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Slack / Private Message Drop, p.297 [SLACK_000511] · slack_pm:msg:03099

Date: 2020-12-06 10:32
Type: chat message · slack
recipient: Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker: Kristian G. Andersen

Recipients on this medium are inferred from channel membership, not per-message addressing.

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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A single line often inverts meaning once you see what it answers, so neighbouring messages are always shown.

2020-12-06 10:15 Kristian G. Andersen open

Lemme check these human sequences against the larger pango/bat alignment I have - since I have all the assemblies for those too.
2020-12-06 10:16 Andrew Rambaut open

Not sure that is the same WH04 - there are some confusing names
2020-12-06 10:16 Kristian G. Andersen open

[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]
2020-12-06 10:17 Kristian G. Andersen open

Lemme get WH04 from GISAID (I have been using MT291829 from NCBI as WH04)
2020-12-06 10:32 Kristian G. Andersen

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...
2020-12-06 10:42 Andrew Rambaut open

hCoV-19/Fujian/8/2020 I EPI_ISL_411060 -> seems to be identical to WA1 and sampled around the same time.
2020-12-06 10:51 Kristian G. Andersen open

SARS splits the differences.
2020-12-06 10:52 Kristian G. Andersen open

Compared to all the pango/bat genomes, those positions appear ancestral to me - Hu-1 and RmYN01 have derived residues in those positions.
2020-12-06 10:53 Kristian G. Andersen open

Here's an alignment - it's pretty messy and some duplicates... [shared file(s): 2020.12.06_pango-bat-sars2_alignment.geneious]

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