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Slack / Private Message Drop, p.150 [SLACK_000364] · slack_pm:msg:01538

Date: 2020-08-29 17:48
Type: chat message · slack
recipient: Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker: Kristian G. Andersen

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Okay, so just for the heck of it, I decided to look at some at Baric's mouse adaptation experiments with SARS-1. Hegrew SARS-1 repeatedly in mice (https://pubmed.ncbi.nlm.nih.gov/19853271/) to gain "mouse adapted" variants. Imagine somebody had done the same for SARS-2 - we'd expect to see at least _some_ of these mutations fixed inSARS-2, right? There are 14 "mouse adapted" mutations in SARS-1. If I compare those to residues in SARS-2, 2/14 are the same between the mouse adapted version and SARS-2, _however_, in both those cases the residues are identical between SARS-2 and RaTG13, so it's the ancestral state. In other words, there's no evidence at all for mouse adaptation of SARS-2 - and in fact, seeing 0/14 'mouse residues' is pretty darn strong evidence against. And as a last check, I looked at whether any of these have reverted/mutated during the pandemic - nope.So we lose one argument, but gain a new one. That's a good day.

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gov https://pubmed.ncbi.nlm.nih.gov/19853271/

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2020-08-29 17:48 Kristian G. Andersen

Okay, so just for the heck of it, I decided to look at some at Baric's mouse adaptation experiments with SARS-1. Hegrew SARS-1 repeatedly in mice (https://pubmed.ncbi.nlm.nih.gov/19853271/) to gain "mouse adapted" variants. Imagine somebody had done the same for SARS-2 - we'd expect to see at least _some_ of these mutations fixed inSARS-2, right? There are 14 "mouse adapted" mutations in SARS-1. If I compare those to residues in SARS-2, 2/14 are the same between the mouse adapted version and SARS-2, _however_, in both those cases the residues are identical between SARS-2 and RaTG13, so it's the ancestral state. In other words, there's no evidence at all for mouse adaptation of SARS-2 - and in fact, seeing 0/14 'mouse residues' is pretty darn strong evidence against. And as a last check, I looked at whether any of these have reverted/mutated during the pandemic - nope.So we lose one argument, but gain a new one. That's a good day.
2020-08-29 17:52 Kristian G. Andersen open

And in case anybody wants to take a look at the alignment, here's the Geneious file - GOF (mouse adapted) variantsin the "Sequence variant" track. [shared file(s): Mouse adaptation.geneious]

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