Slack / Private Message Drop — page 296

[2020-12-06 08:53:07] [Kristian Andersen] Perfect example of how a conspiratorial mind works. Fascinating. It's pretty clear they didn't bring the A-team in for this. [2020-12-06 09:33:59] [Kristian Andersen] [thread - ID: 2020-12-06 09:33:59] Here's the NYT article about China's cover up - it's a very good one, but nothing new: https://www.nytimes.com/202 0/12/06/world/asia/china-covid-origin-falsehoods.html?action=click&module=News&pgtype=Homepage [2020-12-06 09:52:07] [Andrew Rambaut] I was just taking a closer look at the rooting of the pandemic. Our lineage A is definitely 2 nucleotides (1 amino acid) closer to RaTG13 than lineage B (Wuhan-Hu-1). But interestingly WA1 is one nucleotide closer still (out of a 1150-odd, of course). It looks like the some of lineage A had a chance reversion (synonymous). But may be the cause of mis-rooting. [2020-12-06 09:54:46] [Kristian Andersen] In what sites? Lemme check the bam file to see how confident those RaTG13 calls are in those positions [2020-12-06 09:55:21] [Kristian Andersen] There are some low-coverage regions in that genome where you have ambiguous calls [2020-12-06 10:02:33] [Kristian Andersen] Just compared WA1 to Hu-1 and RaTG13. Only three differences between the two, all of them ancestral in WA1 - not Hu-1. [2020-12-06 10:02:56] [Kristian Andersen] What do you use as prototypical Lineage A? [2020-12-06 10:03:03] [Andrew Rambaut] WH04 [2020-12-06 10:03:31] [Kristian Andersen] Lemme include that too - and I should say, all those calls are fully supported in the RaTG13 assembly, so they're good [2020-12-06 10:04:32] [Kristian Andersen] It's that midpoint root.... Some early emergence funkiness. [2020-12-06 10:06:46] [Kristian Andersen] I have WH04 being identical to Hu-1, except the ends - do you have a different sequence? [2020-12-06 10:08:31] [Andrew Rambaut]