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Slack / Private Message Drop, p.1015 [SLACK_001229] · slack_pm:msg:10603

Date: 2021-10-05 16:09
Type: chat message · slack
recipient: Kristian G. Andersen, Edward C. Holmes, Andrew Rambaut
speaker: Robert F. Garry

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https://www.science.org/doi/10.1126/science.1092002?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rf r_dat=cr_pub%20%200pubmed Between the coronavirus sequences of the palm civets (SZ3 or SZ16) and each of the human SARS-CoV sequences, the ratios of the rates of nonsynonymous to synonymous changes (Ka/Ks) for the S gene sequences were always greater than 1, indicating an overall positive selection pressure. However, pairwise analysis of the Ka/Ks for the genotypes in each epidemic group (fig. S6) (_14_) shows that the average Ka/Ks for the early phase was significantly larger than that for the middle phase, which in turn was significantly larger than the ratio for the late phase, which in fact was significantly less than 1 (table S3). These data indicate that the S gene showed the strongest positive selection pressures initially, with subsequent purifying selections andeventual stabilization. For Orf1a, we observed a pattern similar to that for the S gene (table S3). In contrast, Orf1b(nt coordinate: 13,398 to 21,485) seems to be undergoing purifying selection during the whole course of the epidemic. Indeed, it is the most conserved genomic region of SARS-CoV (_7_).

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journal https://www.science.org/doi/10.1126/science.1092002?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rf

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2021-10-05 15:03 Edward C. Holmes open

Thanks Bob. So where does BANAL-20-50 differ most from SC2?
2021-10-05 15:09 Kristian G. Andersen open

Yes. These viruses are about as far from banal as can be...
2021-10-05 15:18 Robert F. Garry open

Not anywhere that I can see at least at the amino acid level. All of the proteins I've looked at so far are very very similar. Just looking at the proteins, you would really be hard pressed to call this a different virus species IMO. I'm guessing that most of the nt changes are third base changes (codon usage).
2021-10-05 15:37 Robert F. Garry open

From the paper - I think most of that minor orf3a difference is the 9 aa indel. [shared file(s): image.png]
2021-10-05 16:09 Robert F. Garry

https://www.science.org/doi/10.1126/science.1092002?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rf r_dat=cr_pub%20%200pubmed Between the coronavirus sequences of the palm civets (SZ3 or SZ16) and each of the human SARS-CoV sequences, the ratios of the rates of nonsynonymous to synonymous changes (Ka/Ks) for the S gene sequences were always greater than 1, indicating an overall positive selection pressure. However, pairwise analysis of the Ka/Ks for the genotypes in each epidemic group (fig. S6) (_14_) shows that the average Ka/Ks for the early phase was significantly larger than that for the middle phase, which in turn was significantly larger than the ratio for the late phase, which in fact was significantly less than 1 (table S3). These data indicate that the S gene showed the strongest positive selection pressures initially, with subsequent purifying selections andeventual stabilization. For Orf1a, we observed a pattern similar to that for the S gene (table S3). In contrast, Orf1b(nt coordinate: 13,398 to 21,485) seems to be undergoing purifying selection during the whole course of the epidemic. Indeed, it is the most conserved genomic region of SARS-CoV (_7_).
2021-10-05 16:11 Robert F. Garry open

The "orf 1b" part is about 99.7% similar between SC2 and BANAL-20-50.

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