3 ms·

These are all very compelling claims. I am wondering if you can provide at least one reference for each. E.g. "There are now many known related sarbecoviruses w

These are all very compelling claims. I am wondering if you can provide at least one reference for each. E.g. "There are now many known related sarbecoviruses which have been found with furin cleavage sites" is a claim that can be referenced pretty easily with a link to papers reporting said sarbecoviruses.

lamontcg 5y ago
https://www.sciencedirect.com/science/article/pii/S1873506120304165 https://www.sciencedirect.com/science/article/pii/S187350612... https://www.biorxiv.org/content/10.1101/2021.01.26.428212v1 https://www.biorxiv.org/content/10.1101/2021.01.26.428212v1 https://www.independentsciencenews.org/commentaries/phylogeographic-mapping-of-newly-discovered-coronaviruses-pinpoints-direct-progenitor-of-sars-cov-2-as-originating-from-mojiang/ https://www.independentsciencenews.org/commentaries/phylogeo... https://www.frontiersin.org/articles/10.3389/fmicb.2020.584717/full https://www.frontiersin.org/articles/10.3389/fmicb.2020.5847... https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006698 https://journals.plos.org/plospathogens/article?id=10.1371/j... https://www.nature.com/articles/s41467-021-21240-1 https://www.nature.com/articles/s41467-021-21240-1 https://www.researchsquare.com/article/rs-871965/v1 https://www.researchsquare.com/article/rs-871965/v1
- areyousure 5y ago
  From your first link: "SARS-CoV-2 is the only virus in subgenus Sarbecovirus having this feature" From your second link: "Finally, the poly-basic (furin) site present in SARS-CoV-2 is absent in both RshSTT182 and RshSTT200." Your third link doesn't discuss furin cleavage sites very much. Your fourth link literally doesn't contain the substring "furin". Your fifth link literally doesn't contain the substring "furin". Your sixth link at least partially supports your claim with a single mention of furin, saying "The two viruses shared part of the furin cleavage site unique to SARS-CoV-2", but the whole truth is that while they have insertions at the S1/S2 cleavage site in the spike protein, they do not contain the full furin cleavage site. https://en.wikipedia.org/wiki/RmYN02 https://en.wikipedia.org/wiki/RmYN02 From your seventh link: "None of these bat viruses harbors a furin cleavage site in the spike." (Protip: in this claim #4 of yours under discussion, you should change "sarbecoviruses" to "betacoronaviruses".)
  - createdapril24 5y ago
    I only reviewed the first link. What I took away from it is that furin cleave sites occur in the family of coronaviruses naturally, but have not been seen in those most closely related to SARS-CoV-2. This note about not having closely related coronaviruses having such a feature is also true of SARS-CoV-1, which also leads evidence to its ability to occur naturally within a given subgenus (unless we posit also original SARS was lab-leak, but I do not think anyone has posited this.) I have not evaluated 2-7.
willupowers 5y ago
I believe the uniqueness has been established by the issue that the specifics of the 12-nt insertion is never found anywhere in a natural setting. Many papers have gone back and forth over this and there's no natural example.
- createdapril24 5y ago
  Can you explain the importance of the 12-nt insertion, and also provide some references regarding it not being evolved naturally?

lamontcg 5y ago

https://www.sciencedirect.com/science/article/pii/S1873506120304165 https://www.sciencedirect.com/science/article/pii/S187350612... https://www.biorxiv.org/content/10.1101/2021.01.26.428212v1 https://www.biorxiv.org/content/10.1101/2021.01.26.428212v1 https://www.independentsciencenews.org/commentaries/phylogeographic-mapping-of-newly-discovered-coronaviruses-pinpoints-direct-progenitor-of-sars-cov-2-as-originating-from-mojiang/ https://www.independentsciencenews.org/commentaries/phylogeo... https://www.frontiersin.org/articles/10.3389/fmicb.2020.584717/full https://www.frontiersin.org/articles/10.3389/fmicb.2020.5847... https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006698 https://journals.plos.org/plospathogens/article?id=10.1371/j... https://www.nature.com/articles/s41467-021-21240-1 https://www.nature.com/articles/s41467-021-21240-1 https://www.researchsquare.com/article/rs-871965/v1 https://www.researchsquare.com/article/rs-871965/v1

areyousure 5y ago
From your first link: "SARS-CoV-2 is the only virus in subgenus Sarbecovirus having this feature" From your second link: "Finally, the poly-basic (furin) site present in SARS-CoV-2 is absent in both RshSTT182 and RshSTT200." Your third link doesn't discuss furin cleavage sites very much. Your fourth link literally doesn't contain the substring "furin". Your fifth link literally doesn't contain the substring "furin". Your sixth link at least partially supports your claim with a single mention of furin, saying "The two viruses shared part of the furin cleavage site unique to SARS-CoV-2", but the whole truth is that while they have insertions at the S1/S2 cleavage site in the spike protein, they do not contain the full furin cleavage site. https://en.wikipedia.org/wiki/RmYN02 https://en.wikipedia.org/wiki/RmYN02 From your seventh link: "None of these bat viruses harbors a furin cleavage site in the spike." (Protip: in this claim #4 of yours under discussion, you should change "sarbecoviruses" to "betacoronaviruses".)
- createdapril24 5y ago
  I only reviewed the first link. What I took away from it is that furin cleave sites occur in the family of coronaviruses naturally, but have not been seen in those most closely related to SARS-CoV-2. This note about not having closely related coronaviruses having such a feature is also true of SARS-CoV-1, which also leads evidence to its ability to occur naturally within a given subgenus (unless we posit also original SARS was lab-leak, but I do not think anyone has posited this.) I have not evaluated 2-7.

willupowers 5y ago

I believe the uniqueness has been established by the issue that the specifics of the 12-nt insertion is never found anywhere in a natural setting. Many papers have gone back and forth over this and there's no natural example.

createdapril24 5y ago
Can you explain the importance of the 12-nt insertion, and also provide some references regarding it not being evolved naturally?