Chat message

Slack / Private Message Drop, p.135 [SLACK_000349] · slack_pm:msg:01379

Date: 2020-08-14 14:32
Type: chat message · slack
recipient: Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker: Kristian G. Andersen

Recipients on this medium are inferred from channel membership, not per-message addressing.

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 tokeep in mind (in this particular point, it's impossible to say whether the virus moved South (as suggested), North, orfrom some completely different location). [shared file(s): Screen Shot 2020-08-14 at 2.29.40 PM.png]

In context

A single line often inverts meaning once you see what it answers, so neighbouring messages are always shown.

2020-08-14 14:26 Kristian G. Andersen open

And yes - my concern exactly relates to whether subsampling has taken out necessary context - combined with bias,of course.
2020-08-14 14:27 Edward C. Holmes open

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'sirresponsible subsampling from NextStrain.
2020-08-14 14:27 Kristian G. Andersen open

Whether correct or not, pretty interesting though - especially given the pretty strong political line that this is due toreturn travelers (could be - but I'm also not sure about that...).
2020-08-14 14:29 Edward C. Holmes open

True! I'm on it. Thanks for pointing this out!!
2020-08-14 14:32 Kristian G. 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 tokeep in mind (in this particular point, it's impossible to say whether the virus moved South (as suggested), North, orfrom some completely different location). [shared file(s): Screen Shot 2020-08-14 at 2.29.40 PM.png]
2020-08-14 14:32 Edward C. Holmes open

My money is on NextStrain screwing it up.
2020-08-14 14:32 Kristian G. Andersen open

And just for reference - here's the wording from our own report [shared file(s): Screen Shot 2020-08-14 at 2.32.03PM.png]
2020-08-14 14:33 Edward C. Holmes open

Bloody Trevor.
2020-08-14 14:51 Andrew Rambaut open

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.

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