Slack / Private Message Drop — page 134

viruses into the UK as compared to Dougless viruses. The fitness effect you see for Doug is relatively minor, so I wonder if little potential confounding factors like these could explain the difference? There's also the peculiar effect of skews towards younger for Doug, which could likely also contribute (cause or effect is pretty interesting here - very difficult, if not impossible, to sort out though). [shared file(s): Screen Shot 2020-08-10 at 3.58.47 PM.png] [2020-08-10 18:06:30] [Eddie Holmes] They asked me as well Kristian but I declined to comment this time....good call as you are much better informed on this than I. [2020-08-11 04:03:09] [Andrew Rambaut] [thread - ID: 2020-08-10 17:10:28] It has annoyed me that the only metric that statistically supports D614G fitter hypothesis is the basic fit to to the number of genomes - the issue is that there are so many confounding factors here. Erik's analysis does try to control for introductions by trying to focus only on local incidence but you have highlighted the issue that our method of inferring introductions is likely biased by the same issues. [2020-08-11 04:04:41] [Andrew Rambaut] [thread - ID: 2020-08-10 17:10:28] @Kristian Andersen I think most of the D lineages (after the very early ones) actually came from Spain in returning holiday makers. There was a large lineage A epidemic there (at the time unnoticed). [2020-08-14 12:10:57] [Kristian Andersen] @Eddie Holmes do you agree with this? I thought Australia was pretty adamant that recent surges were due to tourism - but it's unclear to me whether politics or science might be behind those statements... [shared file(s): Screen Shot 2020-08-14 at 12.09.46 PM.png] [2020-08-14 14:22:24] [Eddie Holmes] The story here is that the outbreak in Victoria was due to an escape from hotel quarantine from return travellers. There's even an inquiry going on that the moment. I can see from the tree that you are suggesting that the virus was in Australia prior to the current outbreak? That is certainly not the narrative here. I will need to ask about this. To clarify, I'm not involved in any of the Australian analysis: it's being done by the public health people in each state. They've shut me out completely. [2020-08-14 14:25:28] [Eddie Holmes] Are we sure that the NextStrain tree is just massively subsampled, missing key background lineages? [2020-08-14 14:25:34] [Kristian Andersen] Yeah, that's what I thought too - returning travelers and quarantine issues. I should have clarified that the statement I shared is from the most recent Nextstrain narrative: https://nextstrain.org/narratives/ncov/sit-rep/2020-08-14. I'm not sure we can really conclude it's local acquired from this data, but I haven't looked at it directly (so I'm not sure whether I agree or disagree with the Nextstrain folks here...) [2020-08-14 14:26:08] [Kristian Andersen] And yes - my concern exactly relates to whether subsampling has taken out necessary context - combined with bias, of course.