Private channel session 298
22 messages over 1h 39m, 2020-08-14 – 2020-08-14.
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.
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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 wasin Australia prior to the current outbreak? That is certainly not the narrative here. I will need to ask about this. Toclarify, 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.
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Are we sure that the NextStrain tree is just massively subsampled, missing key background lineages?
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Yeah, that's what I thought too - returning travelers and quarantine issues. I should have clarified that the statementI 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...)
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And yes - my concern exactly relates to whether subsampling has taken out necessary context - combined with bias,of course.
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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.
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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...).
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True! I'm on it. Thanks for pointing this out!!
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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]
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My money is on NextStrain screwing it up.
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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]
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Bloody Trevor.
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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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@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).
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Yes, that's my guess.
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I will be criticising NextStrain if so. I'm just checking with the Melbourne people now.
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@Eddie Holmes Pretty incompetent analysis. I'm going to enjoy this.
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@Eddie Holmes Does anyone actually pay attention to these 'sit reps'?
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@Eddie Holmes No idea. But the hotel quarantine thing is huge in Australia. There's a formal inquiry at the moment and heads will roll.
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@Eddie Holmes My worry is that these young, talented scientists have squandered a huge opportunity to do great science and help understand the pandemic and instead do silly ephemeral shite like this.
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@Eddie Holmes Completely agree. They are being dragged along by Trevor's ego.
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@Eddie Holmes Andrew, you trained them, so we blame you... :smiling_imp:
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@Eddie Holmes Mostly, I'm just a little confused - because these are big and important questions so we all know that we need to be really careful what we say (especially because of a few prior misfires). And some of these mistakes are really simple - as in, I can spot them and I'm still in elementary school when it comes to these types ofquestions (hence I collaborate with people who graduated already - just so I don't cock up too much).