Slack / Private Message Drop — page 137

[2020-08-15 10:10:09] [Kristian Andersen] Yeah, the time-tree really needs to be ignored - especially if it comes out of TreeTime. For transmissions, we're always just looking at the ML tree and that's how we came to the conclusion that the outbreaks "are likely connected, but we can't determine directionality". One additional (major) issue if focusing on the time tree - we don't have the same sampling period for Baja that we have for San Diego... [2020-08-15 15:39:54] [Kristian Andersen] 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 15:59:56] [Andrew Rambaut] Yeah. The MBK67 has areas of low coverage suggesting a difficult sample. But it has to be survivor relapse/latent infection, surely? [2020-08-15 16:00:55] [Andrew Rambaut] Perhaps which ever bat colony produced the 2018 outbreak had some latently infected bats but seems less likely. [2020-08-15 16:01:39] [Andrew Rambaut] Probability of it happening in the middle of another outbreak in the same region? Weird [2020-08-15 16:05:32] [Kristian Andersen] 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 16:06:48] [Kristian Andersen] 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 16:07:45] [Andrew Rambaut] 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 16:08:23] [Andrew Rambaut] Strong ascertainment bias - EVD will be noticed in that area. [2020-08-15 16:08:54] [Kristian Andersen] 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 16:09:30] [Andrew Rambaut]