Private channel session 827
55 messages over 6h 27m, 2021-01-18 – 2021-01-18.
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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Definitely too early with L452R and I'm annoyed that they put out a press release with no data and before we could actually get a close look at what's going on.The concern I have is that they mentioned this was found in three skilled nursing facility outbreaks with 100% attack rates - if true, then absolutely concerning, but I don't know how good the data is. I should know tomorrow.To the UK variant - this is not great... https://twitter.com/guptar_lab/status/1351181784776634370?s=21
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Now I'm getting concerned. [shared file(s): Image from iOS.jpg]
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Actually the Gupta data fell about where I expected. 3-6 fold reduction is not fantastic for B117, but actually could have been worse. EeeK will likely result in a bigger drop I suspect.
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Yeah, I agree Bob. - right where you might expect it to land. Quite a number of folks with no neuts to either virus aswell. Eeek will for sure be worse and cross the 4x threshold (I believe) is being used in the flu field to trigger avaccine update.
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That's a good analogy to flu - and you're right vaccine update will be needed. Just hoping that most humans can mount a good response to K484.
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Eek + Pooh: ```Accession ID Collection date Submission date Location EPI_ISL_778908 2020-11-30 2021-01-07 North America / USA / Maryland EPI_ISL_791414 2020-11-21 2021-01-08 North America / USA / Maryland EPI_ISL_791426 2020-12-30 2021-01-08 North America / USA / Maryland EPI_ISL_791427 2021-01-01 2021-01-08 North America / USA / Maryland```
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Are they hanging with Nelly too?
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No. Unrelated
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Interesting. I expect we'll see N501Y pop up on that background shortly.
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Bob, to your point about vaccine updates - yes, absolutely going to be needed. However, what's going to be very different here is that we're going to have a gazillion different (partially) vaccine 'resistant' lineages floating around atthe same time because we have sooooo many infections. Are we going to make an updated vaccine for each? Stick'em all together in a single vaccine? How are we going to prioritize?Until we use NPIs to massively drop infections down, I don't think we'll be successful in this game of whack-a-mole.
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I may be extremely pessimistic here, but by the time we have vaccinated enough people to reach herd immunity thresholds, I'm pretty sure we'll be dealing with almost completely resistant SARS-CoV-2 - and multiple different lineages.
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Maybe true - and it may be time to *start lowering expectations*. It's very possible we'll be in a situation [maybe already there] where the vaccines do not prevent infection or spread but offer some protection from severe disease. AKA flu vaccine. This means getting you ~flu~ CoV vaccine each year or maybe even every 6 months.
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In some ways thou the fact that we're seem the same mutations popping up repeatedly is "reassuring" in the sense that it may not take a gazillion.
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Alina was clearly wrong on many levels when she stated "SARS-CoV-2 is well adapted for humans." It's what lead her down the path that SC2 must be engineered or GOF. It's not that well adapted apparently because it keeps mutating. https://www.biorxiv.org/content/10.1101/2020.05.01.073262v1.full.pdf
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Yeah, we'll have to wait and see - maybe SC2 only has a narrow window for escaping (some level of) immunity, but I'm not convinced that's the case - we only need to look to all the ccCoVs.I warned Alina about her "well adapted to human" comments, making it clear that compared to SARS, yes, that might look to be the case, but there's a whole world of viruses out there where what we're seeing (dN/dS) in SC2 isnothing special. We're definitely seeing that play out now.
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https://twitter.com/AdamJKucharski/status/1351228542143651840?s=20
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Starts ~40 mins: https://www.youtube.com/watch?v=Ja_tLG8CLAc
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That's worse than expected. Much worse.
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It's bad indeed - very bad. To me it's not unexpected though - the RSA lineage has multiple mutations that had already been shown to affect immunity, so I can't say I'm surprised (this is unlike b117 - that one has less mutations that seem related to escape). It's much worse than I could have _hoped_ for though. Add to this that I'm getting increasingly concerned that this is because Eek leads to general immune escape and isn't just linked to changing asimple B cell epitope.
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I like this Salim guy though - very very good.
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Salim Abdool Karim - holy smokes, such a good scientific communicator. Probably the best I have seen during the entire pandemic - I feel like an idiot I didn't know about him before watching this presentation. https://en.wikipedia.org/wiki/Salim_Abdool_Karim
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Yes good - I chaired the study section that reviewed the last round of AIDS clinical trials groups grants a few months back. Karim and his wife clearly had the best application of the bunch. Not close.
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I'm impressed.
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Doug, Nelly, Eek and N417T fit - binds to ace2 like hell - and very immune evasive.
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Exactly - Nelly and her bad friends. "In about 50% of cases there was no recognition of the new virus by preexisting antibodies". Some of the most chilling words of the pandemic. Let's not fool ourselves that T cells will come and save the day - this is fucking serious (and is what a good proportion of us have been warning about for months -many months before even seeing these new variants). This is one sly fucker.
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No way to sugar coat it. My expectations are lowered a lot.
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I was unfortunately already there - I hate the fact that my most pessimistic viewpoints tend to be confirmed by this virus over and over again.
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I updated the Christmas Card figure on virological to include P.1. I'm also "done" messing with the new post/figure -Karthik offered no changes [but generated some interesting data on indels that'll be useful later on] and Bill Gallaher suggested several additions which I cut down - incorporating a few. Please let me know if there are any edits that are needed. This whole VoC situation is a rapidly changing mess. Probably be a dozen extra facts that should have been added in a few hours...
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I'll take a look now.
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Fuck
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That's basically the perfect summary.
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If we all dig deep and for a moment forget that we are humans that like other people live in part denial, are we truly surprised by these results? It's a general question, because I have observed this in myself since the very beginningof the pandemic - e.g., in the beginning of it communicating that "maybe it isn't going to be so bad" because at the end of the day that's really what I wanted, but deep down my training was telling me I was a wishful idiot.
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Not surprised it has happened, but surprised it has happened so quickly.
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We do need a spicy Phe to Lys mutation
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> Not surprised it has happened, but surprised it has happened so quickly. One jump. One single jump.
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Bloody glad I live in Australia - NO community cases here yesterday and all the tennis players are locked up
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I know - I'm so bloody jealous. And the model still has to be to drive down transmissions as low as possible - primarily with NPIs, with vaccines also coming in helpful (but the current view is that the vaccines will come in anddo it all - I doubt it).
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I agree. No other way.
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YES - the key message now has to be that the vaccines are NOT going to do it all.
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Totally
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I think most of us have been pushing the "vaccines are not going to be a silver bullet" message for a while - I wonderif people will listen now... Probably not :wink: .
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Bob - I went through the Ruff Draft and made a few edits (all in edit mode) / comments. Looks great!
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I'll have another look today.
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At least this is some encouraging news from Ireland and UK - the emergency break is still there, but we need to pullit harder (I was afraid somebody had cut the cord). [shared file(s):outbreakinfo_epidemiology_data_2021-01-18.png]
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Mad number in the UK though. Jesus.
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Totally bonkers. But I'll take a declining trend over an increasing trend or a plateau (the US favorite) any day.
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True
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@Kristian Andersen Although we have had 4 or 5 cases of spontaneous addition of Eeek to B.1.1.7 - none seem like they are spreading but they are ready to go.
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"Djokovic is a tool," Kyrgios, ranked 47th in the world, said on Twitter after the latest reports.
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I'm loving this tennis thing.
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!channel I suspect that the pending little virological post, which brings most of the PO1 band back together, on sucha hot topic will attract attention...an opportunity perhaps for a bit of public service messaging that "vaccines are not going to be a silver bullet."
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Yes, excellent point.
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@Kristian Andersen @Andrew Rambaut - have you seen any data from the UK about neutralization studies from these variants? It's unclear to me why the data is taking this long, so surely some must have been produced?
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@Kristian Andersen Need to very rapidly get the numbers down as we vaccinate. The point is that NPI do get R<1so with vaccine as well it should be possible to avoid escape..
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@Kristian Andersen Yes - although I prefer the initial drop of R<1 is done by NPIs first, followed by vaccination -not attempt to do the other way around. We'll learn A LOT from Israel.