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Slack / Private Message Drop, p.566 [SLACK_000780] · slack_pm:msg:05912

Date: 2021-03-04 12:55
Type: chat message · slack
recipient: Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker: Kristian G. Andersen

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I see it Eddie - will take a look. We have a few very recent genomes that smell like recombination to me as well - I'm pretty convinced recombination happens quite frequently, so (as discussed before), I'm not surprised. That said, need proper evidence.

In context

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2021-03-04 11:37 Robert F. Garry open

Oh yes - but perhaps a bit of a missed opportunity for more Bullocks on FoxBusiness....Might have been fun but ....
2021-03-04 12:17 Edward C. Holmes open

@Kristian Andersen There's a recombination paper in the bioRxiv queue that would be good if you took a look at. Looks like garbage to me.
2021-03-04 12:35 Andrew Rambaut open

I found some solid examples of recombination with B.1.1.7. No surprises but pretty clear with multiple genomes sequenced in different labs.
2021-03-04 12:39 Edward C. Holmes open

This one does not look very good and talks about enhanced fitness. But I don't have time to look at it now as I haveto do another talk.
2021-03-04 12:55 Kristian G. Andersen

I see it Eddie - will take a look. We have a few very recent genomes that smell like recombination to me as well - I'm pretty convinced recombination happens quite frequently, so (as discussed before), I'm not surprised. That said, need proper evidence.
2021-03-04 12:59 Kristian G. Andersen open

Yeah, junk. "The VOCs have a lot of mutations so they must be recombinants"....
2021-03-04 13:25 Kristian G. Andersen open

*Key* paper from South Africa here - people infected with B.1.351 fully neutralize B.1.351 viruses AND neutralizenon-B.1.351 viruses pretty well. https://www.medrxiv.org/content/10.1101/2021.01.26.21250224v2
2021-03-04 13:27 Kristian G. Andersen open

Also, one very interesting finding - although it's n=1. They had somebody infected by non-B.1.351 _but_ with a virus that had the E484K mutation. The serum from that patient absolutely knocked it out of the park when it came to neuttiers against both B.1.351 and non-B.1.351 - so much so, they had to exclude the individual from most analyses. Ifthis holds up, we might have a winner for near-perfect vaccine antigen - spike + E484K, 2P, and dFCS. That'd becool.
2021-03-04 14:19 Edward C. Holmes open

I finally looked at this carefully. Did you see the BEAST analysis? TempEST found no temporal structure so they went ahead and used a strick clock anyway. On a 440 nt region. [shared file(s): Latrinne.NatComm20.pdf]

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