Slack / Private Message Drop — page 946

MN908947.3 28081 28104 nCoV-2019_93_LEFT 60 +``` [2021-06-19 10:35:55] [Robert Garry] Wang _et al._ (2020a) sequenced PCR amplicons covering nu- cleotide sites 21,563 to 29,674 of the SARS-CoV-2 genome, which spans from the start of the spike gene to the end of ORF10. They also sequenced a short amplicon generated by nested PCR that covered a fragment of ORF1ab spanning sites
15,080 to 15,550. In this paper, I only analyze the region from spike through ORF10 because this is a much longer contiguous sequence and the amplicons were generated by conventional rather than nested PCR. I slightly trimmed the region of interest to 21,570 to 29,550 because many samples had poor coverage at the termini." [2021-06-19 10:36:40] [Andrew Rambaut] Ah - OK so not the ARTIC amplicons then [2021-06-19 10:39:07] [Robert Garry] WA1 is lineage A and has bat-like T8782 and C28144 plus another bat-like snp - what mutation is this? [2021-06-19 10:41:05] [Robert Garry] More top secret stuff - Tony and Francis have arranged a call with Jesse tomorrow - need to sort this out... [2021-06-19 10:42:47] [Robert Garry] C18060T? [2021-06-19 11:33:37] [Andrew Rambaut] ```But the earliest known SARS-CoV-2 sequences, whichare mostly derived from the Huanan Seafood Market, are no-tably more different from these bat coronaviruses than othersequences collected at later dates outside Wuhan. ``` This is incorrect - WA1 is from Wuhan [2021-06-19 11:34:38] [Robert Garry] *Yes from your earlier post (Numbering off by 1) Andrew Rambaut* [12:11 PM] Wuhan-Hu-1: T:8781:C|T:18059:C|C:28143:T WH04: T:18059:C WA1: 0: [2021-06-19 11:34:43] [Andrew Rambaut] So it is they are notably (2 or 3 mutations) more distant from RATG13 than other viruses in Wuhan at the same time [2021-06-19 11:56:30] [Robert Garry] Yes - he's got WA1 in the mix, but yes definitely WA1 early Wuhan for sure. I'm thinking Jesse making much ado about nothing - it's lineage A going to lineage B with WA1 from Wuhan ancestral. [2021-06-19 12:03:01] [Robert Garry] "Rambaut _et al._ (2020) suggest that viruses from the clade labeled "B" in Figure 4 may just "happen" to have been sequenced first, but that other SARS-CoV-2 sequences are really more ancestral as implied by phylogenetic rooting." Uhhh Rambaut is right about this...