Talk:Variants of SARS-CoV-2

Medrxiv sourcing and technical DOI issues

@Jaredroach: I fully understand medrxiv is not a proper Wikipedia reference. I'm glad you've decided to remove medrxiv references which are not based on any peer review. However, one of the articles you removed is actually also published in a reputable journal (Cell (journal)), and should have been updated instead of removed.

The point of my edit was to add in a DOI pointing to the peer reviewed paper. Before my edit, the article had a DOI pointing to the medrxiv preprint, but not the actual paper. Unfortunately, the Template:cite journal does not have a parameter for medrxiv preprints within the same citation, so I moved the preprint link to a separate template within the same footnote to keep the source accessible, since the publisher article is paywalled. I'm not adding any references here, just clarifying the DOI of the authoritative source.

I think your revert was based on a misunderstanding. Finding an article on medRxiv doesn't mean it's *not* peer reviewed, it's just not a sufficient evidence of peer review. 〈 Forbes₇₂ | Talk 〉 22:10, 2 October 2021 (UTC)

That's fine. But in no case should there be any need to reference medrxiv. If an article in medrxiv is published later in a reputable source, one should reference the reputable source. One should not reference medrxiv "pending" the availability of that reputable source. I think it is correct for one editor to remove the medrxiv source, and for another editor to add the new source. The first editor might not easily have the info for next source, nor should they feel obligated to find it before deleting the medrxiv source. After removing the medrxiv source, the material may be unsourced. A "citation needed" tag can be added, and eventually the material can be deleted or someone can add the new reference. Jaredroach (talk) 22:16, 2 October 2021 (UTC)

I agree with you that using preprints as "pending" sources should never be done, and any non-peer reviewed sources used as a reference should be deleted. I'd just point out that arxiv/biorxiv/medrxiv will link from the preprint directly to the published version if it exists, so it's a one-click check to see if the reference is salvageable. I assume you're just objecting to standalone medrxiv references as bad, and not any and all preprint links? Adding a link to the preprint is accepted practice on Wikipedia as long as the underlying peer-reviewed paper is also linked in the same citation. I three options to add the missing peer-reviewed link to the citation:

1. replace the DOI link to the preprint with a DOI link to the reviewed paper, but keep the preprint accessible in a nearby template (what I did before revert)

2. replace the DOI link to the preprint with a DOI link to the reviewed paper, remove the link to the preprint entirely (I would object if medrxiv was the only free source, but since there's a PMC link this doesn't matter much)

3. update the cite journal template so we can include both the DOI link to the paper and DOI link to the preprint in the same template.

I'd say option 3 is ideal, but it would take some time since cite journal is a highly visible, fully protected template. What do you think? 〈 Forbes₇₂ | Talk 〉 23:26, 2 October 2021 (UTC)

Absent explicit assurance that the content of the preprint is identical with the content of the peer-reviewed (published) version, they should not be considered equivalent. Peer review often results in revisions (it's not simply an approval process). — soupvector (talk) 23:42, 2 October 2021 (UTC)

That's a very technical distinction to make. In my experience comparing peer-reviewed papers to preprints, preprints verus published paper end up pretty similar, so I usually prefer to link to both in the case of a paywall. I agree the published one is the authoritative source. I think its a mistake to remove preprint links for peer-reviewed papers, but I've gone ahead and removed the preprint doi altogether in this one case so at least the citation template is correct. 〈 Forbes₇₂ | Talk 〉 01:59, 31 October 2021 (UTC)

No idea how easy it is to update MedrXiv preprints, but updating ArXiv preprints to match the final accepted version (in content, not format, font, etc) is standard practice. This guarantees green open access. Any non-trivial changes in the review process are normally put in the final versions of the preprints, because it's a lot easier to check ArXiv preprints than waste time trying to guess which journals are non-paywalled. Moreover, some papers have mathematical errors introduced by proofreaders that the authors fail to pick up when double-checking the proofs, in which case the version-of-record is wrong and the final preprint is right. The peer review process statistically improves the quality of research papers, but hiding or removing preprint information generally functions as a block against access to verifiable information, especially with journals that are still paywalled. Caveat: the actual practice may vary across disciplines - here I'm talking of astronomy/cosmology - I can't judge MedrXiv. Boud (talk) 06:51, 26 November 2021 (UTC)

"Positive" vs. "Negative" vs. "Neutral" mutations

Could somebody further explain to me what the video in the article means by "positive mutations" and "negative mutations"? What makes a mutation positive or negative? CessnaMan1989 (talk) 01:48, 5 November 2021 (UTC)

Google scholar might help--Ozzie10aaaa (talk) 15:23, 4 December 2021 (UTC)

B.1.1.529

Just saw news of this breaking over the last couple of hours. It's currently listed on the WHO tracking page as a variant under monitoring. I'm not sure what counts as a RS in this topic area yet, I note however that Axios have stated that it's ben found so far in Botswana, South Africa, and Hong Kong. Reuters state 100 specimens in South Africa, and confirm what Axios state for Botswana and Hong Kong but state the Hong Kong case is a traveller from South Africa. Sideswipe9th (talk) 18:19, 25 November 2021 (UTC)

I've added the basic info from the WHO tracking page. Not sure what to cite for more detailed information in the notes section however. Sideswipe9th (talk) 18:25, 25 November 2021 (UTC)

Thanks User:Sideswipe9th for making the addition. I think the sheer number of mutations on the spike protein alone is the most concerning part and perhaps needs to be mentioned. The following news sources state that there are 32 spike mutations. SpookiePuppy (talk) 19:45, 25 November 2021 (UTC)

@PhiLiP: I've just had an afterthought, to ping the Stanford HIVDB team who created those superb genome map figures (https://en.wikipedia.org/wiki/Talk:Variants_of_SARS-CoV-2#Genome_maps) which showed the different SARS-CoV-2 variants, to make them aware of this discussion about the new variant (B.1.1.529). SpookiePuppy (talk) 20:14, 25 November 2021 (UTC)

@SpookiePuppy: Thanks! We are updating our site correspondingly. --PhiLiP (talk) 18:10, 28 November 2021 (UTC)

This reference might be useful, but the situation at the moment is so uncertain that I think it would be better to wait for a statement from the WHO. The effect of these mutations on neutralization needs to be tested. --Fernando Trebien (talk) 00:26, 26 November 2021 (UTC)

Six Southern African countries added to England's red list for travel; "100 cases confirmed through full sequencing of samples, up from just 10 reported on Wednesday, and signs of community transmission," 90% of cases in Gauteng. But still only VUM for WHO, not (yet) VOI or VOC. Boud (talk) 01:01, 26 November 2021 (UTC)

WHO will meet 26 Nov 2021 to decide if upgrading B.1.1.259 from VUM to VOI or VOC is justified.

There are already draconian travel restrictions all over the lot. Once WHO settles on the nomenclature, article drops. This thing came out of the gate fast...! https://www.theguardian.com/world/live/2021/nov/26/covid-news-live-new-variant-sparks-tougher-restrictions-in-india-and-singapore-ahead-of-who-meeting

kencf0618 (talk) 10:19, 26 November 2021 (UTC)

David Nabarro from the WHO: "it is going to be some weeks before we can say for certain whether our fears have any basis" [1] --Fernando Trebien (talk) 14:44, 26 November 2021 (UTC)

Maybe Responses to the COVID-19 pandemic in November 2021 is a good place to write about this subject for now. --Fernando Trebien (talk) 14:53, 26 November 2021 (UTC)

Certainly the UK's addition to their travel red list should be added to that page. Sideswipe9th (talk) 15:50, 26 November 2021 (UTC)

I've added a quick and dirty prècis focusing on Africa, but note that the impact is already global. It'll get its own article and timeline soon enough. (I refer to it as "Variant Nu" inasmuch as WHO hasn't officially announced the nomenclature.) kencf0618 (talk) 17:24, 26 November 2021 (UTC)

It's Omicron. https://www.bbc.com/news/live/world-59426277 kencf0618 (talk) 18:27, 26 November 2021 (UTC)

Proposal to add mutations to variant tables (total and in the spike protein)

Especially regarding the news for Variant B.1.1.529 with 32 mutations in the spike protein (for comparison Delta has 7+) also found in an Israeli Tourist returning from Malawi probably boostered with Pfizer–BioNTech it should be informative to add the info of known total and spike protein mutations to all variant comparison tables, so under Overview variants of concern (VOC) and Alerts for further monitoring (WHO) and maybe if possible also under Nomenclature SARS-CoV-2 corresponding nomenclatures. Understanding the range of mutational variability while remaining infectious of the SARS-CoV-2 virus is of utter importance combined with understanding how it effects natural and vaccine immunity in the variants of concern. --Krahax (talk) 08:54, 26 November 2021 (UTC)

The VOC table is a bit overloaded, but the Alerts table has plenty of space. However, being so atypical for B.1.1.529, I think it would be best to write this in prose for due weight. The number of mutations has theoretical implications - it "may" affect immunity from vaccines and the effectiveness of antibody therapies; but it also may not. Most mutations do not affect these characteristics, some do significantly, and the combined effect is difficult to predict. --Fernando Trebien (talk) 12:18, 26 November 2021 (UTC)

Thx for the response Ftrebien. AFAIK the immunity could be much more effected by the number of mutations in contrast to transmission-rate and severity which should depend more on the type of mutations. But of course any paper/expert review on this is welcome. I can't find the source but found an interesting 2D/3D plot of the mutation differences of Alpha, Beta, Gamma, Delta interesting. I'm not sure if it was in a paper with CC-BY(-SA) licence or in a media article. Not sure if possible but a comparison of the predicted post-Delta Scenarios would be informative to see if one model is close to the future reality. --Krahax (talk) 13:06, 26 November 2021 (UTC)

"Nu" Omicron variant

There are lots of mainstream news reports stating that B.1.1.529 has been named as the "nu" variant by the WHO. However, this seems to be jumping the gun; I see that the meeting to discuss this is happening right now (see [2]), and there is as yet no official word on this. As or when a "nu" variant is declared in WP:MEDRS, it should be added here. -- The Anome (talk) 17:03, 26 November 2021 (UTC)

And here we go: WHO has indeed declared B.1.1.529 a variant of interest, (see [3]) but assigned it the Greek letter omicron, not nu. Perhaps because "nu" sounds like "new"? -- The Anome (talk) 18:11, 26 November 2021 (UTC)

If they are skipping nu, the next should be xi not omicron. Agmartin (talk) 18:15, 26 November 2021 (UTC)

WHO published a statement about classifying B.1.1.529 as Omicron and a Variant of Concern. ― Aidan ⦿ (talk) 18:33, 26 November 2021 (UTC)

WHO recently named the new variant lineage #B11529 as "Omicron," but I have not been able to find here any info on the variant named "Xi", which is the preceding letter ib the Greek alphabet. 108.12.194.196 (talk) 19:00, 26 November 2021 (UTC)

Given that China's current leader is Xi Jinping, I think it's quite unlikely that the WHO will use the letter. I'm also guessing that it's likely that they skipped "nu" because it sounded too much like "new". -- The Anome (talk) 19:04, 26 November 2021 (UTC)

References

WHO skips nu and xi

WHO skips nu and xi.

https://www.rt.com/news/541479-who-nu-xi-omicron-covid/

https://nypost.com/2021/11/26/who-skips-two-letters-in-alphabet-in-naming-omicron-variant/ — Preceding unsigned comment added by 208.98.202.34 (talk) 05:46, 27 November 2021 (UTC)

yes your correct, rather odd on their part--Ozzie10aaaa (talk) 13:16, 28 November 2021 (UTC)

Hong Kong

In the article Hong Kong is said to have reported one case. There have actually been two, from the very moment it was announced that the B.1.1.529 strain was detected in their samples.[4][5][6][7] 1.64.47.144 (talk) 14:37, 27 November 2021 (UTC)

 Not done. 'The Straits Times' reports that it was "brought in by a man who had flown in from South Africa on Nov 11... This patient, 36, then allegedly passed on the virus to another man who was staying in a neighbouring room at the hotel." I think it makes more sense to keep the article saying "one" since there was only one person that brought it to Hong Kong, and saying two would imply otherwise. ◢  Ganbaruby!  (talk) 00:02, 3 December 2021 (UTC)

Source for risk classification

The table under Overview highlights many cells according to some color coding for risk. Is there any source for that, or is it OR? ◅ Sebastian 12:37, 29 November 2021 (UTC)

how would 'color coding' be OR?--Ozzie10aaaa (talk) 15:25, 4 December 2021 (UTC)

@Ozzie10aaaa:: Simple: When someone marks a variant with a color such as red, it means “Very high risk”. That's a statement of fact – and even an extreme and potentially dangerous one – that obviously needs a reference. ◅ Sebastian 22:22, 3 January 2022 (UTC)

Nomenclature

Currently the 2nd sentence of Section #2 Nomenclature is "As of July 2021, no consistent nomenclature was established for it." whose reference (via Twitter) is a January 2021 WHO statement archived from the original on 23 January 2021, retrieved 2 February 2021. Since a later sentence is "After months of discussions, the World Health Organization announced Greek-letter names for important strains on 31 May 2021." (also with a Twitter reference) should "July" be a different month? Maybe https://www.who.int/publications/i/item/WHO-2019-nCoV-genomic_sequencing-2021.1 should be used for the January reference and https://www.who.int/news/item/31-05-2021-who-announces-simple-easy-to-say-labels-for-sars-cov-2-variants-of-interest-and-concern for the May reference instead of Twitter. Mcljlm (talk) 00:56, 1 December 2021 (UTC)

thank you for post--Ozzie10aaaa (talk) 15:26, 4 December 2021 (UTC)

Original strain name

Is there a name for the original strain, eg. "SARS‑CoV‑2 wild-type" or "SARS‑CoV‑2 original" or something like that? Or is its name just "SARS‑CoV‑2", without any qualifiers? There are some older designators, like SARS‑CoV‑2 strain G and SARS‑CoV‑2 strain L; are these differences regarded as being on the same level as the Greek-lettered variants, or as just minor differences within a single variant? -- The Anome (talk) 13:16, 3 December 2021 (UTC)

I could be wrong but I believe its SARS‑CoV‑2--Ozzie10aaaa (talk) 15:25, 4 December 2021 (UTC)

Xi variant is not a "common" last name

It should be noted in the article that Xi is factually not a very "common" last name. While the threshold of "common" can be debated, the point is entirely moot as stated. The surname Mu, an already named variant recognized by WHO, is relatively much more common of a last name.

MU: ~1025k instances, 527th most common (https://forebears.io/surnames/mu)

XI: ~775k instances, 708th most common (https://forebears.io/surnames/xi)

The fact that the current CCP leader's name is Xi, however, remains factually correct. — Preceding unsigned comment added by 73.8.240.69 (talk) 03:32, 4 December 2021 (UTC)

According to China's Ministry of Public Security http://gat.ah.gov.cn/public/7081/40201012.html via Google Translate there are "more than 6,000 surnames in use today" (though https://edition.cnn.com/2021/01/16/china/chinese-names-few-intl-hnk-dst/index.html, based on that has "about 6,000 surnames are in use". According to https://www.scmp.com/news/china/science/article/3157678/lambda-mu-omicron-why-who-skipped-nu-and-xi-name-latest, based on the Ministry of Public Security data, "the Chinese president’s surname is the 296th most common family name" and "Two other surnames that would also be read as “Xi” but read in different tones were more common, ranking 169 and 228". Mcljlm (talk) 08:01, 4 December 2021 (UTC)

New variant detected in France (B.1.640.2)

There are news reports of another variant being detected in Forcalquier in the south of France. It has been provisionally named B.1.640.2. Apparently it was detected in early December 2021 at the IHU Méditerranée, Forcalquier. Scientists are suggesting that the origin may lead back to a person returning from a trip to the Cameroon. SpookiePuppy (talk) 21:03, 3 January 2022 (UTC)

References

And it's likely to become "variant of concern" -Abhishikt (talk) 00:57, 4 January 2022 (UTC)