers as they published themselves in PLOS. Were any of them leaked from the lab? We do not really know, but it seems very likely because same lab has leaked previously a number of other pathogens including SARS. What kind of experiments did they perform on the virus beyond ones described in the PLOS article? I mean such genetic engineering experiments, merely artificial selection for something or whatever. We also do not know, but the Chinese researchers have a sufficient expertise: the head of the group (last author in the PLOS publication) was one of the co-authors in the earlier (in Nature) publication, and that is apparently Shi Zhengli, a director of the Center for Emerging Infectious Diseases at the Wuhan Institute of Virology. Also see this article by Washington Post [8], which tells a lot more than my post here My very best wishes (talk) 15:52, 28 April 2020 (UTC)

Wikipedia should not be promogulating politically motivated conspiracy theories about the virus. Saying that natural selection is unable of creating such an effective virus and therefore it must have been lab created is idiotic and obviously false considering the many pandemics throughout history have happened with no genomic editing technology whatsoever, and the crude nature of current genomic editing technology. The nature of this argument feels similar to that of Ancient astronauts, where of course "primitive" indigenous people can't have created complex works of architecture therefore it must be aliens. It's the same fallacy. We now know that the US Government is pushing this conspiracy theory to cover for their own failures. (Mazzetti, Mark; Barnes, Julian E.; Wong, Edward; Goldman, Adam (2020-04-30). "Trump Officials Are Said to Press Spies to Link Virus and Wuhan Labs". The New York Times. ISSN 0362-4331. Retrieved 2020-04-30.) Hemiauchenia (talk) 16:32, 30 April 2020 (UTC)

@John Maynard Friedman, MarioGom, Hemiauchenia, and EvergreenFir: thank you. This bioweapon / artificially created / leaked theory is not credible according to scientists, who instead of indulging in wild and politically motivated conspiracy theories, are hard at work trying to understand the origin and evolution of this virus. There are now many thousands of scientific papers on this topic, including dozens or hundreds directly relevant to this issue. Those should be the sources we consider. I am dismayed to learn that the few scientists on earth who were intelligent and cared enough to study coronaviruses, understanding their danger to humanity, are now the very same people being blamed for this catastrophe by politicians who have done little or nothing to help. -Darouet (talk) 17:51, 30 April 2020 (UTC)
  • According to NYT article, "Most intelligence agencies remain skeptical that conclusive evidence of a link to a lab can be found, and scientists who have studied the genetics of the coronavirus say that the overwhelming probability is that it leapt from animal to human in a nonlaboratory setting, as was the case with H.I.V., Ebola and SARS.". I guess it summarizes this well. Of course, just "being skeptical" and "probability" shows that people do not know really know it for sure. Given the secrecy in China, this could be finally disproven by finding the actual population of bats or other animals where COVID-19 originated. There is none so far. Or perhaps further studies of this virus, which is highly unusual according to some virologists [9], will be able to finally resolve this question. My very best wishes (talk) 22:45, 30 April 2020 (UTC)
But why all these suspicions at the first place? That's because the entire purpose of the research by Dr. Zhengli was to discover something like SARS-CoV-2 in her lab prior to the actual pandemics. Apparently, she did not succeed. But she is going to succeed in the future [10]:
Despite the disturbance, Shi is determined to continue her work. “The mission must go on,” she says. “What we have uncovered is just the tip of an iceberg.” She is planning to lead a national project to systematically sample viruses in bat caves, with much wider scope and intensity than previous attempts. Daszak’s team has estimated that there are more than 5,000 coronavirus strains waiting to be discovered in bats globally. “Bat-borne coronaviruses will cause more outbreaks,” Shi says with a tone of brooding certainty. “We must find them before they find us.”
.
So, she now will be looking for a super-COVID-19. And what they will do when they find it? Leak to the outside world, exactly as they did with SARS twice in the Wuhan lab? This seems to be very dangerous for humanity. My very best wishes (talk) 23:01, 30 April 2020 (UTC)
Well, since you are clearly so fond of conspiracy theories, then of course you will give the same credence to the equally bat-shit-crazy idea that a US military operative brought it to Wuhan last October. In the meantime, read up about virology: scientists are studying viruses in labs all over the world, trying to get ahead of the next one. How do you think the annual flu vaccine gets specified, oh wait, don't tell me, you don't believe in vaccines either? --John Maynard Friedman (talk) 09:57, 1 May 2020 (UTC)
  • You and some other people above are using the Straw man argument. Please check the original question at the top of the thread. Now, speaking about the science, there is no scientific proof right now it was not leaked from the lab and even that it could not be created in a lab. Yes, I think it probably was transmitted to a human directly by a bat (there is no really a proof of that), but it could be created in a lab with modern technologies. As correctly posted here (this is not an RS), If you hear anyone claim “we know the virus didn’t come from a lab”, don’t buy it — it may well have. Labs around the globe have been creating synthetic viruses like CoV2 for years. And no, its genome would not necessarily contain hallmarks of human manipulation: modern genetic engineering tools permit cutting and pasting genomic fragments without leaving a trace. It can be done quickly, too: it took a Swiss team less than a month to create a synthetic clone of CoV2.. And the quick creation of the synthetic clone of COVID-19 [11] is a scientific fact. It proves that anything is possible, unless the exact origin of the virus (such as the specific population of bats it came from) has been established. It was not. My very best wishes (talk) 14:55, 1 May 2020 (UTC)
@John Maynard Friedman: why get your COVID19 news from peer-reviewed scientific journal articles when you can get it from the website [12] of a far-right antisemitic party [13] that wants access to nuclear weapons [14]? -Darouet (talk) 14:59, 1 May 2020 (UTC)
Well, your first ref is an interview with well known researcher (who studied COVID-19) by RFE/RL. Two others are not on this subject. What I cited above was Scientific American. Blog posts like that one are generally not good, but they may be useful for finding better sources. That one I think is especially helpful if anyone is interested in the subject. My very best wishes (talk) 15:52, 1 May 2020 (UTC)
There is no scientific proof that it didn't come from an alien landing either. Science 101: it is impossible to prove a negative. Now can we stick to hard evidence and lose the Trump2020 campaigning. Per WP:NOTFORUM, I will not contribute further to this nonsense thread. --John Maynard Friedman (talk) 16:17, 1 May 2020 (UTC)
Oh no, Science 101: it is usually possible to study where viruses came from and how, and that one is not an exception. That is assuming that Chinese scientists are not re-introducing the COVID-19 back to a selected population of bats right now to find them later and thus prove the origin of the virus. My very best wishes (talk) 16:30, 1 May 2020 (UTC)
And just to elaborate on "virus hunters" (quotation above). Peter Daszak just said [15]: “Let's find all of these viruses, find out the genetic sequences, design vaccines that work against all of them so we're protected against all future pandemics. That's the vision.” What? Does not he know that main stage in vaccine development is large-scale testing, which will not be done unless there is an actual pandemic? Consider the amount of effort spent to develop the vaccine for COVID-19 or any other important vaccine that actually work. They are not going to develop any proven vaccines. That sounds like Lysenkoism. Will they leak the pathogens to population? Yes, that had already happen with many pathogens. My very best wishes (talk) 17:54, 1 May 2020 (UTC)
John Maynard Friedman, you are using a straw man argument, that's disingenous. Reputable sources have reported the hypothesis, although labeling it as 'purely speculative'. We should register it as a minority view, with a caveat that it has been dismissed. The circumstantial evidence of previous cover-ups, and previous leakages in labs, calls for an independent investigation on the hypothesis. What we have looks like someone ate some cookies in the kitchen, there are no clues on who did it, but a children appears suddenly with his mouth and lips full of cookie chips. The sensible thing to do, instead of asking the children if he ate the cookies and take his word, is to conduct an independent research. Now that is Science 101. --Forich (talk) 15:56, 2 May 2020 (UTC)

Should an origin section be added?

I'm proposing that we add a section that includes the debate on how COVID-19 originated.

Respectfully, Thanoscar21 (talk) 22:26, 5 May 2020 (UTC)

But the point is that we don't know how it originated we know that its ultimate origin is probably in bats, which is mentioned in the lead. Such a section, if created should not give WP:UNDUE weight to politically motivated claims that the virus escaped from a lab, which there is no evidence for. Hemiauchenia (talk) 22:48, 5 May 2020 (UTC)
Evidence is not required to meet WP:DUE only coverage in the press is. We have seen widespread coverage on these issues. Jtbobwaysf (talk) 06:32, 6 May 2020 (UTC)
Of course you are free to explore any subject you want, as long as it has good sources. With a controversial topic, it might be good to explore it on the talk page first. The controversy surrounding the bat and weapons lab origins are likely DUE. There are a couple of links to sources higher up on this talk page that I added here Talk:Severe_acute_respiratory_syndrome_coronavirus_2#Investigations_China_Lab_Theory. I suppose there are a few theories, and it would be encyclopedic to cover those that have significant press coverage. Jtbobwaysf (talk) 09:01, 6 May 2020 (UTC)

Investigations China Lab Theory

Call for investigation by Austraila [16] and response by PRC. I recall there was also some talk of this by the US. Let's see if this develops to multiple countries. Jtbobwaysf (talk) 19:36, 29 April 2020 (UTC)

A WHO Advisor is now supporting this this china lab theory. Jtbobwaysf (talk) 11:30, 2 May 2020 (UTC)

Well, I am reading this. Some of the mentioned facts are well known and were published elsewhere. Such as the refusal to allow an independent investigation or the synthesis of SARS-like coronaviruses to analyze if they could be transmissible from bats to humans (the publication in Nature Medicine). Actually, if their stated goal was Let's find all of these viruses, find out the genetic sequences, design vaccines that work against all of them so we're protected against all future pandemics (said Dr. Daszak, see another thread above), then they absolutely needed to study if and how the found viruses can be transmissible to humans and possibly even generate artificial fusion versions of viruses as a part of vaccine development. But we simply do not know for sure what they did. My very best wishes (talk) 15:43, 2 May 2020 (UTC)
In addition to the secrecy by Chinese government, there are numerous suspicious details around this. Consider this publication in Science which makes a reference to this expert discussion, where one should look through all replies. As Science tells, Richard H. Ebright "questioned the accuracy of Bedford’s calculation that there are at least 25 years of evolutionary distance between RaTG13—the virus held in the Wuhan virology institute—and 2019-nCoV" (and of course he is right, this is something obvious), but it appears during discussion that the lab in Wuhan withheld the sequence of RaTG13 during 7+ years prior to the deposition in a public database in January 2020. According to Richard H. Ebright, the lab in Wuhan keeps a lot of other unpublished/withheld coronovirus sequences for years (and perhaps some of them are closer to the COVID-19 than RatG13?). Doing so is extremely unusual; such sequences are typically released prior to any publications. The only possible explanation in my mind would be involvement of the lab in a secret or military project(s) with these sequences. I am not sure though how things are done in China. Maybe they have a First Department. My very best wishes (talk) 20:21, 2 May 2020 (UTC)
Excellent, thank you! I suppose we can just about create a section on this. Jtbobwaysf (talk) 09:37, 5 May 2020 (UTC)

Russia joins in on discussion and Fauci says no. More than enough discussion here for a DUE controversy. Jtbobwaysf (talk) 09:20, 6 May 2020 (UTC)

The national intelligence services of US, CA, UK, AU, NZ (together known as the Five Eyes network) say that there is no evidence in this case of an accidental, let alone deliberate, release from the Wuhan virus lab.[1] Accidental virus and bacterial releases certainly happen so it could have happened, but right now it is pure speculation and inappropriate for this article (try Conspiracy theories). Please apply Occam's razor. --John Maynard Friedman (talk) 09:46, 6 May 2020 (UTC)

Why is the Guardian article hiding its sources's identity? I am legitimately curious.--Forich (talk) 00:57, 7 May 2020 (UTC)

References

  1. ^ Dan Sabbagh (4 May 2020). "Five Eyes network contradicts theory Covid-19 leaked from lab. No current evidence to suggest coronavirus leaked from Wuhan research lab, agencies say". The Guardian.

We have built a UCSC genome browser for the SARS-CoV-2. I know that all human gene pages already have outlinks in the info box to our human UCSC Genome Browser, but on the info box on this page, there only is a link to the NCBI Genome Browser. Does anyone have an idea who I would have to talk to to get a link to another genome browser added to the "genomic information" infobox? --Maximilianh (talk) 23:01, 4 May 2020 (UTC)

@Maximilianh: hello! Hope you're well. Some templates have parameters that let you override the default values. I took a look at the documentation for Template:Infobox genome. Looks like taxID automatically links NCBI, and the documentation doesn't clearly state how to link to another genome browser. Do you mind linking some examples of human gene pages [that] already have outlinks in the info box to our human UCSC Genome Browser? Maybe we could take a look at some of those pages, see what's going on there, and simply replicate it here.
Edited 02:28, 5 May 2020 (UTC) to add: You may also want to check out the associated WikiProject at Wikipedia:WikiProject COVID-19.
Also, headsup: your userpage shows you've had this account for a while and clearly, you list an individual email address on your userpage, but just to be super safe, I'd avoid using "we"/"us" and stick to "I"/"me". Sometimes, use of first-person plural hints at a shared account, which falls afoul of our account policies. Also, some employers have policies about speaking on their behalf. This is, admittedly, a nanoscopic point, especially since you are following the rules, but better to be unambiguous about it. Rotideypoc41352 (talk · contribs) 02:17, 5 May 2020 (UTC)
@Rotideypoc41352: Hello! Yes, this taxId tag always links to NCBI. Our browser is linked from chromosomal locations, on most human gene pages, e.g. PITX2 or P53, in the infobox, under "location (UCSC)". And yes, this is my account, it's fine by my employer (who's a University) but I'm saying "we" because there are many people working on the genome browser, and I don't want to create the impression that it was all my work. I can add my work email to my talk page. --Maximilianh (talk) 12:40, 5 May 2020 (UTC)

I need to add that the current link only goes to the Genbank entry and no visual browser. our link would be https://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1 since wuhCor1 is the name of our assembly (it predates the international naming recommendation to SARS-CoV-2) — Preceding unsigned comment added by Maximilianh (talk • contribs) 12:49, 5 May 2020 (UTC)

Hmm...to be frank, I am still sorting out my thoughts on what I've found, so please bear with me. So those pages use a different infobox, Template:Infobox gene. To my understanding, it calls (?) Module:Infobox gene, which generates the infobox using the gene's information as stores on the centralized depository (?) at Wikidata. While updating the genome's Wikidata entry would be great (it uses the same login; the folks there can provide better help than I can), I tried using Infobox gene on the bacterial gene mecA, and it didn't work well. Admittedly, the Wikidata entry on mecA is paltry, but it looks like Infobox gene is geared toward human genes and their mouse orthologs. The Module code seems to generate the URL based on chromosome position, so I don't know if we can get that URL you have there.
At this point, I'm wondering if our best bet is to just edit the genome infobox to do what you want. We might be able to edit the template directly as long as we don't break anything. My concern is that the genome infobox parameter will only see use on this page, which kind of defeats the point of a template, haha. I'm also concerned that someone may undo the addition, but based on my experience, using a non-existent infobox parameter only generates an error in preview, not when someone is simply reading the article.
Let me fool around with Infobox genome and maybe the Wikidata entry for SARS-CoV-2 genome. See what happens. Rotideypoc41352 (talk · contribs) 18:51, 5 May 2020 (UTC)
I've linked the UCSC genome browser in the genomic info infobox. Still haven't poked around Wikidata. Likely not needed, but I like to cover my bases. Rotideypoc41352 (talk · contribs) 23:28, 5 May 2020 (UTC)
Hey great, that seems like a very simple change! one note: the tag for the link is called "assembly". That's a very general term, UCSC is not the only group providing assemblies and the UCSC codes often differ from other databases, almost every database has their own identifier system. If you modify it again, I would change the "assembly" tag to "ucsc_assembly" to make sure that editors understand that the identifier is specific to this website. By the way, can I find pages that use this info box? We have around 200 assemblies, so I can now easily add the links for the other infoboxes. (BTW it is reassuring that this wikidata connection is also confusing to you, I found it very surprising. :-) ). --Maximilianh (talk) 11:30, 6 May 2020 (UTC)
Does take some getting used to, especially when you remember when enwp hosted such data locally, but it does make more sense for the different language Wikipedias and other Wikimedia projects to pull (pool?) shared data from one place. You or your colleagues might take a look at Wikidata. I see GLAMs (galleries, libraries, archives, and museums) engaging with it but don't edit Wikidata enough to know how other parts of, say, a university can use it.
Special:WhatLinksHere/Template:Infobox genome. That page lets you filter results by namespace, too.
I changed the parameter name as you've suggested as well. Rotideypoc41352 (talk · contribs) 17:22, 6 May 2020 (UTC)
@Maximilianh: hello again! I amend part of my previous comment. Please seriously consider also editing Wikidata. You mentioned the UCSC has around 200 assemblies and almost every database has their own identifier system. Adding the UCSC genome browser identifier to, for example, d:Q87901425 and the other 200 would be a great boon. One, anyone pulling data from Wikidata would then have easy access to the UCSC genome browser, which would be great for the university. Two, it would link said party to a potentially useful resource. Three, if somehow Infobox genome goes the way of Infobox gene, the relevant Wikidata entries will already have the UCSC identifier (and whoever's involved in building the new template/module would have an easier time implementing that part). I should repeat that I don't edit Wikidata much (though it shares a login with enwp), so the community there could have info and knowledge that I don't and decide against opening the floodgates to all identifier systems, so to speak. I don't see the harm in trying a few pages and asking active Wikidatans for input. Stay well, Rotideypoc41352 (talk · contribs) 05:36, 7 May 2020 (UTC)

Weasel words in the article

This section:

Several sources consider these terms racially charged and state they contribute to the xenophobia and racism caused by the outbreak.

is problematic. Who are the "sources"? Citing "sources", "experts", "authorities", etc. isn't acceptable especially for what is obviously just a point of view. These are textbook cases of weasel words. --RaphaelQS (talk) 15:43, 2 May 2020 (UTC)

 Not done: it's not clear what changes you want to be made. Please mention the specific changes in a "change X to Y" format and provide a reliable source if appropriate. Rotideypoc41352 (talk · contribs) 17:37, 2 May 2020 (UTC)
I'm not asking you (or anyone) for anything, please do not use this template, it's inappropriate. I'm opening up the discussion and if any action is to be taken it will be in a second stage. I think that the necessary corrections are obvious: either removing the section with the weasel words, or substituting the weasel words with an acceptable attribution of the point of view, but I'm waiting to get the views of other contributors on the matter. --RaphaelQS (talk) 18:20, 2 May 2020 (UTC)
Aren't the sources listed right after that sentence? Enivid (talk) 09:53, 3 May 2020 (UTC)
This is not the same as an attribution of a point of view. For example it's not enough to say "some sources say this thing is bad" even with a bunch of media sources all saying a variation of "yes, this thing is bad". --RaphaelQS (talk) 18:16, 4 May 2020 (UTC)

@RaphaelQS:, I wrote this sentence. The reason it was added is the adding the hot term "China/Chinese virus" without the context that it widely considered derogatory would be unencyclopedic. The reason that "Chinese virus" is even in the article in the first place is because of a 2 month discussion pushed by several persistent users (most notably the currently blocked Symphony Regalia, who is regarded by most who have interacted with him as persistent time waster) that the terms "wuhan virus" and "China virus" should be used in the lead as alternate names for the virus. That ended up making its way to the NPOV noticeboard, the result of which being that "China virus" and "wuhan virus" should not be used in the lead as alternative names, but could be discussed in a terminology section. This then resulted in more edit warring between me and Symphony Regalia about the nature of the terminology section, with the above discussions Talk:Severe_acute_respiratory_syndrome_coronavirus_2#Symphony_Regalia_edit_warring_again_over_"China_virus" and Talk:Severe_acute_respiratory_syndrome_coronavirus_2#Hemiauchenia's Interference with NPOV discussion board results, which were resolved by outside editors to the sections current form. After two months arguing about China virus I've quite had quite enough honestly. Hemiauchenia (talk) 18:57, 2 May 2020 (UTC)

I cleaned it up a bit. Having trouble finding WP:DUE statements in this. Removed a few sources that were not WP:RS for this. We arent going to name Mr. Woo, who is CEO of a toy factory. I suppose this not notable Mr. Kennedy from the notable organization Center for Strategic and International Studies is ok for now. Certainly the NYT stating that the statements by the Chinese govt is clearly WP:DUE. I dont object if anyone wants to remove the CSIS. This was a very weaselly statement, and needed to be cleaned up. Thanks! Jtbobwaysf (talk) 18:43, 4 May 2020 (UTC)
I agree in retrospect that some of the sources that I added to support the statement were borderline and not due weight, thanks for the cleanup. Hemiauchenia (talk) 18:52, 4 May 2020 (UTC)
And then 20 minutes later you added the content back here. Correct? I'll remove the bad sources again. Refrain from the WP:BATTLE. Re-added here, with a link [17]. We dont use words such as "many", the weasel words got even worse. Thanks! Jtbobwaysf (talk) 09:28, 5 May 2020 (UTC)
@Jtbobwaysf: I didn't add the sources back, @Rotideypoc41352: did. Please fully read the edit history before making accusations. This was my edit, which only added the term "public health expert" and added a third reliable source from the Washington post, here's Rotidey's edit, which re-added back all the references. My point was that suggesting that the Chinese government is the only one who is complaining about the term "Chinese virus", rather than many ethnic minorities, borders on WP:POV insertion. Hemiauchenia (talk) 13:46, 5 May 2020 (UTC)

Apologies, I re-added your Washington Post source with a specific person based upon below logic.

  • Harvey Dong: Apparently not even a tenured professor and no BLP.
  • Charissa Cheah, professor of psychology at UMBC who is doing a study. No BLP article.
  • Gilbert Gee, UCLA’sSchool of Public Health. “Now, they’ve basically made it okay to have anti-Asian bias.” Has BLP, thus maybe WP:DUE. I chose to add this one since he has a BLP.

Maybe we can add more here. I suspect there will be more notable people and we can add or subtract based upon WP:DUE. I dont share the concern about Asian vs. Chinese, as the controversial WP:ALTNAME is the China virus, not the Asian virus. Thanks! Jtbobwaysf (talk) 15:37, 5 May 2020 (UTC)

@Jtbobwaysf:, what about Celeste Ng and Jeremy Lin? Who are mentioned in the Guardian article. Hemiauchenia (talk) 16:42, 5 May 2020 (UTC)
@Hemiauchenia: we have no quarrel between us; I've just always been a direct person, which often translates poorly across the Internet. When I responded to your NPOVN discussion citing WP:MEDRS, Jtbobwaysf called the content guideline established through consensus (!) nonsense. I say this not to be uncharitable, but to point out a lack of understanding of policy. Their subsequent behavior has turned this ignorance into a pattern.
I see flaws with their criteria. For example, are we going to add George Takei, too? He has a BLP, has spoken out against the term. Sure, he's nikkei and this is not the Asian virus, but the Japanese-Americans have been stalwart defenders of civil rights. Just look at when people were talking about locking up Arab Americans after 9/11 and more recently on the inclusion of questions on legal status on the census. Anyway, he's alive, notable, said something, but is not Chinese. Do we include his opinion?
Also, when have we valued the speech of celebrities over those who have devoted years and decades to studying and working for this? Just because the person doesn't have a BLP, we should disregard their expertise? That applies to almost every author of every scientific paper we've painstakingly built this article with. BLP simply means notability, and as often mentioned at AfD, doing your job well isn't necessarily notable. Conversely, you can fail inclusion for criteria and have well-informed statements people should heed.
Again, no quarrel between us, Hemi. Like you and many others across the COVID-19-related pages, I'm tired. These topics have been a time sink, and this article is a month's worth of MEDRS behind on a fast-moving research subject. But I realize you may not have the context I do but have shown a pattern of listening to anything reasonable even when you disagree, so I chimed in. Thanks, and stay well, Rotideypoc41352 (talk · contribs) 18:17, 5 May 2020 (UTC)
@Rotideypoc41352: I don't really significantly disagree with your edits Rotidey. The comment wasn't an attack on you or your edits, and I didn't realise it would come off that way, for that I apologise. My issue wasn't with your edit, but with Jtbobway accusing me of making them, my comment was simply to clarify that I didn't. I agree that we shouldn't really be citing random celebrities as evidence that the term "Chinese virus" is racist, but just saying "many people have said the term is racist" does feel like a bit of a blanket statement that needs further clarification. As an additional note I have added a link to this discussion over at Wikipedia talk:WikiProject COVID-19 so hopefully more contributors will come to resolve this. Hemiauchenia (talk) 18:29, 5 May 2020 (UTC)
A basketball player an obscure author would not qualify for inclusion here, that would be UNDUE. Thanks! Jtbobwaysf (talk) 19:08, 5 May 2020 (UTC)
@Hemiauchenia: no harm done! I just wanted to point out flaws in Jtbobway's reasoning 'cause I didn't see anyone else do so yet. I just have the subtlety of a charging bull, alas.
And from one tired editor to another: when are we going to finish this and move on to the research? Moxy linked a RdRP paper above; I keep telling myself to check the paper on TMPRSS2 (the protease) and check other sources to update the viral load and viral shedding data. I've also heard some paper found the virus might downregulate ACE2. Fascinating stuff. That's another discussion, though. (Then there's that strain vs. virus edit request above. Viral taxonomy hurts my head.) Rotideypoc41352 (talk · contribs) 19:13, 5 May 2020 (UTC)
WP:NOTFORUM applies to to lovefest going on. I'll split into two sub-sections to allow more room for all the people that want to pile on to the objections. Jtbobwaysf (talk) 19:17, 5 May 2020 (UTC)
Clarifying talk page comments or discussing adding article content does not come under WP:NOTAFORUM. What you consider to be due weight for attributed opinion and reliable sources for statements is ultimately your own judgement, and this is why we need the opinions of outside contributors in order to come to a concensus that most people who contribute to the project agree upon. Hemiauchenia (talk) 19:29, 5 May 2020 (UTC)
Correct relating to the obvious that wikipedia is about the opinions of multiple editors. Keep your personal discussions to your personal respective talk pages. Jtbobwaysf (talk) 19:31, 5 May 2020 (UTC)
I'm not sure how any comments I've made on this talk page were "personal". Theres no need for the sharp-elbowed tone with me either. I didn't criticise you, that was Roidey, whose comment also acted like you weren't an active contributor to the discussion, which I think was pretty rude and uncalled for, and created a hostile atmosphere for discussion. Hemiauchenia (talk) 19:56, 5 May 2020 (UTC)
Sorry for escalating the situation here. I've struck my comments. Rotideypoc41352 (talk · contribs) 20:58, 5 May 2020 (UTC)
@Rotideypoc41352: I think you have valuable contributions to make to this discussion, and should unstrike the parts of that don't involve criticsm of Jtbobway, which were largely fair and reasonable. Hemiauchenia (talk) 21:11, 5 May 2020 (UTC)
In this section we are discussing weasel words and this china virus altname. Please try to keep the comments relating to this discussion. You can always create another section to discuss these other protease points. Second, lots of editors engage in conversations on their personal talk pages, it is a great place to do that for subjects that are off topic. Jtbobwaysf (talk) 21:26, 5 May 2020 (UTC)
Unstruck part of my comments. Rotideypoc41352 (talk · contribs) 16:40, 7 May 2020 (UTC)

There's definitely value in documenting the politicial debate around the virus name. I've summarized the discussion to cover key chronology and details. I've also added a link to an existing entry in a related topic. This medical topic (see the content above and below the Terminology section) is not the appropriate place for a deep dive into U.S. politics. I'd suggest expanding the existing discussion of this subject in one of these non-medical topics:

- Wikmoz (talk) 04:31, 7 May 2020 (UTC)

I agree, that this article should only have limited content on the subject and wikilink. There are two separate issues.
  • The first is the interim name Wuhan Virus (武汉肺炎) name that was an unofficial location based interim name used for the virus. This has to be kept in connection to the medical name as it is encyclopedic and reflects that the location based naming system was not used in this case, as apparently is no longer the standard. This name had widespread usage in both China and outside China, including Xinhua News Agency an official state propaganda agency. It is encyclopedic since it is interesting that while Spain was blamed for the Spanish Flu (maybe incorrectly) that China was not blamed for the Wuhan flu (that also may not have originated in Wuhan, so says at least some). Thus the naming convention part of this is absolutely WP:DUE.
  • On to the second name, China Virus. This name seems to be a political name pushed by Trump and seems to have existed after the virus was officially named. I havent read anything that suggests that China Virus name was referring to the medical term for the virus. I think it may as Wikmoz points out be referring to some politicized name for the COVID19 pandemic, which is not the subject of this article and has its own articles that are suitable for extended content on this China Virus POV subject. One (or two sentences max) for NPOV here would be fine, and not a list of all the basketball players and barely notable authors that object to it. The weasel words were evidence of an attempt to jam content into the article that probably didn't belong.
Thanks! Jtbobwaysf (talk) 10:59, 7 May 2020 (UTC)
(While 武汉 certainly means "Wuhan", 肺炎 means "pneumonia", not "virus". <joke>Just in case someone wants a tattoo that says "love", but the tattoo artist shows them those characters instead.</joke>) Rotideypoc41352 (talk · contribs) 16:40, 7 May 2020 (UTC)

My additions of additional names weren't things I was massively keen on either, it was more to highlight the disjointedness of attributed opinions in that section, and I am glad they have been removed entirely. I am happy with the section in its current form as Wikimoz has edited it, there are better places for expanded discussion of controversy regarding terminology. Kind regards Hemiauchenia (talk) 14:48, 7 May 2020 (UTC)

Removal of cited statement concerning materials used in retention study

A while ago, I added some information on this page, as well as another, from an NIH study about the stability of coronavirus on various surfaces. It seemed to have been completely removed in subsequent edits, and due to edit volume I was not able to figure out which specific diff took it out. Since there isn't any discussion about it on the talk pages, I'm adding it back to both articles. It seems to have been removed accidentally -- if there is a reason for this information to be removed, I'll take it back out. { } 03:58, 8 May 2020 (UTC)

@Jacob Gotts: found it.

these terms are used in the appendix of the paper, but the paper itself uses "plastic" and "stainless steel" without attempting to restrict the applicability of its conclusions in this way
— User:Dekimasu 12:45, 9 April 2020 (UTC)

Still looking for the COVID-19 article. I'll comment that article's talk when I find it. Cheers, Rotideypoc41352 (talk · contribs) 19:59, 8 May 2020 (UTC)
Thanks. I see the point here, which was why I had put the specific materials in parentheses. Most citations I've seen for the study just say "plastic and steel", which to me implies it was tested on a variety of polymers/alloys rather than just two -- so I think it might be prudent to note this (I was surprised to find they'd only measured it for one plastic). { } —Preceding undated comment added 00:13, 9 May 2020 (UTC)

Coronavirus 2 and T-cells

In a Google search I ran across this web page (April 16, 2020) which claims that SARS-CoV-2 attacks T-cells like HIV, yet there is nothing about this in this Wikkipedia article. Does anyone know whether this is "fake news"? Should it be included? I also found this article "This HIV/AIDS Specialist Explains Its Similarities — And Differences — To COVID-19", which appears to be more balanced. --Robert.Allen (talk) 20:36, 14 May 2020 (UTC)

The first link looks like click bate. There is some evidence that Covid-19 infects T cells, but there is little evidence that this has clinical consequences. If anything, Covid-19 overstimulates the immune system (or at least part of it) resulting in damage to the lungs and other organs. Covid-19 is bad enough, we don't need to invent other problems that don't exist. Claims that it attacks the immune system like HIV are indeed "fake news". Boghog (talk) 21:07, 23 May 2020 (UTC)

Semi-protected edit request on 8 May 2020

Krypstick (talk) 14:26, 8 May 2020 (UTC)

There is a major inaccuracy on this page.The section - "A phylogenetic network analysis of 160 early coronavirus genomes sampled from December 2019 to February 2020 revealed 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".[64][65]" - is factually incorrect and is entirely based on a source that was debunked by the scientific community (see e.g. https://twitter.com/arambaut/status/1248387395201847296).

Also the statement of an origin in late 2019 - "The virus shows little genetic diversity, indicating that the spillover event introducing SARS-CoV-2 to humans is likely to have occurred in late 2019.[19]" - would benefit from an additional reference: https://www.sciencedirect.com/science/article/pii/S1567134820301829

 Not done: Twitter is not a reliable source. One cite is enough to source that statement. Don Spencertalk-to-me⛅ 19:59, 8 May 2020 (UTC)
 Partly done: removed flawed PNAS phylogeny study per two letters in that same journal https://www.pnas.org/content/early/2020/05/06/2007062117 and https://www.pnas.org/content/early/2020/05/06/2007295117 (full disclosure: as cited in https://twitter.com/arambaut/status/1258532977241292801) Rotideypoc41352 (talk · contribs) 20:34, 8 May 2020 (UTC)
Krypstick's request does not withstand scrutiny and the deletion should be reverted. In detail, following the links to the PNAS paper and to Cambridge University (April 2020), it is clear that the two debunking letters have been debunked in the Reply published alongside - evidently the critics had simply misread the paper, confusing the A, B and C types, etc. Then, following Krypstick's link to Krypstick's preferred paper (the Balloux paper May 2020) shows that Krypstick's preferred paper in fact confirms the start of the epidemic around November 2019. 86.161.82.133 (talk) 11:15, 23 May 2020 (UTC)
 Undone: This request has been undone. I do see the reply to the articles mentioned by 86.161.82.133, and have undone the changes as requested by that editor. As DonSpencer1 originally stated, Twitter is not a reliable source. — Tartan357  (Talk) 14:11, 25 May 2020 (UTC)

Requested Move to capitalized Severe Acute Respiratory Syndrome Coronavirus 2

I'm not going to make this an official request, just some friendly advice from a computer person and former member of WikiProject Medicine. Having the name in lower case looks bad and reflects out of date ideas and discussion on talk pages regarding WP:Capitalization. Similar discussion on renaming Boeing 737 MAX to Max. There 3 lengthy no concensus debates to change the name away from the official plane designator, just because of a 2 decades old policy (not just Zoom->ZOOM). Previous move requests are were done by lay people not knowing the difference between a vector and an illness trying to call it the covid virus.

In a technical sense, there will be no problems on the backend with old links not having capitalization. They will all redirect right to this page right here and it won't cause any problems. Technophant (talk) 23:09, 2 June 2020 (UTC)

But why? Wikipedia:Manual of Style/Capital letters#Animals, plants, and other organisms suggests the use of lowercase for commons names of organisms just as for the species part of scientific names. (I know that a virus is not considered a complete organism, but this is the closest thing in the guidelines.) The official name is lowercase. Why does it look bad, according to you? All those capitals make the text more crowded, so lowercases enhances readability. Bever (talk) 14:28, 3 June 2020 (UTC)
Hello! Hope everyone's well. The official naming from the experts of ICTV's Coronavirus Study Group: Here, we present an assessment of the genetic relatedness of the newly identified human coronavirus3, provisionally named 2019-nCoV, to known coronaviruses, and detail the basis for (re)naming this virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which will be used hereafter. Lowercase it is. Stay safe, Rotideypoc41352 (talk · contribs) 15:47, 3 June 2020 (UTC)

I have linked this discussion at Wikipedia talk:Manual of Style/Capital letters#Current so that people who care about capitalization style can discover it. Dicklyon (talk) 15:08, 3 June 2020 (UTC)

Diseases, syndromes, conditions, etc. are generally lower case in Wikipedia and elsewhere with the exceptions of proper names that are part of them. So, for example, Lyme disease after Lyme, Connecticut and Ebola after the Ebola River, but without a proper name, lower case. SchreiberBike | ⌨  19:32, 3 June 2020 (UTC)
Per SchreiberBike. An opinion that it "looks bad" is not a substantial arguement for its move. Regards, Cinderella157 (talk) 23:41, 4 June 2020 (UTC)

SARS-CoV-2 possibly a hybrid

The virus is likely to be a hybrid of viruses from two different species. See the research paper and a link for a general overview here. •Shawnqual• 📚 • 💭 06:46, 3 June 2020 (UTC)

@Doc James: is this WP:DUE? Jtbobwaysf (talk) 21:25, 8 June 2020 (UTC)

"Severe acute respiratory syndrome coronavirus 2.0" listed at Redirects for discussion

Information icon A discussion is taking place to address the redirect Severe acute respiratory syndrome coronavirus 2.0. The discussion will occur at Wikipedia:Redirects for discussion/Log/2020 June 17#Severe acute respiratory syndrome coronavirus 2.0 until a consensus is reached, and readers of this page are welcome to contribute to the discussion. Pandakekok9 (talk) 08:39, 17 June 2020 (UTC)

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