A single line often inverts meaning once you see what it
answers, so neighbouring messages are always shown.
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WA1 has three differences to both WH04 and Hu-1 - all three ancestral.
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Lemme check these human sequences against the larger pango/bat alignment I have - since I have all the assemblies for those too.
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Not sure that is the same WH04 - there are some confusing names
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[and I'll see if I can get the raw data for WA1 so I can check the assembly for that one too - although it's been sequenced multiple times, so I assume it's correct]
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2020-12-06 10:17
Kristian G. Andersen
Lemme get WH04 from GISAID (I have been using MT291829 from NCBI as WH04)
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Comparing to all the pango/bat sequences here is interesting - in two out of the three positions (8782 (C/T) and(18060 C/T) where WA1 is ancestral compared to RaTG13, all the other pango/bat genomes have the same asRaTG13 - so definitely ancestral. HOWEVER, RmYN01 has the same derived residues in those positions as WA1. (Ican't check the third position - RmYN01 has bad sequencing around that position). Checking SARS...
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hCoV-19/Fujian/8/2020 I EPI_ISL_411060 -> seems to be identical to WA1 and sampled around the same time.
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SARS splits the differences.
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Compared to all the pango/bat genomes, those positions appear ancestral to me - Hu-1 and RmYN01 have derived residues in those positions.