Private channel session 1663

15 messages over 1h 11m, 2021-11-30 – 2021-11-30.

A “conversation” here is an activity session — a run of messages with under 60 minutes of silence inside it. The channel had no native conversation boundaries.

2021-11-30 14:15 Andrew Rambaut open PDF p.1035

Had a few journalists saying that omicron started in September. Ian Semple said he had got this from you @Kristian Andersen ? That is way to old in my opinion
2021-11-30 14:16 Andrew Rambaut open PDF p.1035

Blue is Capetown. Orange is Netherlands
2021-11-30 14:18 Andrew Rambaut open PDF p.1035

Here is our current tree - and the outgroup at the bottom is probably dodgy stuff [shared file(s): omicron_2021-11-29_179-Italian.masked.ml.tree.png]
2021-11-30 14:18 Kristian G. Andersen open PDF p.1035

Agreed - it's based on what Kai put in the Science article. I didn't talk to Ian, but our media departed reached outmentioning that more recent estimates seem to converge around mid-October, with a large degree of uncertainty.
2021-11-30 14:20 Kristian G. Andersen open PDF p.1035

NL, ex-RSA in the tree, correct? (given recent - "IT WAS WIDESPREAD IN EUROPE OVER THE SUMMER!!!")
2021-11-30 14:20 Andrew Rambaut open PDF p.1035

Yes. Marion says most of them came from Capetown which is eminently plausible in that tree.
2021-11-30 14:21 Kristian G. Andersen open PDF p.1035

So this bloody things is widespread _all_ over South Africa and presumably most of Southern Africa as well... Bloody hell, it took off fast.
2021-11-30 14:21 Andrew Rambaut open PDF p.1035

@Kristian Andersen Missed this - where was that?
2021-11-30 14:23 Kristian G. Andersen open PDF p.1035

@Kristian Andersen This: https://twitter.com/dmaccannell/status/1465526465336950784?s=20. Duncan taking it on because it's being amplified in US media and everybody is getting pinged about it.
2021-11-30 14:25 Andrew Rambaut open PDF p.1035

Yes - two independent travellers from Mozambique (Italy and Reunion)
2021-11-30 14:25 Andrew Rambaut open PDF p.1036

All within the Gauteng/Botswana diversity
2021-11-30 14:35 Kristian G. Andersen open PDF p.1036

Do we understand what's going on here? Moritz mentioned that places like Gauteng had ~80% attack rates in previous waves, so I'm almost certain immunity is massively eroded. Question is - do we have increased transmission of Omicron to add to that? My gut tells me yes - simply given the speed here.
2021-11-30 15:00 Andrew Rambaut open PDF p.1036

I would be surprised if inherent transmissibility is higher than delta. My gut tells me this is due to massive number ofnew susceptibles and complete lack of any NPIs.
2021-11-30 15:10 Kristian G. Andersen open PDF p.1036

I agree on the massive number of new susceptibles, but some of those mutations in the FCS and NTD + outside the spike - not sure those are only involved in immune escape.
2021-11-30 15:26 Andrew Rambaut open PDF p.1036

NSP6del + Nelly + Pooh is Alpha like .