Private channel session 301

16 messages over 48m, 2020-08-15 – 2020-08-15.

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.

2020-08-15 15:39 Kristian G. Andersen open PDF p.137

So interesting: https://virological.org/t/two-ebola-virus-variants-circulating-during-the-2020-equateur-province-outbreak/538 Man, Ebola evolution has gotten so weird since 2014. It used to be such a well-behaved virus with a logical clock, but that's certainly changed. How interesting.
2020-08-15 15:59 Andrew Rambaut open PDF p.137

Yeah. The MBK67 has areas of low coverage suggesting a difficult sample. But it has to be survivor relapse/latentinfection, surely?
2020-08-15 16:00 Andrew Rambaut open PDF p.137

Perhaps which ever bat colony produced the 2018 outbreak had some latently infected bats but seems less likely.
2020-08-15 16:01 Andrew Rambaut open PDF p.137

Probability of it happening in the middle of another outbreak in the same region? Weird
2020-08-15 16:05 Kristian G. Andersen open PDF p.137

Yeah, MBK67 is super weird, but I talked to Mike earlier in the week and it sounds like it's basal on the clade - I can't quite suss it out from the tree as it's displayed. If that is the case, then it might not actually be a survivor relapse, but rather a new spill-over from the very same reservoir. Very interesting indeed - let's touch base on it with Mike next week too.
2020-08-15 16:06 Kristian G. Andersen open PDF p.137

And yes, from a probability standpoint - two separate outbreaks starting essentially at the same time? Clearly not impossible, but definitely seems risk overall is just up for Ebola - people encroaching on animal habitat I guess.
2020-08-15 16:07 Andrew Rambaut open PDF p.137

I wouldn't trust the basal thing - it has lots of low coverage areas including over quite a few SNPS internal to the outbreak.
2020-08-15 16:08 Andrew Rambaut open PDF p.137

Strong ascertainment bias - EVD will be noticed in that area.
2020-08-15 16:08 Kristian G. Andersen open PDF p.137

Ah, okay - I asked Mike if that sequence had any of the human diversity from the previous outbreak and he said no.But if it's a low coverage sample, who knows. Very very interesting (and so messed up...)
2020-08-15 16:09 Andrew Rambaut open PDF p.137

I will take another look before our chat.
2020-08-15 16:10 Kristian G. Andersen open PDF p.138

Also, interestingly - more cases of vaccinees getting primary Ebola, only to relapse later on after having receivedmAbs... This definitely needs some further looking into.
2020-08-15 16:15 Andrew Rambaut open PDF p.138

Yeah, not coming out basal for me... [shared file(s): image.png]
2020-08-15 16:17 Andrew Rambaut open PDF p.138

Don't have all the 2018 genomes there for some reason.
2020-08-15 16:26 Edward C. Holmes open PDF p.138

Very weird indeed. Can we rule out a fuck-up?
2020-08-15 16:27 Andrew Rambaut open PDF p.138

The genome has a lot of low coverage bits. Are we sure they weren't doing some retrospective sequencing of 2018 samples and contaminated?
2020-08-15 16:28 Andrew Rambaut open PDF p.138

But then there are 11 nuc differences.