Chat message

Slack / Private Message Drop, p.59 [SLACK_000273] · slack_pm:msg:00594

Date: 2020-06-06 10:35
Type: chat message · slack
recipient: Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker: Kristian G. Andersen
Topics: Furin cleavage site and molecular features Intelligence community assessments

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

Actually, this just occurred to me and I'm wondering if the UK dataset could help investigate. Is it possible that the furin site is advantageous during high passage scenarios (transmission) but maybe not so much within host? In that scenario, maybe the furin cleavage site is maintained during exponentially increasing outbreaks (like we have observed up until about a month ago), but might be lost during more low-transmission periods? (as is the case insome places currently).In the bioRxiv paper above, they observe loss of the site in a subset of patients, but only intra-host, so based onthat, it might be possible that the site _can_ be lost in human infections too, and not just in tissue culture. To see ifthere's a link to transmissions, if we look at viruses sequenced in low-transmission places (or during low-transmission times) vs viruses sequenced in high-transmission places (or times), is there an association with the former showing more evidence of furin site loss than the latter? Would be pretty cool if that was the case...

Extracted statements

Rule-extracted, not adjudicated. The grade says what may be done with each one; read the document above before relying on any of them.

Statement	Grade	Attribution	Stance
Is it possible that the furin site is advantageous during high passage scenarios (transmission) but maybe not so much within host?	needs context	uncertain explicit hedge	questions
In that scenario, maybe the furin cleavage site is maintained during exponentially increasing outbreaks (like we have observed up until about a month ago), but might be lost during more low-transmission periods?	needs context	uncertain explicit hedge	questions
To see ifthere's a link to transmissions, if we look at viruses sequenced in low-transmission places (or during low-transmission times) vs viruses sequenced in high-transmission places (or times), is there an association with the former showing more evidence of furin site loss than the latter?	needs context	speaker_own	questions

Statement

Grade

Attribution

Stance

Is it possible that the furin site is advantageous during high passage scenarios (transmission) but maybe not so much within host?

needs context

uncertain explicit hedge

questions

In that scenario, maybe the furin cleavage site is maintained during exponentially increasing outbreaks (like we have observed up until about a month ago), but might be lost during more low-transmission periods?

needs context

uncertain explicit hedge

questions

To see ifthere's a link to transmissions, if we look at viruses sequenced in low-transmission places (or during low-transmission times) vs viruses sequenced in high-transmission places (or times), is there an association with the former showing more evidence of furin site loss than the latter?

needs context

speaker_own

questions

In context

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

2020-06-06 09:22 Kristian G. Andersen open

Here's the alignment of furin site ENaC and SARS-2 [shared file(s): Screen Shot 2020-06-06 at 8.58.49 AM.png]
2020-06-06 09:49 Andrew Rambaut open

So only one codon the same. I got to say - Bill's HKU9 source still seems good to me. But perhaps it did happen in amink/ferret/pangolin/civet/cat/etc.
2020-06-06 10:14 Kristian G. Andersen open

Yeah, I think Bill's explanation is basically the "hairpin followed by polymerase slippage in flu" CoV equivalent. Issueis - it could have happened anywhere.... I'm thinking a theory involving a farm isn't completely crazy - I believe Drosten is leaning that way too (and thought maybe even SARS1 could have started that way)
2020-06-06 10:20 Andrew Rambaut open

Farm sounds good to me.
2020-06-06 10:35 Kristian G. Andersen

Actually, this just occurred to me and I'm wondering if the UK dataset could help investigate. Is it possible that the furin site is advantageous during high passage scenarios (transmission) but maybe not so much within host? In that scenario, maybe the furin cleavage site is maintained during exponentially increasing outbreaks (like we have observed up until about a month ago), but might be lost during more low-transmission periods? (as is the case insome places currently).In the bioRxiv paper above, they observe loss of the site in a subset of patients, but only intra-host, so based onthat, it might be possible that the site _can_ be lost in human infections too, and not just in tissue culture. To see ifthere's a link to transmissions, if we look at viruses sequenced in low-transmission places (or during low-transmission times) vs viruses sequenced in high-transmission places (or times), is there an association with the former showing more evidence of furin site loss than the latter? Would be pretty cool if that was the case...

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