Private channel session 295
2 messages over 56m, 2020-08-10 – 2020-08-10.
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.
-
@Andrew Rambaut - reading your Doug paper in a little more detail since the NYT folks asked about it... Question for you - looking at this figure, I largely see overlap in cluster sizes _earlier_ in the epidemic. Since Dougless camein early and Doug came in later - where, importantly there was A LOT more ongoing transmission - is it possible that when you measure "cluster sizes" (or any of the downstream phylodynamic estimates) that it's possible that a largersubset of Doug clusters that you assign to transmission within the UK could be due to multiple introductions ascompared to Dougless? Reading the methods, I'm wondering if you have multiple examples of, say, a cluster actually being made up of two introductions of identical viruses from neighboring countries, but then gets counted asa single introduction on your tree?I assume this effect would be more significant for later clusters - before mitigation - and could therefore skew cluster size towards Doug's being larger because they're more likely to be due to multiple introductions of identical viruses than Dougless'. One way to control for this would be to either make sure that clusters are all from the same city/region - but I assume you run out of power if you start dividing the dataset like that. Separate to a potential skew due to time, there's also a potential skew due to source. If you look at introductions from the same time period, Dougless would primarily be coming from China (less travel), while Doug would becoming from neighboring countries - again, this'd increase the likelihood of multiple introductions of identical Doug 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]
-
They asked me as well Kristian but I declined to comment this time....good call as you are much better informed onthis than I.