Private channel session 808
70 messages over 9h 0m, 2021-01-15 – 2021-01-15.
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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@Andrew Rambaut - do you guys have any concerns about L452R?
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I wasn't until you just asked me.
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Oh boy. What did I do - anything in your data? We saw it yesterday here in San Diego, but Charles Chiu just told meit's at 25% in LA
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What the hell is going on with this binding affinity thingamajig. https://arxiv.org/pdf/2005.14669.pdf
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86 with L452R in England.
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Recent and on B.1.1.7 background?
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(and I said LA - it's actually Northern California)
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A few from lineage A with N501Y too: Denmark/DCGC-22492/2020,2020-12-14,A,synSNP:A361G|orf1ab:P286L|synSNP:C2509T|synSNP:C8782T|orf1a b:D2980G|orf1ab:N3651S|synSNP:A11326G|synSNP:C16293T|orf1ab:P5401L|synSNP:A18366G|synSNP:A20262 G|S:L18F|synSNP:G22468T|S:L452R|S:*N501Y*|S:A653V|S:H655Y|S:D796Y|S:G1219V|ORF3a:V50A|synSNP:C2 7247T|ORF8:L84S|N:S202N|synSNP:T29344A|N:D358N England/PHEC-150B87/2020,2020-12-23,A,synSNP:A361G|orf1ab:P286L|synSNP:C2509T|synSNP:C8782T|orf1a b:D2980G|orf1ab:N3651S|orf1ab:T4265I|orf1ab:Q4392H|synSNP:C16293T|orf1ab:P5401L|synSNP:A18366G|orf1a b:L6082F|orf1ab:A6544V|synSNP:A20262G|S:L18F|synSNP:C21658T|synSNP:G22468T|S:L452R|S:*N501Y*|S:A6 53V|S:H655Y|S:D796Y|S:G1219V|ORF3a:V50A|synSNP:A26154G|synSNP:C27247T|ORF8:L84S|N:S202N England/PHEC-150B96/2020,2020-12-23,A,synSNP:A361G|orf1ab:P286L|synSNP:C2509T|synSNP:C8782T|orf1a b:D2980G|orf1ab:N3651S|orf1ab:Q4392H|synSNP:C16293T|orf1ab:P5401L|orf1ab:K5542R|synSNP:A18366G|orf1 ab:L6082F|orf1ab:A6544V|synSNP:A20262G|S:L18F|synSNP:C21658T|synSNP:G22468T|S:L452R|S:*N501Y*|S:A 653V|S:H655Y|S:D796Y|S:G1219V|ORF3a:V50A|synSNP:A26154G|synSNP:C27247T|ORF8:L84S|N:S202N
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Danish one seems related too
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One in combo with E484K: England/MILK-D74161/2020,2020-12-26,B.1.1.10,orf1ab:L446F|synSNP:C3037T|orf1ab:M1378I|synSNP:C4543T|s ynSNP:G8179T|orf1ab:P2739L|orf1ab:Y3063S|orf1ab:P3767L|synSNP:C12406T|orf1ab:P4715L|synSNP:C14805T| orf1ab:T5131I|synSNP:C19170T|synSNP:C19269T|synSNP:G19509A|synSNP:C21811T|S:L452R|S:*E484K*|S:D6 14G|S:Y1155F|S:V1228L|synSNP:A26927G|synSNP:G28079T|N:R203K|N:G204R
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Hmmm. Also L18F
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Yeah just looking at the structure L452R could definitely affect ACE2 binding.
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All are recent too. I'll put that on the list of "ones to watch". I don't want to do this every time a g'damn mutation comes up! We also need somebody to gather all the informationwe have on the various SNPs - binding, Ab escape, structures, etc. - so we can have a simple SNP table... I'll put that on the list.
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shared file(s): L452R variant
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Very fitting. [shared file(s): Screen Shot 2021-01-15 at 11.19.03.png]
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just tell me when i can update my christmas card
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shared file(s): image.png
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Yeah, please keep that confidential for now - the zoo is freaking out... That genome is identical to a zookeeper, sono change of the virus going to the gorilla. We're getting additional samples.
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Will do - test some monkeys too. Maybe the tamarins. They are my favorites.
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It'll be interesting to see if the whole zoo goes down with covid....
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@Kristian Andersen We are building a website that will track 'constellations' rather than variants. Combinations ofmutations of known or predicted importance. Were you can cross cut the data to see where those combinations have arisen and in what contexts (independent of the phylogenetic history).
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@Kristian Andersen Yeah, that'll be important to have, however, I'd love to have a way to "look up" particular mutations - e.g., E484K telling me it increases affinity and is involved in immune escape - so more on the functional side to make sense of the phylogenetic data. Would be similar to Jesse's 'maps', but with much more information. Not an easy task at all though...
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Would be sad - my three favorite zoos happen to be in NOLa, San Diego and Sydney.
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Separately - can I just point out that it's 85 degrees in San Diego today. I thought it was winter..?! :beach_with_umbrella:
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I'm particularly partial to gibbons.
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Possibly the second best thing on Twitter today (after Andrew's Variant Rant) https://twitter.com/mbeisen/status/1350181257313882112?s=20
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Wow.
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I guess Mike won't be invited to comment on the microbial programs...
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Pass the sick bag: https://www.nytimes.com/2021/01/14/theater/lauren-gunderson-the-catastrophist-nathan-wolfe.html?action=click&module=Features&pgtype=Homepage
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I can't look - ok I'm going to look, but please have look at the "quick" virological post on indels. It's fleshed out A LOT but needs input. Proposed author list is a reverse of PO1 with delBL and addition of ProfBill [for fun] and a couple ofstudents who contributed to the Vero passage. THOUGHTS PLEASEhttps://docs.google.com/document/d/1UMQokOz_gDqE0s9keyI7ES8bC7-55EOFuA4UiznEP08/edit?usp=sharing
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What do we reckon - a fishing attempt to hack my account? I am sure is a legit email: [shared file(s): image.png]
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It seems more specific than random phishing. They are definitely targeting you in particular. My guess: someone wearing a tinfoil hat looking to entrap you into some sort of response that will look like you're open to a bribe from the CCP. Maybe you should inquire if the offer includes a "honeypot?"
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Maybe 2.
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I hadn't thought of that - I was thinking more of the one I heard about where they give you a fake zoom or teams link which ends up giving them access to your system.
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But actually the trying to get an incriminating email is an interesting thought. @Eddie Holmes, @Kristian Andersen did you get this?
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I don't know man - enquire about the excellent honorarium first...
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... I didn't receive it.
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Perhaps say they have to pay the honorarium first into my paypal and then I have some excellent dirt about Holmes and Andersen
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That's worth at least a hundred grand!
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Maybe more $$$
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$100K - can't buy a decent boat for that.
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I got this a few weeks ago. Deleted it. It's an attempt to trap us.
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Full slide deck from Ian Wilson's recent talk - quite useful for looking at some of these mutations: https://www.dropbox.com/s/jrxhtnndvf2fdd8/Wilson%20DiscoBio%20Retreat%202021%20for%20DiscoBio%20.pptx?dl=0
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@Robert Garry I'll take a look the Virological post today. Apologies! It's the summer hols here and I am chilling in the Blue Mountains.
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Not a problem - chilling in the mountains does sound incredibly wonderful! Any feedback welcome gents!
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Some of the stuff about the conspiracy crowd should be toned down a bit, but - inspired by Angie R - I put some of itin for now.
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Will try to take a look over the weekend but it may not be until Monday
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Not a bad spot [shared file(s): Image from iOS.jpg]
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AWESOME - Enjoy Eddie - you deserve it!
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Latest version of the figure [shared file(s): image.png]
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Got it Bob!
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""The Catastrophist" tells the story of Wolfe's upbringing by a father who, along with other relatives, shares aparticular medical vulnerability. It follows his quest as a virus hunter whose early career was spent in Africa and Asia looking for clues to the next major pandemic". Surely it should be "The Bullshitter"?
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Do you know why GISAID are claiming that they releasing the first genome on January 10th? This is a complete fabrication. A journalist pointed me to it: [shared file(s): Screen Shot 2021-01-16 at 12.14.27 pm.png]
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@Robert Garry @Andrew Rambaut @Kristian Andersen Massive shit is about to hit the fan.... [shared file(s): Fwd FACT SHEET Activity at the Wuhan Institute of Virology.pdf]
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Reading it carefully, I see a rather vague set of accusations with no smoking gun. The idea that the WIV were working on pangolins seems totally bizarre. "With symptoms consistent with both COVID-19 and common seasonal illnesses"? Could mean anything. The timing speaks volumes from me...passing shot from Pompeo?
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Bannon, Pompeo, etc laying the groundwork for the next push.
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I agree. The statement about pangolins is ridiculous...and then they throw in the military links....
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From my NYT journo friend "Pompeo is getting ready to join the presidential race in four years, so he's laying all kinds of markers and booby traps to show he's tough on China."
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That so called "Fact Sheet" seems completely bogus to me - there's no _actual_ information in there other than they did lab work... No specific allegations, no specific data - pure bs.
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Yup, pure BS. On the subject of BS...why are GISAID claiming that they released the sequence on the 10th?? Their data were uploaded on the 12th.
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Yeah, I was really confused about that too - I talked to Peter on the phone and he mentioned it. I don't remember that at all, but then again, I wouldn't have checked GISAID on that day. I'm sure it's pure BS - everybody got that fucking sequencing from Virological and your post! I mean, that post has more views than our Proximal Origin post....
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Plus, WHO say it was the 12th. I remember the chain of events well. [shared file(s): Screen Shot 2021-01-01 at 12.00.41 pm.png]
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Better evidence is this: [shared file(s): Screen Shot 2021-01-16 at 1.26.54 pm.png]
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Rewriting history during/following a pandemic - it's the standard playbook. Gotta push back!
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This Tweet came out and I remember looking on GISAID and I couldn't see them. Then the WHO tweeted the 2nd tweet (above) and they were there. Standard pandemic history rewrite as you say. I'll leave it. Just weird.
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Speaking of PO1 - we are back to #2 [shared file(s): image.png]
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I think it's the citations that keep coming....
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:beer:
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We were #4 last week!
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Might owe Mike Pompeo a beer.