Slack / Private Message Drop — page 135

[2020-08-14 14:27:13] [Eddie Holmes] [thread - ID: 2020-08-14 14:27:13] I'm going to ask around about this. At face value it's either a massive fuck-up by the people analysing the data or it's irresponsible subsampling from NextStrain. [2020-08-14 14:27:41] [Kristian Andersen] Whether correct or not, pretty interesting though - especially given the pretty strong political line that this is due to return travelers (could be - but I'm also not sure about that...). [2020-08-14 14:29:50] [Eddie Holmes] True! I'm on it. Thanks for pointing this out!! [2020-08-14 14:32:12] [Kristian Andersen] You bet - definitely worth an extra (careful...) look. They made some conclusions on our Baja / SoCal sequences that are definitely not correct though, so something to keep in mind (in this particular point, it's impossible to say whether the virus moved South (as suggested), North, or from some completely different location). [shared file(s): Screen Shot 2020-08-14 at 2.29.40 PM.png] [2020-08-14 14:32:46] [Eddie Holmes] My money is on NextStrain screwing it up. [2020-08-14 14:32:48] [Kristian Andersen] And just for reference - here's the wording from our own report [shared file(s): Screen Shot 2020-08-14 at 2.32.03 PM.png] [2020-08-14 14:33:28] [Eddie Holmes] Bloody Trevor. [2020-08-14 14:51:10] [Andrew Rambaut] [thread - ID: 2020-08-14 14:27:13] The issue here is that this is NextStrain's 'Oceania' site. This has a focus on Oceania genomes and down-samples the rest of the world which means it will over sample Australia. [2020-08-14 14:56:20] [Kristian Andersen] [thread - ID: 2020-08-14 14:27:13] @Eddie Holmes And they don't check to see if these genomes are shared outside Australia? For that types of question, one really needs to look outside the sandbox... (this reminds my of the ever-occurring issue of people taking short reads and blasting them against viral databases to conclude that they have viruses in their samples... Only to realize later that they are human reads). [2020-08-14 15:36:31] [Eddie Holmes] Yes, that's my guess. [2020-08-14 15:37:45]