libera/##covid-19/ Tuesday, 2021-01-26

bin_bashyeah on the one hand im glad they got it, but on the other i am a bit skeptical of emergency authorizations in general00:00
LjLbin_bash, my parents are between 70 and 80 and the day doesn't feel close at all (or even vaguely known) when they'll get vaccinated. the EU isn't exactly shining in the eyes of people, despite media being like "the EU went to the next level in the way it's handling this in a united way with the vaccines and the recovery funds"... yeah, except the vaccines aren't coming, and how to bind use of the recovery funds has broken up my government00:00
DocScrutinizer05>>"conditional market authorization" takes longer than the "emergency use authorization"<< that been what? 2 weeks? MEH!00:01
DocScrutinizer05I'd rather question why a proper conditional approval was almost as _fast_ as an emergency approval00:02
LjLwell fact remains, the US and UK are vaccinating much faster than the EU, and they have at least two vaccines approved instead of just one00:04
DocScrutinizer05we also have two, no?00:04
LjLdifferent strategies, but for now, the EU one isn't looking like a winning one, especially with the variants now threatening to take the R well above 100:04
LjLDocScrutinizer05, Italy has only received Pfizer00:05
LjLi don't know about other countries, i thought only Pfizer was being used in the EU for now00:05
DocScrutinizer05nope, moderna is shipping afaik00:05
LjLi wasn't aware of that, or i forgot. but the EU (or at least Italy) has ordered a comparatively very small number of Moderna doses compared to others00:05
LjLthe other day, TV was suggesting that we'll be looking at Sputnik and Sinovac to fill in the gaps. that doesn't make me feel great00:06
de-factobtw have you read about the moderna trial of the Moderna one being effective with limited neutralization against the SA variant even and that they plan to do an update to their mRNA?00:06
de-factoi linked it above00:06
LjLyes00:07
de-facto.title https://investors.modernatx.com/news-releases/news-release-details/moderna-covid-19-vaccine-retains-neutralizing-activity-against00:07
Brainstormde-facto: From investors.modernatx.com: Moderna COVID-19 Vaccine Retains Neutralizing Activity Against Emerging Variants First Identified in the U.K. and the Republic of South Africa | Moderna, Inc.00:07
LjLi've also read comments that it's bit of a mixed message. they want to show that their vaccine still works, but in practice they're thinking of having a "third booster" to properly deal with the variants00:07
de-facto"While the Company expects these levels of neutralizing antibodies to be protective, pseudovirus neutralizing antibody titers were approximately 6-fold lower relative to prior variants. These lower titers may suggest a potential risk of earlier waning of immunity to the new B.1.351 strains."00:08
de-facto"the Company is advancing an emerging variant booster candidate (mRNA-1273.351) against the B.1.351 variant first identified in the Republic of South Africa. The Company is advancing mRNA-1273.351 into preclinical studies and a Phase 1 study in the U.S. to evaluate the immunological benefit of boosting with strain-specific spike proteins."00:08
LjLi'm paraphrasing comments, not my own opinion, but it seems unfortunately reasonable given the much reduced activity against that strain00:08
de-factoits very good that they do that (not only for their stock price)00:09
de-facto.title https://www.biorxiv.org/content/10.1101/2021.01.25.427948v1 <-- the paper with details 00:10
Brainstormde-facto: From www.biorxiv.org: mRNA-1273 vaccine induces neutralizing antibodies against spike mutants from global SARS-CoV-2 variants | bioRxiv00:10
LjLwell, i was really hoping for better protection against current variants. if it's already shaky on current variants, what will happen as more variants develop? (and they will, there's already this study on the "californian variant", and similar sets of mutations are just coming up in various places)00:10
DocScrutinizer05I heard a re-certification of VoC-adapted mRNA vaccines is ultrafast or not needed at all? o.O00:10
LjLmaybe it was an overoptimistic hope00:10
LjLi'm not often overoptimistic, but i just want to see an end to this at some point00:10
de-factoyeah PEI was asked about that too, they said something about template approval, not sure what exactly that means, but probably something like they only would have to demonstrate that the changes behave in the expected way or such?00:11
BrainstormNew from NPR: South Dakota Health Leader On How The State Has Gotten Its Vaccine Out: South Dakota has administered roughly 80,000 of the 106,000 doses it has received so far, or 75%. Dr. Shankar Kurra in Rapid City says a centralized system helped for coordination. → https://is.gd/En4hrp00:11
de-factowhat exactly that means in practice i am not so sure00:11
DocScrutinizer05I hope they will move to a mixed mRNA cocktail in Moderna and BNT00:12
de-factoeventually we have to get MASSIVELY more production capacity and a tight feedback loop rolling that constantly integrate the latest sequences of concern into a polyclonal vaccine00:13
DocScrutinizer05for the first and 2nd shot, not a 3rd booster00:13
de-factoyeah but we dont have nearly enough production cap to even deliver a monoclonal (Wuhan S-protein variant only) to satisfy demands by many orders of magnitude00:14
de-factohow about the updates then?00:14
de-factoDocScrutinizer05, that was exactly one of my proposals earlier, "bruteforce" new escape mutants in cell cultures under selection pressure of a representative mix of current prevalent antibodies to get their sequences and integrate them into vaccines prior to their occurrence in the wild00:15
de-factoi am still not sure if selection behaves deterministic enough for that, yet the independent occurrence of variants would suggest something like that (e.g. N501Y appearing several times more or less independently)00:16
de-factoor that Y453F mink variant also occurred several times independently00:17
LjLi can't remember all these numbers00:17
de-factohow about the new ones E484K et al?00:17
DocScrutinizer05I guess they could use a "racemic" approach in production00:17
raccoon_dogAn equal proportion?00:18
DocScrutinizer05>>"bruteforce" new escape mutants in cell cultures<< smart! :-)00:18
LjLsmart, in a level 4 lab00:18
LjLso smart but not doable everywhere00:18
DocScrutinizer05raccoon_dog: yep, mix the mRNA variants, then multiply00:19
LjLbut i agree it sounds like a possible way ahead in the longer term00:19
de-factoboth SARS-CoV-2 and SARS-CoV-1 have a proofreading capability related to the NonStructuralProteins-14 and NSP-10, so for SARS-CoV-1 it was possible to destroy that proofreading cap hence increase mutation rate by 20-fold00:19
raccoon_dogAnd the mutations you get, are those the same ones you'd encounter later in the wild?00:19
LjLthat's the idea, there would be no guarantee00:19
de-factoso maybe if something like that also was possible for SARS-CoV-2 one may gain some time advantage from that in cell cultures for "bruteforcing" escape mutants? i am not sure if that is possible though00:19
LjLbut they'd be subject to similar selective pressures00:19
de-factoprobably the normal mutation rate already is sufficient if the antibody titers are always kept below a neutralizing concentration 00:20
LjLde-facto, i'd *really* want to make sure they do that in BSL4 facilities though. the fact it mutates *slowly* has so far worked in our favor (at least until the vaccines were almost ready and we were like "yay" and then "oh crap")00:20
LjLif a version of this virus without proofreading abilities ended up in the wild, *shudder*00:21
bin_bashbut first BSL4 facilities need to be overhauled00:21
de-factoraccoon_dog, thats a very good question, i am not sure if the mutations are predictable enough to allow for all of that to be useful00:21
bin_bashotheriwse it's just a matter of time before another pathogen gets leaked by accident00:21
raccoon_dogde-facto: Right.00:21
raccoon_dogbin_bash: One with possibly a much higher mortality rate than this one, much more infections, too. :S00:21
DocScrutinizer05LjL: absolutely. I'd oppose even going that route at all00:22
DocScrutinizer05there are other means to increase mutation rate00:22
DocScrutinizer05reversible means00:22
bin_bashraccoon_dog: yep it'll happen00:22
bin_bashthis isnt even the big one00:22
raccoon_dogNowhere near it, yeah.00:23
bin_bashit's sick that facing this reality is considered "political"00:23
bin_bashdoesnt matter where the lab is, it needs to be fully secure. there are bsl4 labs in the US that arent00:23
BrainstormNew from Bloom Lab: @jbloom_lab: R to @jbloom_lab: Here are impacts of mutations at some key sites on REGN-COV2 antibodies (REGN10933 and REGN01987), LY-CoV555, and LY-CoV016:E484: mutations reduce binding by LY-CoV555 and to lesser extent REGN10933, little effect on REGN01987 or LY-CoV016. (5/n) → https://is.gd/olabwz00:23
bin_bashit's not a chinese-specific problem00:23
bin_bashi think a lot of ther governmental corruption makes it more difficult and more susceptible but plenty of places in the US have made mistakes to00:24
bin_bashtoo*00:24
LjLthink of how comparatively trivial a problem Chernobyl was in comparison to what happened here (assuming it's a lab leak, hence comparing human accidents)00:24
de-factoLjL, i am not that scared about the proofreading deficient occuring in the wild, if that was such a big advantage it already would have happened00:25
bin_bashLjL: yeah00:25
de-factoi think it even could make it dysfunctional  00:25
de-factonsp14 is highly conserved for some reason00:25
de-factobut yeah sure it should be done in BSL-3 anyhow00:26
DocScrutinizer05there's a name for that in cosmology, sth like "the technological bottleneck" which will allow a civilization to extinguish itself00:26
de-factothe great filter00:27
de-factofermi paradox00:27
de-factohttps://en.wikipedia.org/wiki/Great_Filter00:27
bin_bashofftopic but it's not even a paradox idk why it gets called that00:29
LjLlots of paradoxes aren't00:30
bin_bashthat's the most famous one that I can think of off-hand00:33
DocScrutinizer05I meant this https://en.wikipedia.org/wiki/Global_catastrophic_risk#Anthropogenic  still missing the correct term for it. I *think* it was "technological bottleneck"00:33
BrainstormUpdates for Guernsey: +38 cases (now 359) since a day ago00:33
DocScrutinizer05the cause for the question to aliens >>how did you manage to survive?<<00:35
LjLmy understanding is that the technological bottleneck, or similar terms, is a possible "implementation" of the great filter00:35
BrainstormNew from The Lancet (Online): [Comment] The need for a global COVID-19 maternal immunisation research plan: There is evidence that COVID-19 threatens maternal and perinatal health. Pregnant women, especially in the second half of pregnancy, are at increased risk of complications—eg, severe pneumonia, hospitalisations, admission to intensive care [... want %more?] → https://is.gd/PBL0GX00:36
DocScrutinizer05zje idea being: the the more technology we invent, the higher the risk we will kil us with it00:36
LjLthe great filter says, since we haven't heard any aliens, then maybe at some point along the way from "no life" to "intelligent life capable of colonizing the universe" always something happens that makes life destroy itself00:36
LjLat which point that happens, we don't know00:36
de-factoi think its not nuclear war or such that is likely to cause an extinction level event, its may very well be a pathogen though, hence i think improving our capabilities in terms of biosecurity is very important and this pandemic is an excellent chance to learn and improve00:36
de-factobtw its also an excellent motivation to become a multi-planetary species00:38
DocScrutinizer05that's when we got behind the bottleneck. That'S why it's called bottleneck and not... dead end00:39
de-factoi really think the importance to use this chance to learn and improve bio-security capabilities from this pandemic can not be underestimated00:40
DocScrutinizer05and very figuratively we're out of the bottle then ;-D00:40
de-factonot because of SARS-CoV-2, we will get that under control, but because of the future in general00:40
DocScrutinizer05obviously00:41
DocScrutinizer05we should rethink our complete security concept00:42
de-facto*can not be overestimated00:42
raccoon_dog> we will get that under control00:42
raccoon_dogWill we?00:42
DocScrutinizer05of course00:43
de-factoyes i think so00:43
raccoon_dogI mean, I certainly hope so.00:43
raccoon_dogAnd I want it to be true.00:43
de-factoand we will learn a lot on the way00:43
DocScrutinizer05really, worst case it won't be a tenth of the black plague, and in ten years we forgot about 202000:44
DocScrutinizer05we WILL survive this, as species00:44
de-factothis one yes00:44
raccoon_dogHere's the thing, though.00:44
DocScrutinizer05yes THIS one00:44
raccoon_dogSurviving a pandemic as a species can just as well mean "there are two fertile individuals left alive".00:45
de-factohehe better be one of those two then :D00:45
raccoon_dogI don't mean to sound pessimistic, but "surviving something as a species" has that as the minimum.00:45
de-factoactually it would be a problem, because only two is not enough genetic diversity00:45
raccoon_dogWell, yeah.00:46
DocScrutinizer05as I said, it won't get anywhere near that00:46
de-factoi think they estimated how many would be needed to colonialize Mars, i dont remember exactly anymore, was it like 50k or such?00:46
raccoon_dogTo have a healthy genetic diversity?00:47
raccoon_dogOr what.00:47
DocScrutinizer05a simple look at numbers tells us this virus has no potential to kill more than maybe 10% of population00:47
raccoon_dogThose are the people it kills, though. Then there are the people with potentially permanent lung damage.00:48
de-factoyeah there is a minimum for a species to survive as healthy genetic pool of diversity00:48
de-factoi dont know the exact numbers00:48
raccoon_dogI see.00:48
de-factoif we would have compartmentalized bio-security probably one of such compartments would survive (depending on minimum transmission times between them)00:50
LjLall business no play00:57
pigughsMonday health officials announced a case of the variant found in South Africa had been recorded in New Zealand in a returned traveler who had been released from hotel quarantine after twice testing negative.   Apparently just found in Minnesota also01:00
DocScrutinizer05LjL: now mainstream news have >><65 problems. AZ denies<<01:00
BrainstormNew from NPR: Gorilla Gets Monoclonal Antibody Therapy For COVID-19: An older silverback gorilla in San Diego, Calif., received an array of treatments after it and others in the troop contracted the coronavirus. The therapy came from a supply meant for non-humans. → https://is.gd/XLKb6U01:00
LjLDocScrutinizer05, well someone was bound to pick it up, since it was on Reuters... but is there some more clarity on what the sources are?01:01
DocScrutinizer05I read "Bild and $someothernewspaper tabloids" or whatever01:02
DocScrutinizer05BILD is a pile of BS newspaper01:02
LjLyes but it was Reuters saying that01:02
LjLReuters was just reporting from a German tabloid01:02
LjLbut then if something is on Reuters it will be certainly be picked up by mainstream media01:02
DocScrutinizer05it's all maximum obscure01:02
raccoon_dog... But Reuters is a news agency.01:02
raccoon_dogAnd if a news agency has that.01:03
raccoon_dogThen eventually everyone will.01:03
raccoon_dogIt's like Associated Press.01:03
LjLthat's what i'm saying raccoon_dog01:03
raccoon_dogYes.01:03
de-factothere see DocScrutinizer05 said it too Bild is toilet paper01:03
raccoon_dogLjL: That's ... not good. :/01:04
LjLso i'm not surprised it's been picked up, but i hope the fact it's been picked up will make someone eventually figure out what the source for this claim is01:04
DocScrutinizer05I still recall the Datex-P username and password of Reuters' account back from 1985 ;-P01:04
raccoon_dogIt does make me wonder why Reuters are using a German tabloid as a source.01:04
raccoon_dogI'd have thought their journalistic standards were a bit higher ...01:04
LjLmeh01:05
DocScrutinizer05well Reuters is just an aggregator, they're supposed to cover this. They basically don't filter01:06
DocScrutinizer05I doubt Reuters has many journalists01:07
DocScrutinizer05my take on it01:08
raccoon_dogI'm not sure what "aggregator" means in this context, but my understanding was that a news agency has their journalist (who may work part time for them) go out and collect material and then type up the article. This is a basic, more or less just-the-facts article which is then sold to news outlets who may or may put their spin on it.01:09
raccoon_dogI thought this was how a news agency worked.01:09
raccoon_dogmay or may not*01:09
DocScrutinizer05not sure, Partially for sure, but then they also feed through all the news from other media as well01:10
de-factothey never ever provide sources, i really hate that about them01:11
sanehatterDocScrutinizer05, about reuters, "It employs some 2,500 journalists and 600 photojournalists in about 200 locations worldwide."01:11
DocScrutinizer05ok, thanks for fixing my idea in this regard01:11
sanehatternews agencies like AFP, AP, reuters have journalists all around the world and they write news that smaller news outlets subscribe to for republication01:12
DocScrutinizer05anyway this was tagged "from BILD"01:12
LjLReuters is a *large* company01:13
DocScrutinizer05so you need to "ask" BILD where from they got this "info"01:13
raccoon_dogsanehatter: Right.01:15
raccoon_dogThat was my understanding as well.01:15
DocScrutinizer05LjL: sure they are large, but nevertheless I can't recall a simgle journalistic revelation where they been mentioned as one of the co-authors01:15
sanehatterDocScrutinizer05, they have exclusive stories on a daily basis on their website01:16
DocScrutinizer05never heard of one01:16
LjLthat's because they sell them01:17
LjLthey don't routinely get public-facing attribution01:17
LjLevery news source makes it look like it's their own thing, they certainly don't say "GO TO ROUTERS TO FIND MORE OF THESE RIGHT WHEN THEY COME OUT"01:18
DocScrutinizer05then it would still mention "Reuters" in the authorship. I never heard "Minister X told in an interview with Reuters that blablabla..."01:18
DocScrutinizer05whatever, this was BILD01:19
DocScrutinizer05Reuters is tangential here01:19
raccoon_dogRight. And BILD is a so-so source, yes?01:20
sanehatterDocScrutinizer05, https://www.reuters.com/search/news?blob=exclusive&sortBy=date&dateRange=all <- the first page of results are all from today for example01:20
DocScrutinizer05Bullshit Is Literally 'Dis01:20
raccoon_dogHah! Nice one.01:21
raccoon_dogYeah, I see.01:21
de-facto.tite https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)32661-1/fulltext01:21
raccoon_dogSo I guess we can take it with a grain of salt.01:21
LjLbut meanwhile, someone already made a fake post on worldnews <Brainstorm> New from r/WorldNews: worldnews: AstraZeneca vaccine found to only protect the elderly 8%, not acceptable to use in that group of people → https://is.gd/1gqLsy01:21
LjL(no need to click, that's Bild, in german)01:21
LjL(already reported it as non-english, but more of them will come)01:21
raccoon_dogI saw that, LjL, but before seeing that I saw the refutation from AZ themselves.01:22
raccoon_dogSo fortunately I was like *rolls eyes*01:22
LjLraccoon_dog, from what, that tweet? because i don't have a "real" source for the refutation either...01:22
raccoon_dogo.o01:22
LjLi mean, what i read was basically "AstraZeneca refutes claim of 8% blah blah"01:23
LjLi had never heard the claim before01:23
de-facto.title https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)32661-1/fulltext01:23
LjLand i also don't know where AZ actually refuted it01:23
Brainstormde-facto: From www.thelancet.com: Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK - The Lancet01:23
LjLexcept on a copypasted image in a tweet (copypasted from where? dunno)01:23
raccoon_dogLjL: https://globalnews.ca/news/7598547/astrazeneca-coronavirus-vaccine-reports-incorrect/ 01:23
raccoon_dogI don't know how trustworthy this is, mind.01:23
de-factoat a quick scroll i could not see them doing separate analysis for the age groups there01:23
LjLde-facto, convenient01:24
de-factoLjL,  what was the other link where we talked about their table layout? it was some UK gov site afair01:24
de-factothey had some more details there right?01:24
LjLyes, the MHRA approval. there is also a PDF version without those table issues01:24
LjLlet's see if i'm lucky01:24
LjL%links MHRA astrazeneca01:25
BrainstormLjL, Sorry, nothing found. Try with broader keywords 01:25
LjLno luck for me01:25
de-facto%links AZD122201:25
Brainstormde-facto, https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20 (Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial)31604-4/fulltext), encouraging preliminary results from the Oxford/AstraZeneca adenovirus-vectored vaccine, showing an acceptable safety profile and [... want %more?]01:25
BrainstormNew from r/WorldNews: worldnews: Covid: Curfew riots hit Netherlands for third night → https://is.gd/kwj83s01:25
de-facto%more01:25
Brainstormde-facto, [...] unit, invasive mechanical ventilation—and death from COVID-19 compared with age-matched non-pregnant women.1–3 Existing evidence also suggests that pregnant women with COVID-19 are at higher risk of having a preterm delivery and that their neonates are three times more likely to be admitted to hospital than those born to mothers without COVID-19. → https://paste.ee/p/mHhDp01:25
Brainstormde-facto, [...] strong immune response after a booster, while https://blogs.sciencemag.org/pipeline/archives/2020/07/20/new-data-on-the-oxford-az-vaccine (Derek Lowe's "In The Pipeline" blog provides a critical commentary) on it; in November 2020 https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20 (Safety and immunogenicity of ChAdOx1 nCoV-19 [...] → https://paste.ee/p/9fec401:25
LjLi'll grep logs01:25
de-factoprobably around 30 Dec or such? when they got approved in the uk01:26
LjLde-facto, it was this i think https://www.gov.uk/government/publications/regulatory-approval-of-covid-19-vaccine-astrazeneca/information-for-healthcare-professionals-on-covid-19-vaccine-astrazeneca but this is not the PDF version01:26
DocScrutinizer05raccoon_dog: got another nice one for you. The tag of everyone burying their face in a BILD in subway: "Brain Is Likely Dead" ;-D01:28
raccoon_dogDocScrutinizer05: Lol01:28
LjLde-facto, it does say "Efficacy and safety data are currently limited in individuals ≥65 years of age (see sections 4.8 and 5.1). No dosage adjustment is required."01:29
de-factoyes i think that was it that a b table i remember01:29
LjLso if nothing else, AZ's rebuttal of "100% of adults showed immune response!" is misleading01:29
LjLimmune response != not getting COVID01:29
de-factoyes of course01:30
LjLso i'd like their "not true!" to be a bit better established as not true, honestly01:30
de-factoimmune response just means they have measured something, not if its protective or not01:30
de-factoEMA for sure got the raw data of all those 01:31
de-factounder non-disclosure probably01:31
DocScrutinizer05quite possible there is something hiding there. Wasn't it AZ who got that flawed 62% -> 90% = 70% study?01:35
DocScrutinizer05or was that JJ?01:36
DocScrutinizer05can't remember01:36
BrainstormNew from https://covid19.specops.network : ljl-covid: Change badly readable link to MHRA page that also links to the better… → https://is.gd/B7ZKEJ01:37
DocScrutinizer05anyway AZ seems a pretty shady company, see their cutback on delivery for EU01:37
de-factohmm nothing about age group separated protection from symptomatic covid in there01:38
de-factoDocScrutinizer05, AZ yes01:39
LjLde-facto, the PDF is at https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/951851/uk-clean-spc-covid-19-vaccine-astrazeneca-reg174.pdf with much better-looking tables01:39
LjLi also updated the links as you can see, %links mhra will show it next time01:39
LjLDocScrutinizer05, it was AZ01:39
de-factoyeah indeed they look better01:40
LjLanyway, Sanofi are delaying their own adenovirus vaccine because it pretty much doesn't work on people over 5501:40
LjLso i wouldn't be *incredibly* surprised if AZ turned out to be similar, and they just made it non-apparent in the data01:40
de-factowell according to the lancet paper we dont have any data for half dose full dose schemes in any age over 55 at all01:41
de-factohence it was full dose full dose for all of those01:41
LjLde-facto, but then eventually it was approved at full dose anyway...01:42
de-factohttps://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)32661-1/fulltext table 101:42
de-factowas it? is the approval about full dose -> full dose?01:42
LjLurr01:42
LjLi seem to remember that way01:42
LjLbut i also thought Moderna wasn't approved in the EU01:42
de-factocoudl be i dont know01:42
LjLso i'm not very confident with my memory01:43
de-factomoderna got approved on jan 6th01:43
LjLmy logs seem to indicate it was approved as full dose01:44
LjLbut i'm still reading some past discussions01:45
de-factohmmm idk id rather say that this phase III trial does not give us appropriate data for low dose / high dose for any age over 55, and we know the high dose / high dose scheme did not work very well01:45
LjLanyway... if the half-dose+full-dose scheme didn't have any >55, while the other one DID, then wouldn't the fact the former gave 90% efficacy and the latter just 62% indicate potentially disastrous efficacy on >55?01:45
de-factowe also know that it works better in the young, hence we really would need low dose / full dose in the age > 55 or 65 group01:46
LjLalso i'll remind you and myself01:46
LjLfreenode/##covid-19/2020-12-08.log:[20:25:58] <LjL> de-facto, the lower end of the confidence interval for people who took two full doses is below 50% (45%ish). that's the number that worries me, unless and until we figure out what makes the half-dose+full-dose group better, for which they *admitted* they need another trial01:46
LjLi kind of want to stress here that they had seemed to intend to want to run another trial because this was such a mess01:46
LjLin the end they said "naaah"01:46
LjLi have honestly lost any confidence i had01:46
de-factowell i want to know how low dose / full dose works in age > 6501:47
de-factoat east that part in the trial with 18-55 of LD/SD gave ~90% in COV002?01:48
BrainstormUpdates for France: +5669 cases (now 3.1 million) since 22 hours ago01:48
de-facto*at least01:48
LjL2020-12-30.log:[20:01:39] <LjL> de-facto, i think they should insist with AZ about making sense of this half-dose vs full-dose mess. they can't just swipe it under the rug and pretend they didn't make those claims before, and now just go ahead with "it's 70% effective, forget what we said before"01:49
LjLthis is making me think we had eventually understood they'd use full dose01:49
de-factohopefully they kept track of the ones that received it in the uk so no further time is wasted with another full trial01:49
LjLbut i am not finding an explicit statement of that01:49
de-factocant they just integrate those that received it now in the UK into their trial data and somehow complete it with that? they just would have to get a control group somehow01:50
de-factoprobably difficult to get a control group now, especially since now the elderly could receive real protection01:51
de-factohmmm01:51
LjLi think we should concentrate on ramping up Pfizer a lot01:52
LjLwe can't have a sketchy vaccine with 70% protection *maybe*, maybe really less, when we are also getting variants that escape them01:52
LjLforget that, it won't get us anywhere near herd immunity01:52
de-factoyes but the AZ one is important too, it does not need the cold supply chain01:52
de-factoif i was offered to get it tomorrow i probably would take it too at the LD/SD schema01:54
de-factoif it works better in the young (we dont know that) so why not use it for the young then (15-55)?01:56
LjLi don't think i have any reason to believe the 90% from that schema is anything but a fluke01:56
de-factoyeah thats what i would like to know too01:56
de-factobtw their trials were in those countries were we now have the new variants, UK, SA and Brazil (but thats probably unrelated)01:58
dTalI agree about Pfizer01:59
dTalIt's a politically and economically charged situation but hell, Pfizer wins and we don't have time for half measures01:59
dTallet's get 95% effective vaccines into everyone02:00
dTalalso, what UK is doing terrifies me02:00
dTalHalf doses for everyone is a disaster02:00
dTallike not finishing your course of antibiotics02:00
dTala breeding ground for mutations that will escape vaccination02:00
LjLde-facto, exactly and only those three countries?02:00
raccoon_dog... the UK are doing that? O.O02:01
dTalraccoon_dog, yeah02:01
LjLde-facto, i think you kind of said yourself that nothing would be better to breed new mutation that a vaccine that half-works?02:01
dTalin practical terms02:01
LjL(well, or maybe someone else did)02:01
raccoon_dogdTal: Jesus. :/02:01
dTalyou're supposed to have a booster after 3 weeks but they're now saying upwards of 12 weeks02:02
BrainstormNew from r/WorldNews: worldnews: Moderna begins work on booster to protect against South African variant | Coronavirus → https://is.gd/KM8MTp02:02
LjLso if it was actually trialed in exactly those three countries, honestly, i'm not sure i'd go "probably unrelated"02:02
de-factoLjL, yeah well theoretically yes02:02
dTalmost people who've had one shot don't even have a second one schedules02:02
LjLwas it not trialed in India, where they produced a lot of it?02:02
bin_bashyes the UK may very well be dooming the world with its half-cocked scheme02:03
bin_bashtheyre better off not vaccinating anyone02:03
bin_bashthan giving everyone a half dose02:03
dTalLjL, beware of common cause correlation - maybe those countries have good testing infrastructure or something, and that's why vaccine testing was done AND why new variants were discovered there02:03
bin_bashit's so infuriating02:03
de-factothe lancet said COV001 (UK) COV002 (UK)  COV003 (Brazil) COV005 (South Africa)02:03
raccoon_dogIt's psychologically messed up. People will go out thinking their half-vaccination is as good as a full dose, and voilà, we have a bazillion new variants.02:04
raccoon_dogWhy are they doing that? 02:04
raccoon_dogLike.02:04
dTalto extend supplies02:04
raccoon_dogTo ration.02:04
dTalthey reckon it's better to give twice as many people poor immunity02:04
raccoon_dogI see.02:04
raccoon_dogYes -- poor immunity that'll make them think they can go out and about. Jesus Christ.02:04
dTalwhich might be a reasonable calculus, were it not for the mutation risk02:04
raccoon_dogExactly.02:04
raccoon_dogAll the variants.02:05
de-factoyeah id also not go for any correlation yet, but i just thought that list of countries is in the news right now too. they had pretty high prevalence there, hence they also were chosen for the trials, yet also breeded on those mutations (because of many infections occurring in general)02:05
dTalright so the common cause is "high rates"02:05
de-factoyeah 02:05
dTalpossibly.02:05
bin_bashthe thing that's so crazy and also sad in the US is the number of vaccine doses that get wasted02:06
bin_bashbecause of people not showing up02:06
dTalraccoon_dog, I tend to agree; people are likely to regard their vaccination as carte blanche02:06
raccoon_dogdTal: Exactly.02:06
dTaland they've been so hyped up for it as a panacea02:06
bin_bashit's terrifying frankly02:06
LjLdTal, the UK sequences a lot, and the same is true of South Africa, according to what i see on nextstrain. in Brazil, it's kinda true, but not really relative to their population, at a glance02:08
raccoon_dogbin_bash: Exactly. I've had multiple conversations with that topic as the thing that made me realize, "This person I know has gone insane." Typical exchange: "I heard you had an appointment for the first shot?" "You don't believe that's a thing, do you?" "The pandemic ... ?" "The virus. The virus is a hoax. Come on, you knew this."02:08
raccoon_dogThere is more than one person who's tried to have this conversation with me.02:08
de-facto.title https://covidcg.org/?tab=global_sequencing02:08
Brainstormde-facto: From covidcg.org: COVID CG02:08
bin_bashyeah and that's about the point i revoke their personhood and walk away02:08
bin_bashfortunately for me i havent been blood reated to anyone like that 02:09
dTalIn Israel they go out at the end of the day and vaccinate anyone they can pull in off the street02:09
dTalno wasted doses even with no-show appointments02:09
raccoon_dogbin_bash: It's easy if you don't have to meet them every Thanksgiving and winter holiday season. Lol02:09
de-factoand they guarantee second dose in time for those lucky ones in Israel02:09
bin_bashthat's not something you can do here dTal 02:09
raccoon_dogI don't have that fortune.02:09
dTalhow come, bin_bash?02:09
pigughsanti-vaccine-ism was a thing before covid, some places started having Measles outbreaks, cause parents refused the vac for kids02:09
bin_bashraccoon_dog: yeah im not blood related so i can just have my own thanksgiving02:09
raccoon_dogpigughs: Right. It's been around a while.02:10
dTalbecause of low population density?02:10
bin_bashdTal: why can't you just yank people off the street and give them vaccinations without consent? Because it's illegal.02:10
dTalno, not without consent, duh02:10
LjLdTal, but what worries me is that from the little i've been able to understand, people who understand more than me are a bit perplexed as to how variants with several mutations seem to have come up all at once, without known intermediate stages (even in countries that sequence a lot). so one theory was that variants may develop inside just one patient, like someone who is partially immunocompromised, just enough to still have working antibodies against the 02:10
LjLvirus, but not enough to eliminate the virus completely, making for a human lab. if that hypothesis is plausible, then, i'd think, so is that of a half-baked vaccine causing a similar course02:10
dTalyou *offer* it to passers by02:10
de-factoUK 44.1 seq/1000 cases, SA 1.91 seq / 1000 cases, Brazil 0.19 seq / 1000 cases02:10
pigughsprolly grew about the same time as Infowars, and AM hate radio 02:10
dTaljeez, I thought that was obvious02:10
bin_bashwhat passers-by?02:11
raccoon_dogThere's distinct variations on it; some people are just anti-vaxx in general, even if they do accept the virus and the pandemic is an issue. Those people often come from the MMR-autism nonsense. Then there's another group that doesn't even accept the virus as being real, that think it's some NWO ploy to get people implanted with some "chip". Crazy beliefs.02:11
bin_bashhospitals and clinics don't have people just going around outside saying "hey want a vaccine?"02:11
dTalLjL: but in wildly distant continents?02:11
bin_bashBut in some cases you can call up and make an appointment for if there's a cancelation or something02:11
dTalbin_bash: that's the point; they should02:11
raccoon_dogbin_bash: Right -- especially when there's a shortage and frontline essential workers need it first.02:12
dTalthere's no reason not to02:12
LjLdTal, i don't understand why you ask that question. the variants are not identical. whether it was caused by "special patients", or by a half-baked vaccine in a few thousands people, yes... it could be in three separate continents. except, if those also happen to be the places where just such a vaccine was tested, my antennæ kinda ræise up02:12
dTal"We got 5 no-shows today, go find 5 people who want the vaccine"02:12
bin_bashright let's just have essential personnel standing outside yelling "VACCINES! GET YOUR VACCINES HERE FOLKS!" i'm sure it'll go swimmingly. /s02:12
dTalnot complicated02:12
pigughsJ&J results are due out soon, with some luck it will be 1 shot , effective and not require -40C ?02:12
bin_bashdTal: do you typically just have people sitting around?02:13
de-factoLjL, well there also might be a threshold for the first immunity waning off and start of occurrence of (asymptomatic) reinfections, so that also might become only common enough after some time to breed under (non-neutralizing) selection pressure02:13
dTalbin_bash: why don't you go look at what Israel is doing before accusing me of not thinking things through02:13
dTalthey are literally doing this02:13
de-factoso that also could be an effect explaining the delay of occurrence of new partly evading mutants maybe02:13
dTalit works02:13
dTalnearly 0 vaccine wastage02:13
bin_bashi have. netanyahu just got banned from facebook for trying to get phone numbers of unvaccinated people over 6002:13
LjLde-facto, but that does not explain why those three particular places. dTal's theory "they sequence a lot" kinda does, but i'm concerned02:13
LjL(by variants of concern)02:14
dTalLjL: I asked the question because you said the mystery was multiple variants arising simulatenously02:14
LjLdTal, did i?02:14
LjLdTal, i think you misunderstood me02:14
dTalah perhaps I didn't quite absorb the "no intermediate stages" part02:14
dTalI think I understand now02:14
LjLdTal, okay. yes, that02:15
de-factoi guess such variants could occur in all countries with antibodies waning off and reinfections occurring now, viral replication under (non neutralizing) selection pressure for some generations02:15
dTalso the mystery is sudden leaps in genotype02:15
dTalthere's some unexplained phenomenon there02:15
dTalanother possiblity might be zoonotic reservoirs?02:15
LjLdTal, basically, if you're sequencing decently, you expect to see N501Y in one patient... then another guy has N501Y *and* the other thing... and then... and then... not 5 new mutations that all seem to be meaningful, popping up at once02:15
de-factothats why i was talking about a possible window of time to bring it down by NPIs and hold it low by doing as many vaccinations as possible in as short time as possible globally synchronized02:16
de-factoand yeah i know its unrealistic unfortunately02:16
LjLdTal, yes, i guess that's another possibility, no idea how likely. i'm reporting this theory of immunocompromised patients because i've read it (on virological.org or some such place)02:16
dTalso it circulates in some population that isn't tested at all, like pangolins or cats or something02:16
dTaljesus de-facto I hope you're wrong02:16
dTalabout literally everything you say02:17
de-factome too02:17
LjLdTal, but still, fine, let's have that as another theory. not just the UK, SA and Brazil have pangolins! (or at all?) but alright let's just keep it in one corner of our brains that at some point it would be nice to know if the fact these three countries are the same as the other three countries is just a coincidence02:17
de-factoLjL, yes that jump in mutation rate, but that also could just mean it evolved somewhere else where it was not on mutation radar at all, then maybe got imported and exploded under the mutation radar02:17
de-factowell or sure it also could mean it did that locally in some weird environment02:18
bin_bashthe uk has a big problem with outdoor cats so it's not unlikely that it's circulating amongst them02:19
bin_bashand then people bring them into their homes for cuddles02:19
raccoon_dogWai, what?02:19
raccoon_dogWait*02:19
bin_bashbrazil does too actually02:19
raccoon_dogCats? Cats can get the virus?02:19
bin_bashoh yes02:19
raccoon_dogI heard about the gorilla lately.02:19
bin_bashwe've known that for a year02:19
BrainstormUpdates for United Kingdom: +16998 cases (now 3.7 million), +497 deaths (now 98531) since 18 hours ago — Canada: +4790 cases (now 753571), +117 deaths (now 19187) since 23 hours ago02:19
raccoon_dogBut *cats*? The pets people keep at home and snuggle with in bed??02:19
bin_bashsome tigers got it at the bronx zoo02:19
raccoon_dogWhat!02:19
bin_bashyes02:19
bin_bashthats been known for almost a year02:19
raccoon_dogWell. That's not a housecat -- that's a distinct felid. I mean housecats.02:20
bin_bashso do i02:20
raccoon_dogBut have there been documented cases of housecats having the virus?02:20
bin_bashcats are not all that genetically diverse. housecats are only partially domesticated, unlike dogs02:20
bin_bashyes!02:20
LjLcats can get the virus and pass it to each other02:20
raccoon_dogAnd can they pass it to us?02:20
de-factoyeah (house) cats, minks, golden hamsters, ...02:20
LjLraccoon_dog, yes, and also passing it to other cats, as that was explicitly experimented on02:20
raccoon_dogWHAT.02:20
raccoon_dog?!!??!?!02:20
bin_bashyep02:21
LjLraccoon_dog, that is not known, nobody tried :P02:21
de-factoracoons? no idea02:21
raccoon_dogo.o02:21
LjLraccoon_dog, have you missed the whole mink event?02:21
bin_bashright now is probably the worst time ever to allow your cats outside. i mean it's always been bad for the environment and ecology but now it's also bad for everyone02:21
LjLexcept if you have a cat that's used to go outside, it'll be hell to try to keep it inside...02:22
bin_bashidk i would never let my cats outside alone02:22
LjLfair enough02:22
de-factoits pretty easily jumping between humans and some species, so such a ping pong event could explain a jump because in such animals it would replicate in a completely different environment (slightly different proteins, different immune system etc)02:22
dTalthere is a strange cat that comes into my parent's kitchen and licks the butter02:22
LjLbut if someone already does, it's hard to stop that behavior02:22
bin_bashew02:22
bin_bashLjL: yeah fair02:22
bin_bashi havent experienced it so idk02:22
raccoon_dogThis is extremely disturbing to me.02:22
raccoon_dogI had no idea about any of this.02:22
dTalit is the smartest little shit I have ever had to match wits with02:22
bin_bashcats are pretty willful though so id imagine it would be a painful training experience02:22
raccoon_dogI thought the gorilla case from this week was something bizarre.02:23
bin_bashraccoon_dog: nope old news02:23
de-factofor example in the mink population the mutation  Y453F occured independently in several mink populations because the ACE2 receptor is a slightly different molecule in minks (but still similar enough)02:23
dTalI don't wanna catch covid from contaminated butter02:23
dTalthat would be such an ignominious way to die02:23
bin_bashdTal: how is it even getting in there02:23
LjLraccoon_dog, it is disturbing enough that one of the countries with the top mink fur production in the world decided to kill all their mink to stop the variant that had developed in mink from propagating to more humans (some humans already had it)02:23
LjLthat country being Denmark02:23
raccoon_dogI actually did think that since gorillas and humans have some shared DNA from ancestral times from a common ape ancestor, it may have been due to that.02:23
dTalbin_bash: cat flap02:23
raccoon_dogBut apparently that's not a requirement ...02:23
bin_bashhave you tried sealing it shut dTal 02:23
LjL%wik Cluster 502:23
dTalmy parents have a cat02:23
bin_bashor electrifying it02:23
de-factoand it did spread back in Denmark (Cluster 5), so they could find Y453F in some humans later then02:23
BrainstormLjL, from English Wikipedia: "Cluster 5", also referred to as ΔFVI-spike by the Danish State Serum Institute (SSI), is, or was, a variant of SARS-CoV-2, the virus that causes COVID-19. It was discovered in North Jutland, Denmark, and is believed to have been spread from minks to humans via mink farms. On 4 November 2020, it was [... want %more?] → https://en.wikipedia.org/wiki/Cluster_502:23
bin_bashwell then that's not any beetter :P02:24
dTalso the cat flap is kind of important02:24
raccoon_dogLjL: Sheesh.02:24
bloody_noob259[mIf cats might be drivers of the pandemic shouldnt we also See high Rates on Crete?02:24
dTalour cat is not gregarious to other humans or cats so there's no danger in letting him outside, directly02:24
bin_bashthe risk to the ecology and environment is still there02:24
dTalbut the cat flap is an entry point for this other little furry bastard02:24
bin_bashbut that's a topic for another time. 02:24
raccoon_dogThere's actually an island near Japan I think. Cat Island.02:24
bin_bashyou know there are flaps that respond to chips02:25
bin_bashand dont unlock for other animals02:25
raccoon_dogHas God knows how many cats.02:25
dTalyeah I know02:25
bin_bashah figured it was worth a mention at least02:25
dTalon the ecosystem topic I would be shocked if this cat can catch anything at all02:25
de-factobloody_noob259[m, probably cats are not drivers, we would know that by now02:25
bin_bashi would be shocked if it didnt kill stuff everyday tbh02:25
dTalhe's an old cat02:25
dTalvery very slow02:26
dTalcomically slow02:26
LjLde-facto, i think there's a lot of things that one is tempted to say "we would know by now" about, and yet we don't02:26
dTalmaybe if he waited by a mouse hole or something but he ain't catching birds02:26
dTalanyway02:26
LjLde-facto, for a positive test of this: do we know of any country where people who test positive have their animals routinely tested too, to see if that could be the case?02:27
LjLi think if that's not being done, then "we would know by now" doesn't hold02:27
bin_bash^^i think that's a good point. 02:27
LjLi think it's very possible that most mammals will be drivers to some extent, obviously more so the ones who live close to men (rats and mice have already been raised as a concern)02:28
de-factoLjL, well yeah but for example if cats would be the drivers (hence by definition contribute a significant part to new infections) the correlation bloody_noob259[m just asked have shown up in the data when it was known  that cats can get infected, so for example why dont we have crazy high rates in Crete then?02:28
bin_bashand theyve found that cats recover quickly, so the cat may not show any serious symptoms but still passing it on02:28
de-factoor other places with lots of stray cats02:28
bloody_noob259[m<de-facto "bloody_noob259, probably cats ar"> There are alot of cats on Crete, havent checked infections for a while though. But then again  most cats on Crete live outside02:28
bin_bashi dont think cats are the drivers, but it wouldnt surprise me if they didnt contribute in some way02:28
LjLde-facto, i would say "the drivers", in humans, are definitely other humans. doesn't mean cats can't be "drivers" without the02:28
raccoon_dogLjL: And what's ironic is that cats have been historically kept -- as vermin control.02:28
dTalI doubt cats pass it to humans very effectively02:28
raccoon_dogLjL: And now there's a possibility they themselves are a driver.02:28
dTalthey don't talk02:28
dTalthey're the wrong height02:28
bin_bashthey lick themselves all the time and then people pet them02:28
bin_bashand then they tocuh their faces02:28
bin_bashor they cuddle with the cats or give them hugs or kisses02:29
raccoon_dogdTal: They groom themselves with their own tongues.02:29
raccoon_dogAnd then humans snuggle with them.02:29
dTalthat's a good point02:29
LjLraccoon_dog, or to see it another way, both cats and mice were calmly going on about their business without any virus getting in the way, until humans decided to play with bats and create this whole virus issue for them02:29
raccoon_dogHeh, yeah.02:29
dTalI don't think the mice were very calm about it02:30
de-factolol02:30
LjLdTal, did they have toxoplasmosis?02:30
raccoon_dogWell, I'm certainly going to be more mindful of petting stray/feral cats from now on. :|02:30
bin_bashtoxoplasmosis is a big problem in a lot of places02:30
raccoon_dogYeesh.02:30
bin_bashanother reason i dont allow my cats out lol02:30
dTalokay the ones with toxoplasmosis were calm02:30
dTaltouche02:31
LjLi've stopped touching outside cats since the pandemic began02:31
LjLdTal, hehe02:31
de-factoraccoon_dog, i knew it and i did pet stray cats (they are so cute :), but i did not touch anything until i washed my hands very good after touching that cat02:31
raccoon_dogde-facto: This is what bothers me -- why did I not know this? Everyone here was as sure as 2 + 2 = 4 when I brought it up.02:32
raccoon_dogI guess the media may not have paid much attention to it here.02:32
LjLraccoon_dog, because we spend too much time in this channel fueling our anxiety02:32
de-factoyeah true02:32
LjLwhile sometimes reminding each other that it doesn't help our immune systems02:32
LjLut we do it anyway02:32
de-factoits abit addictive tbh02:33
LjLit has been widely publicized in media02:33
LjLbut like02:33
LjLLOTS and LOTS of things about COVID have been "widely publicized" in media02:33
LjLit's hard to remember what media were saying months ago02:33
raccoon_dogYeah. And it's hard to separate what's BS from what's credible.02:33
LjLthe thing about cats has not been on media's radar in a while02:33
raccoon_dogRight.02:33
LjLnot just that, it's simply overload02:34
raccoon_dogIndeed. It's SO much.02:34
raccoon_dogIt's like a dump.02:34
raccoon_dogEvery single hour. 02:34
de-factosame with the onslaught of new preprint papers, its awesome but its also too much to read all of them02:34
LjLraccoon_dog, there are definitely studies on mental health that give us worrying prospects on how that makes us feel02:34
LjLalthough i haven't read them02:35
LjLbecause i'm honestly like02:35
LjLEXTREMELY INTERESTING = skim the whole study02:35
LjLVERY INTERESTING = read the abstract02:35
raccoon_dogLjL: Oh, yeah. The lockdown and quarantine measures definitely do have a toll on mental health.02:35
LjLINTERESTING = read the headline and assume it's misleading02:35
LjLraccoon_dog, yeah but i think it's also this continuous reminders02:35
LjLhard to separate i guess02:35
LjLand hard to not continuously remind ourselves, either. even if you keep the TV off and stay off news site and off this channel, you still have to remember to sanitize your hands and put on your mask and disinfect your groceries or whatever you do02:36
bin_bashThe biggest toll on my mental health is watching fucktards going about their lives as if nothing is happening02:36
LjLwhich are reasonable things to do, but also constant reminders of the non-normalcy and danger of this situation for us02:36
bin_bashbecause it's illegal to kill them still02:37
bin_bash:(02:37
raccoon_dogYeah, exactly.02:37
raccoon_dogLike the very act of existing, of living, has this thing as an integral part.02:37
raccoon_dogIt's part and parcel of living now.02:37
raccoon_dogWell, except for the idiots bin_bash mentioned.02:37
raccoon_dogThey're pretending nothing's wrong.02:37
raccoon_dogTo the detriment of themselves AND those around them.02:37
LjLbut let's not kill anybody even if someone makes it legal, please02:37
BrainstormNew from r/WorldNews: worldnews: Moderna is designing a new version of its COVID-19 shot to fight the variant first found in South Africa → https://is.gd/WmTJCB02:37
LjL(i know that's not the american way, but i'll say it anyway)02:37
bin_bashin 1918 there was a case of a health department guy shooting a guy who refused to wear a mask02:38
bin_bashand that's the america i believe in02:38
bin_bashi would probably try to argue that it was self-defense. if having sex with someone without a condom is assault then not wearing a mask is too02:39
bin_bashbut anyway i digress02:39
raccoon_dogbin_bash: What was the context? I mean if the dude without a mask was deliberately being obnoxious about it, coughing on people, screaming about "his rights" or whatever ... not saying it's justified, but I'm saying a court could argue it may have been self-defense.02:39
bin_bashhttps://www.theatlantic.com/ideas/archive/2020/03/how-fragmented-country-fights-pandemic/608284/02:41
LjLi'm sorry that's the america you believe in02:42
bin_bashLjL: i was being sarcastic, sorry it didnt come through02:43
bin_bashi need to use /s more02:43
LjLno02:43
LjL/s is dumb02:43
raccoon_dogHow does one show sarcasm, then?02:43
LjLbut it seemed like you were actually half-condoning the act, so...02:43
raccoon_dogXD02:43
LjLraccoon_dog, i think the whole point of sarcasm is more or less to see if the other parties spot it on their own.02:43
bin_bashwell it was a bit of dark humor with a defeatist attitude of if you cant convince em then kill em02:43
bin_bashbut not from a real practicality standpoint02:43
LjLokay02:44
raccoon_dogLjL: The thing is, in a world where people genuine believe diametrically opposing things, it can be hard to distinguish sometimes.02:44
raccoon_doggenuinely*02:44
bin_bashbut yeah i can see how it would come across as actually condoning it02:44
LjLraccoon_dog, well, i prefer to find out by getting a mental picture of a person naturally, even if that takes time, over labelling every act of speech with something02:44
bin_bashin a perfect world it would be cut and dry. people who wore masks and monsters who didnt but thats not the real world02:44
raccoon_dogThis is IRC, that's easier in real life, LjL. I only have text here.02:45
raccoon_dogReal life, of course, is harder nowadays because of the very topic of this channel. XD02:45
LjLi've only had text for many years and i much prefer it to real life :P02:45
raccoon_dogYou got that right ...02:45
LjLit's not true i prefer it to real life, or at least i would have to elaborate on that - but i think there are many clues about things and people over text, too, they are just different clues than the ones you have in person (they may also be more prone to noise in the signal, i'll grant that)02:46
LjLanyway, my uh "charter" for this channel (which was really a half-baked thing i did in reaction to people wanting explicit rules, and me not wanting them) says that it should also be a place for people to try to feel better instead of worse. i think we currently fail at that. maybe it's because we factually only have (overwhelmingly, at least) bad news... or that we have no channel-resident psychologist02:48
LjLbut i wonder, like, if raccoon_dog is a bit terrified from learning about cats and tons of other animals carrying the virus, and it seems like a dump of scary information... i believe in information, but is there something we can do also to counterbalance that to avoid going all crazy?02:49
LjLit's an open question02:49
LjLand it's not for me, i'm already crazy, but it may matter to the rest of y'all!02:49
raccoon_dogI'm afraid of it, and it doesn't seem good, but I accept that if this is what the evidence shows, it is real and happening and we need to adjust our lives accordingly.02:50
raccoon_dogIn my case, for example, trying not to interact with outside cats.02:50
LjLraccoon_dog, i'm sure you realize there is a corollary to the fact it's in a bunch of animals, though, and i really don't like that corollary... and i appreciate your attitude of acknowledging and accepting reality, other people sometimes tell me i should do that more :P02:50
raccoon_dogLjL: Yes. It's a ... messy corollary.02:51
LjLlet's just say Pfizer and Moderna won't be out of a job any time soon02:52
LjL(not so sure about AZ unless they learn to do a better job)02:52
dTalLjL: I don't think the goals of "inform people about the latest covid news" and "cheer people up" are even remotely compatible02:59
LjL"cheer people up" is not what i've said, though03:00
LjLas an example, albeit likely not a sufficient one, ending up feeling like you know what are the best masks to use and other good ways to protect yourself, instead of feeling lost, could be a good thing for people03:01
LjLit's still about the virus, but constructive instead of destructive03:01
LjLbut when we start nitpicking on the best way to deal with things we often end up not agreeing anyway, and i'd assume we'd agree even less with the general population, so someone passing by here might end up feeling *more* lost and confused, which wouldn't help. so i don't know, but *if* it worked, it would be an example03:03
de-factofor the the Moderna paper and press release was good news today03:05
de-factoi was very worried about the E484K (had bad mood for days) and them showing that their vaccine still is effective (even with reduced neutralization) against it and them working on an update to make sure it does not wane off too soon in the future kinda calmed me a bit about all this03:08
de-facto(sorry about my sentences broken sometimes, maybe i should try to read them again before hitting enter)03:10
LjLi see all that more negatively, but it's probably just the way i am03:12
BrainstormNew from r/WorldNews: worldnews: Moderna says it believes vaccine will work against new variants → https://is.gd/X4YzAx03:13
LjLaaaaand one more03:14
LjLwe saw the Category before, but this wikipedia article has a few useful "conversion tables" https://en.wikipedia.org/wiki/Variants_of_SARS-CoV-203:27
raccoon_dogIt's going to be harrowing seen that article grow over tiem .............03:29
raccoon_dogs/seen/seeing03:29
raccoon_dogs/tiem/time03:29
raccoon_dogChrist, my spelling.03:29
LjLthat article growing will mean we *know* about specific variants that are of particular concern, meaning we also know what we should target vaccines at03:31
raccoon_dogYeah, that's true.03:32
LjLraccoon_dog, in the also ever-growing channel links list there is a github page of someone who's actually trying to track all "variants of concern" where concern is defined more broadly than the ones "notable" to wikipedia. that is already jarringly long03:34
raccoon_dogo.o03:34
LjL%link mutations of interest03:35
BrainstormLjL, https://www.cogconsortium.uk/wp-content/uploads/2020/12/Report-1_COG-UK_19-December-2020_SARS-CoV-2-Mutations.pdf (COG-UK update on SARS-CoV-2 Spike mutations of special interest) comes after the https://www.reuters.com/article/uk-health-coronavirus-britain-strain/uk-says-new-coronavirus-strain-is-more-infectious-but-vaccines-should-still-work-idUSKBN28T0KL (UK government [... want %more?]03:35
LjLblaaaah03:35
LjLhttps://github.com/emmahodcroft/cluster_scripts03:35
de-factooh wow that wikipedia is very much up-to-date (as of course is Dr Emma Hodcroft as always)03:42
LjLde-facto, i think the table at https://en.wikipedia.org/wiki/Variants_of_SARS-CoV-2#Summary is slightly out of date in that surely the antigenicity of the SA variant is not just "undergoing investigation", we know it is much less sensitive to some neutralizing antibodies03:43
LjLbut while i have the Moderna study handy, i don't have... i think before the Moderna stuff there was another study that first showed neutralizing antibodies didn't work on it, no?03:44
LjLnot sure if just a preprint still (Wikipedia doesn't accept those)03:44
de-facto.title https://www.biorxiv.org/content/10.1101/2021.01.15.426911v1 <-- you mean this? 03:50
Brainstormde-facto: From www.biorxiv.org: mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants | bioRxiv03:50
de-factothe preprint of Rockefeller University, New York03:51
LjLah, preprint, no go then03:54
LjLthanks though03:54
BrainstormUpdates for Switzerland: +53 deaths (now 9146) since 12 hours ago — New Zealand: +2 cases (now 2290) since 22 hours ago04:05
de-facto.title https://www.youtube.com/watch?v=lj3NhPgOoX4&list=PLGhmZX2NKiNldpyRUBBEzNoWL0Cso1jip&index=1 <-- these are such cool lectures about virology, they even document the pandemic along 2020 with a short intro before each lecture04:05
Brainstormde-facto: From www.youtube.com: Virology Lectures 2020 #1: What is a Virus? - YouTube04:05
de-factothankfully he talks pretty slow so one could ramp up to 2x speed then each lecture is just ~30min04:06
de-factoand he got really really awesome graphics and animations in his lectures04:07
de-factoits fascinating how much of it actually is geometry04:08
de-factoand information of course04:09
BrainstormNew from NPR: A New Coronavirus Variant From Brazil, Is Found In Minnesota: A Twin Cities resident contracted a new variant of the coronavirus after traveling to Brazil. The new strain is believed to be more transmissible. → https://is.gd/xUB1cq04:16
de-factoyeah maybe we should promote airtravel even more, congratz04:19
de-facto:/04:19
de-facto.title https://www.youtube.com/watch?v=wC8ObD2W4Rk04:45
Brainstormde-facto: From www.youtube.com: SARS-CoV-2 UK variant: Does it matter? - YouTube04:45
de-factocomment from Vincent Racaniello on 2020-12-2104:45
de-factoprettty interesting about mutations in general04:46
de-facto.title https://www.youtube.com/watch?v=FPo2BAq4H-8 <-- btw the mutants are also addressed around minute 20 here 05:12
Brainstormde-facto: From www.youtube.com: TWiEVO 64: Seeing the lineages for the variants - YouTube05:12
de-factoLjL, they talk about the Rockefeller Uni NY paper i linked above05:14
de-factovery interesting they talk about first signs of convergent viral evolution (independent emergence of selection for the same mutations in different places)05:18
de-factoand Vincent Racaniello just got his Moderna shot in his arm 05:19
ryoumawhich i guess is a good ad for that brand05:20
de-factoi dont think they need any ads though, they need to scale production as does Pfizer/BioNTech and all the others 05:27
ryouma(i was not implying shenanigans but rather praising vincent is all)05:31
CoronaBot04/r/coronavirus: Biden: Anyone who wants a COVID vaccine will be able to get a COVID vaccine by "this spring." (10530 votes) | https://www.complex.com/life/biden-american-wants-vaccine-be-able-get-one-spring?utm_campaign=complexmag&utm_source=twitter.com&utm_medium=social | https://redd.it/l4z9uz05:34
gigasu_shidade-facto: wouldn't you just love a world in which all passports are revoked =)05:57
de-factono but a world in which biosecurity is not ignored anymore 06:03
gigasu_shidai'll be the first to admit it if i become a walking biohazard 06:19
BrainstormNew from The Indian Express: World: Airlifted COVID vaccines to 9 countries, will gradually supply to WHO’s COVAX facility: India at UN → https://is.gd/NN9MtH06:19
BrainstormUpdates for Thailand: +959 cases (now 14646) since 22 hours ago — Germany: +548 deaths (now 53325) since 22 hours ago06:27
de-factolol06:30
de-factoi guess its all by intention, huh?06:30
de-factoi guess they should just let air-travel passengers sign a paper that they really really do promise not to import an asymptomatic infection with a new variant :P06:40
BrainstormNew from The Indian Express: World: Lebanese in impoverished north protest coronavirus lockdown → https://is.gd/KWnLT306:46
de-factooh wait they do that already, and also that they promise to stay in home quarantine. well i guess then we can relax, because that sounds like a proper biosecurity concept.06:51
CoronaBot04/r/covid19: PRINCIPLE trial finds no benefit from antibiotics, azithromycin and doxycycline for COVID-19 patients (80 votes) | https://www.nihr.ac.uk/news/principle-trial-finds-no-benefit-from-antibiotics-azithromycin-and-doxycycline-for-covid-19-patients/26680 | https://redd.it/l50vpr06:53
BrainstormNew preprint: mRNA-1273 vaccine induces neutralizing antibodies against spike mutants from global SARS-CoV-2 variants by  et al, made available as preprint on 2021-01-25 at https://biorxiv.org/cgi/content/short/2021.01.25.427948 [... want %more?]07:03
BrainstormUpdates for C. Valenciana, Spain: +19462 cases (now 264742), +176 deaths (now 4192) since 2 days ago — Andalusia, Spain: +19378 cases (now 368220), +155 deaths (now 5925) since 2 days ago — Castile y Leon, Spain: +6573 cases (now 174017), +33 deaths (now 5473) since 2 days ago — Galicia, Spain: +4287 cases (now 86829), +31 deaths (now 1616) since 2 days ago07:23
BrainstormNew from Il Sole 24 Ore: Moderna affila nuove armi contro le varianti del virus: La ricerca della azienda Usa punta da una lato ad aumentare le difesa con una terza dose del vaccino oggi disponibile, le difese, dall'altro prevede un “richiamo” mirato per quella o altre variabili  che potrebbero presentarsi → https://is.gd/C12Dtw07:27
BrainstormNew from r/WorldNews: worldnews: Moderna vaccine appears to work against new Covid-19 variants → https://is.gd/wHt38107:56
BrainstormNew from r/Coronavirus: Daily Discussion Thread | January 26, 2021: The WHO pages contain up-to-date and global information. Please refer to our Wiki for additional information. → https://is.gd/Up7YB509:05
BrainstormUpdates for Germany: +550 deaths (now 53327) since 18 hours ago09:15
BrainstormNew from BBC Health: (news): Coronavirus: EU to tighten vaccine exports amid row with AstraZeneca → https://is.gd/oXRItq09:41
BrainstormNew from NPR: Anti-Curfew Protests Flare Up in The Netherlands: At least 150 people were reportedly arrested amid violent protests against coronavirus restrictions in the Netherlands. → https://is.gd/3DgmVv10:06
BrainstormNew from EMA: What's new: Medicine: Human medicines European public assessment report (EPAR): COVID-19 Vaccine Moderna, COVID-19 mRNA Vaccine (nucleoside modified), COVID-19 virus infection, Date of authorisation: 06/01/2021, Status: Authorised → https://is.gd/ApJcx910:19
BrainstormNew from BBC Health: (news): Coronavirus: EU to tighten vaccine exports amid row with AstraZeneca → https://is.gd/oXRItq10:31
BrainstormNew from Medical Xpress: Minnesota case marks 1st detection of Brazil variant in US: A new Brazilian variant of the coronavirus has made its first known appearance in the United States in a person who recently returned to Minnesota after traveling to Brazil, state health officials announced Monday. → https://is.gd/ppMeYa10:43
BrainstormNew from Medical Xpress: COVID-19 variant brings new dimension to Europe's pandemic: In the first week of December, Portugal's prime minister gave his pandemic-weary people an early Christmas gift: restrictions on gatherings and travel due to COVID-19 would be lifted from Dec. 23-26 so they could spend the holiday season with family and friends. → https://is.gd/3AAtzN10:55
BrainstormNew from BBC Health: Covid: UK virus deaths top 100,000 since pandemic began: Another 7,700 deaths registered with Covid on death certificate, bringing total to nearly 104,000. → https://is.gd/CnVMT911:07
BrainstormNew from BBC Health: (news): Coronavirus: EU to tighten vaccine exports amid row with AstraZeneca → https://is.gd/oXRItq11:19
BrainstormNew from BBC Health: (news): Covid-19: Vaccine minister 'confident' of supplies amid production delays → https://is.gd/w4p9Xq11:32
BrainstormNew from BMJ: Universal basic income and covid-19 pandemic: The gulf between the wealthiest and poorest had been increasing even before the covid-19 destroyed the globe’s health and economies.1 Recent research indicates a growing depth of poverty, and women... → https://is.gd/N8sw4011:44
BrainstormUpdates for UAE: +3601 cases (now 285147), +7 deaths (now 805) since 23 hours ago11:50
zutt%cases israel11:51
Brainstormzutt: In Israel, there have been 607445 confirmed cases (6.6% of the population) and 4498 deaths (0.7% of cases) as of 4 hours ago. 10.2 million tests were performed (5.9% positive). Fatality can be broadly expected to lie between 0.8% (assuming prevalence as in tests) and less than 0.8% (considering only deaths and recoveries). See https://offloop.net/covid19/?default=Israel for time series data.11:51
BrainstormNew from Variants of SARS-CoV-2 on Wikipedia: ArcMachaon: correct V to GV; cleanup hatnotes per WP:1HAT: correct V to GV; cleanup hatnotes per WP:1HAT ← Previous revision Revision as of 10:48, 26 January 2021 Line 1: Line 1: {{short description|Different variants of SARS-CoV-2}} {{short description|Different variants of SARS-CoV-2}} {{COVID-19 [... want %more?] → https://is.gd/xKhE7Z11:55
BrainstormNew from BMJ: Covid-19: New UK variant may be linked to increased death rate, early data indicate: The new UK variant of SARS-CoV-2 may be associated with an increased risk of death, emerging data are suggesting.In a briefing paper published on 22 January the government’s New and Emerging... → https://is.gd/1WY3LQ12:20
bittersweetsymphIf it is found in the sewerage it sounds like it is in the community even if there are no detected cases I guess unless it's from old cases that are shedding12:50
BrainstormNew from Scientific American: COVID Vaccine Rollout Pits Fairness against Speed: People wait in line in a Disneyland parking lot in Anaheim, Calif., to receive COVID-19 vaccines on the opening day of the the park’s Super Point-of-Dispensing (POD) site on January 13, 2021. → https://is.gd/lyTyra13:09
BrainstormUpdates for Saint Lucia: +99 cases (now 921), +2 deaths (now 13) since 16 hours ago13:10
BrainstormNew from BBC Health: Coronavirus: Vaccine supply fears grow amid EU export threat: The EU calls for "fair" distribution after vaccine companies cut back on pledged supplies. → https://is.gd/oXRItq13:10
BrainstormNew from r/WorldNews: worldnews: EU demands that vaccine makers honor their commitments → https://is.gd/bIg3Un13:21
BrainstormUpdates for Lesotho: +3 cases (now 8047), +12 deaths (now 146) since 20 hours ago13:23
BrainstormNew from StatNews: Regeneron says monoclonal antibodies prevent Covid-19 in study: The drug maker Regeneron said its monoclonal antibody cocktail prevented Covid-19 in a clinical trial — a finding that could one day make the treatment an option for individuals who are… → https://is.gd/XE0hYR13:34
g2`Click bait13:41
g2`Immunocompromised13:43
BrainstormNew from BBC Health: (news): Covid-19: Vaccine minister 'confident' of supplies amid production delays → https://is.gd/w4p9Xq13:46
BrainstormNew from r/WorldNews: worldnews: Covid 19 vaccination drive: India’s one million shots in 6 days is world’s fastest rollout | India News - Times of India → https://is.gd/r3e9Rc13:59
DocScrutinizer05LjL: could you please check the regex/whatever to adjust the *bold* in those >>New from BBC Health: <b>(news):</b> Coronavirus: EU to tighten vaccine <<?14:09
DocScrutinizer05>> New from EMA: What's new: <b>Medicine:</b> Human medicines E...<<14:11
BrainstormNew from BBC Health: Coronavirus: Vaccine supply fears grow amid EU export threat: The EU calls for "fair" distribution after vaccine companies cut back on pledged supplies. → https://is.gd/oXRItq14:11
DocScrutinizer05weird it works for >>New from BBC Health: <b>Coronavirus: Vaccine supply fears grow amid EU export threat:</b> The EU calls for..<<14:14
DocScrutinizer05maybe add a {25,} somewhere?14:21
DocScrutinizer05discontinuity in daily-reported for D, RKI today14:24
BrainstormNew from BMJ: Covid-19: Use social media to maximise vaccine confidence and uptake: We echo Hanif and colleagues’ concerns that some communities, such as ethnic minority groups and those of lower socioeconomic standing, may be left behind in the UK’s vaccination programme.1 Social... → https://is.gd/5gA2MQ14:24
DocScrutinizer05or rather yesterday?14:24
DocScrutinizer05yesterday X[t_now] ~= X[t-7d], today it's back to decline and even massive decline, way more than the ~20%/week we had for the last weeks14:26
DocScrutinizer05bottom line: sth is happening but absolutely unclear what14:27
BrainstormUpdates for Germany: +574 deaths (now 53351) since 23 hours ago14:32
BrainstormNew from BBC Health: (news): Covid-19: Vaccine minister 'confident' of supplies amid production delays → https://is.gd/w4p9Xq14:37
Arsaneritisn't there some artefact on corona.rki.de due to which the recent days always appear to show a decline?14:44
ArsaneritHamburg only reports 24 cases on corona.rki.de, that would be the lowest value since 25 August 2020, probably something missing there14:46
Arsaneritor rathe ryesterday compared to day before14:46
CoronaBot04/r/covid19: New data show treatment with Lilly's neutralizing antibodies bamlanivimab (LY-CoV555) and etesevimab (LY-CoV016) together reduced risk of COVID-19 hospitalizations and death by 70 percent (90 votes) | https://investor.lilly.com/news-releases/news-release-details/new-data-show-treatment-lillys-neutralizing-antibodies | https://redd.it/l5cxht14:50
mjensen[m]Can the news stories that the bot(s) post be deduplicated?  It's kinda annoying to see the same story 5 times. 15:01
BrainstormNew from NIH Director's blog: Nanoparticle Technology Holds Promise for Protecting Against Many Coronavirus Strains at Once: It’s truly encouraging to witness people all across our nation rolling up their sleeves to get their COVID-19 vaccines. That is our best chance to end this pandemic. But this is the third corona-virus to emerge and cause [... want %more?] → https://is.gd/Vntjbu15:02
jacklswwhich bot?15:02
jacklswmight some people keep posting the same news on reddit15:02
mjensen[m]Brainstorm15:03
mjensen[m]Or am I just seeing duplicates because of matrix?15:04
mjensen[m]For example, this one15:05
mjensen[m]New from BBC Health: (news): Covid-19: Vaccine minister 'confident' of supplies amid production delays → https://is.gd/w4p9Xq15:05
ArsaneritIt just needs to learn to be smart enough when recognising different headlines cover the same story ;-)15:05
mjensen[m]Those have the same headline, same link, right?15:07
mjensen[m]I'm on my phone, so it's hard to compare exactly. 15:07
ubLIX[m]those? you only posted one line?15:09
ubLIX[m]i'm on matrix and that link only appears once in my scroll15:09
ubLIX[m]ah. it's posting the text AND a screenshot which includes the text. i'm using text only client so i didn't see that15:12
ubLIX[m]^ LjL interesting fine tuning opportunity15:14
BrainstormNew from Medical Xpress: COVID-19 vaccine hesitancy can be overcome with the right messaging, researchers find: The battle against COVID-19 vaccine hesitancy—an issue for nearly a quarter of Americans recently polled—can be won if messages promoting vaccination suggest most people will take it and political motivations did not rush its development, [... want %more?] → https://is.gd/bAbGhY15:14
BrainstormUpdates for Switzerland: +1884 cases (now 515483), +94 deaths (now 9187) since 23 hours ago15:15
ubLIX[m]mjensen: i guess you're more concerned with the triple post than the text redundancy in each post?15:15
izhave you guys seen this aplidin news?15:17
izhttps://www.sfchronicle.com/health/article/Cancer-drug-Aplidin-shows-promise-as-COVID-15896461.php15:18
ubLIX[m]hm. my bash script log viewer (faster than in-client search) already de-duplicates so i didn't see the triple post15:22
ubLIX[m]maybe Brainstorm should scan previous 48 hours (oughta cover it) posts for de-duplication15:23
mjensen[m]<ubLIX[m] "mjensen: i guess you're more con"> Just the redundant posts. 15:23
ubLIX[m]i recall that Brainstorm's fetching of Guardian articles should to be responsible for a lot of redundant posts, but that seemed to be because the Guardian changed a single word here or there. these three latest do seem to be identical15:24
ubLIX[m]s/should/used/15:24
mjensen[m]ubLIX are you seeing the same news stories posted multiple times?15:26
BrainstormNew from StatNews: Pharma: STAT+: Pharmalittle: Regeneron says its antibody prevented Covid-19 in a trial; EU threatens to impose vaccine export controls → https://is.gd/K9gGqs15:27
ubLIX[m]well not on this occasion, because i just connected, and the client only fetches the last 10 or so posts15:28
ubLIX[m]but looking through raw log (after just now remembering that my log viewer de-duplicates) i did indeed find that triply redundant post15:29
ubLIX[m]iirc Brainstorm is almost entirely python. fixing duplicate posts would depend on LjL finding time to add some regex test for new posts. idk if he has a rationale for having the post re-foreground news posts. wait to see what he says15:36
ubLIX[m]*the bot15:36
mjensen[m]I just logged on in my browser, it's less annoying to me here because it isn't displaying previews.  15:43
mjensen[m]It seems basing it off the URL would be good enough.  There are times when a title or maybe some content in the story might change, but I personally don't want to be notified each time that happens.  I'd like to hear about the rationale too...15:44
mjensen[m]There's another example15:45
ubLIX[m]eliminating exactly identical posts seems relatively straightforward, low hanging fruit. in cases where a word or two or a url has changed but the essences hasn't, it gets thornier15:50
mjensen[m]In this case, filtering by URL would catch most of them.15:55
ubLIX[m]if LjL is anything like as chaotic a script writer as i am, the difficulty will be in bringing oneself to open the script files in the first place ;p16:03
BrainstormNew from StatNews: STAT+: STAT+ Conversations: A conversation with vaccine expert Paul Offit: STAT's Matthew Herper sits down with vaccine expert Paul Offit to discuss the ongoing Covid-19 vaccine rollout. → https://is.gd/yg2KEO16:03
BrainstormNew from Medical Xpress: Dismay in France, land of Pasteur, over vaccine flops: News that France had fallen further behind in the race to develop COVID-19 vaccines caused dismay on Tuesday, reigniting a debate about the country's standing in the world and its scientific prowess. → https://is.gd/Ae6RkG16:16
BrainstormNew from Variants of SARS-CoV-2 on Wikipedia: Another Believer: order: order ← Previous revision Revision as of 15:20, 26 January 2021 Line 242: Line 242: {{Portal|COVID-19}} {{Portal|COVID-19}} {{Wiktionary|COVID}} {{Wiktionary|COVID}} + ⚫ * [[RaTG13]], the closest known relative to SARS-CoV-2 * [[International Committee on Taxonomy of Viruses]] * [... want %more?] → https://is.gd/xKhE7Z16:29
BrainstormNew from Medical Xpress: Biden sets new goal of 1.5 million COVID vaccinations a day: President Joe Biden upped the country's daily coronavirus vaccination goal to 1.5 million on Monday, even as more infectious variants surfaced across America. → https://is.gd/2idXyV16:54
BrainstormUpdates for Netherlands: +3958 cases (now 959976), +71 deaths (now 13672) since 23 hours ago17:07
BrainstormNew from ClinicalTrials.gov: (news): Direct Topical Lung T3 Treatment to Improve Outcome & Sequelae of COVID-19 Acute Respiratory Distress Syndrome → https://is.gd/DlNLCy17:20
BrainstormUpdates for Canada: +5123 cases (now 755303) since 23 hours ago17:44
LjLubLIX[m], mjensen[m]: i am a chaotic script writer indeed, and as i've said before, the RSS feeds module is one that i've written particularly badly. but it's not like i haven't *tried* to suppress these duplicate posts... of course i check the link, i also check the unique ID (when present, since not all sources are so kind as to actually include it), i check the timestamp to exclude older entries, and i even use an edit counter to match headlines that 18:09
LjLare *almost* identical but not quite. yet it sometimes happens anyway. it had seemed to subside after i removed... i think it was CNBC, which had a particularly nasty way to lie about their RSS timestamps and lacked IDs18:09
BrainstormNew from Variants of SARS-CoV-2 on Wikipedia: Yadsalohcin: Revised 20H & 20I clades into the body of the text: Revised 20H & 20I clades into the body of the text ← Previous revision Revision as of 17:06, 26 January 2021 Line 110: Line 110: |first9=Andrew |last9=Rambaut |first9=Andrew |last9=Rambaut |first10=Jeff |last10=Barrett |first10=Jeff [... want %more?] → https://is.gd/xKhE7Z18:09
LjL<ubLIX[m]> ah. it's posting the text AND a screenshot which includes the text. i'm using text only client so i didn't see that  ←  no, it's not. that's mjensen[m]'s client doing the screenshot thing. i believe i have URL titling/screenshotting disabled by default in the room, but i also believe the mobile client ignores that18:10
LjLubLIX[m], mjensen[m]: have a peek at what happens https://paste.ee/p/pxjjN18:19
DocScrutinizer05>><Arsanerit> isn't there some artefact on corona.rki.de due to which the recent days always appear to show a decline?<<  nope, I refer to this https://i.imgur.com/Uzp4Cld.png18:19
DocScrutinizer05Arsanerit: there probably _is_ some artifact or hickup, but it's not systemic, it's probably a mistake somewhere again18:21
BrainstormNew from NPR: European Union Warns AstraZeneca Over Reduction In Vaccine Shipments: "The companies must deliver. They must honor their obligations," the European Commission's president said after both AstraZeneca and Pfizer said they were experiencing shipping issues. → https://is.gd/mstXGq18:22
DocScrutinizer05>><mjensen[m]> Can the news stories that the bot(s) post be deduplicated?  It's kinda annoying to see the same story 5 times. << I suggested keeping a list of last 24h posts and do a error tolerant "grep" to detect and filter headlines that are 90%+ identical to previous ones18:23
DocScrutinizer05haha >><ubLIX[m]> maybe Brainstorm should scan previous 48 hours (oughta cover it) posts for de-duplication<< yeah :-D18:27
ubLIX[m]DocScrutinizer05: my viewer implemented in bash does that for 100% match (except it ignores timestamps and nick) and apparently catches a few. i don't speak python though :(18:27
ubLIX[m]without wishing to pressure LjL, is python string parsing/comparison easier in python than bash?18:27
LjLubLIX[m], probably18:28
ubLIX[m]no pressure now, lol18:28
LjLDocScrutinizer05, please read what i stated on the matter18:28
LjLeveryone thinks they know the obvious solution to this18:28
LjLbut i'm DOING what you say18:28
ubLIX[m]but but but18:29
LjLthe code has a bug somewhere, that means i'm a bad coder, but not that i'm a complete idiot18:29
LjL    elif latest.text == previous.text or SequenceMatcher(a=latest.text, b=previous.text).ratio() > 0.8:18:29
LjL       try: utils.log("Not updated: {new} == {old}".format(new=latest.text, old=previous.text))18:29
LjL       except: utils.log("Not updated: (can't print what)")18:29
LjL       updated = False18:29
LjLi only compare against one previous entry, and this can fail to work if BBC is utterly dumb. however BBC does provide unique IDs so those should work to disambiguate18:30
LjLand i'm keeping the last 4096 seen IDs stored18:30
LjLanyway, i've already changed the ids storage thing so that in addition to the IDs, it also stores URL and text of the previous 4096 entries to check for duplicates on that. but i think there's a bug somewhere else, i might have found it, but i've thought so a number of times before18:32
ubLIX[m]rewrite it in bash18:32
LjLprobably not found it18:33
LjLlook, you're all welcome to spot the bug in my messy code18:33
LjL%source feeds18:33
BrainstormLjL: Module feeds does not exist!18:33
LjLyes it does18:33
LjLexcept it does in a different bot18:34
ubLIX[m]is this Brainstorm's Hal 9000 moment?18:34
ubLIX[m]"I'm sorry LjL, I can't let you do that"18:34
BrainstormNew from BBC Health: Covid deaths: UK passes milestone of 100,000: A total of 100,162 people have died with coronavirus since the pandemic began, according to government figures. → https://is.gd/5dzvZr18:35
LjLmore or less18:35
LjLa lot of things broke when i divided the bot into three for speed/flexibility18:35
LjLfather son and holy shit how buggy18:35
LjLi'm not entirely sure i can let info.py run on all three bots without horribad duplication of output, but i'll do it anyway18:36
LjLBrainstorm, reload feeds18:36
BrainstormLjL: <module 'feeds' from '/home/brainstorm/brainstorm/bot/modules/feeds.pyc'> (version: 2021-01-26 17:36:32)18:36
LjLnot that one18:36
LjLBrainstorm, reload info18:36
BrainstormLjL: <module 'info' from '/home/brainstorm/brainstorm/bot/modules/info.pyc'> (version: 2020-05-26 03:49:25)18:36
LjL%source feeds18:36
BrainstormLjL, source code for module 'feeds' can be found at https://paste.ee/p/DSGK8 18:36
BrainstormUpdates for Cuba: +786 cases (now 22614), +3 deaths (now 200) since a day ago — United Kingdom: +24005 cases (now 3.7 million), +1764 deaths (now 100162) since 21 hours ago18:40
DocScrutinizer05(me humbly suggests edit distance based grep in a circular buffer, and https://reader.elsevier.com/reader/sd/pii/S0019995885800462?token=AD94F55C20CE9658BCDC06BAF78609935944CBEC63AE6A3092E7B4720A4F5C8EEB0A4BE2BD885E60DF3460CCB82B2139 | https://www.sciencedirect.com/science/article/pii/S0019995885800462?via%3Dihub etc. Sorry, finding a (python) implementation aka lib will take some more time18:45
BrainstormNew from r/WorldNews: worldnews: The megarich have already recovered from the pandemic. It may take the poor a decade to do so → https://is.gd/pgTc4z18:47
BrainstormNew from The Guardian: Politics: UK Covid live: Johnson 'sorry for every life lost' and takes 'full responsibility' as death toll passes 100,000 → https://is.gd/JdpcbH18:47
DocScrutinizer05sth along https://en.wikipedia.org/wiki/Levenshtein_distance18:48
LjLDocScrutinizer05, sigh18:48
LjLSequenceMatcher *uses* Levenshtein distance18:48
LjLalso, the problem that occurred that ubLIX[m] and mjensen[m] were complaining about was with a BBC piece that never changed its headline at all18:48
LjLso using some rocket-science-based edit distance will make no difference to the simple levenshtein distance i'm suing18:49
LjLand using18:49
LjLanyway i found the bug with the ID matching i think18:49
LjL(if i won't have to say actually no for the nth time)18:49
DocScrutinizer05LjL: ooh >>SequenceMatcher *uses* Levenshtein distance<< :-D you're a smart one :-)18:50
DocScrutinizer05didn't know18:50
DocScrutinizer05did you find a lib for it?18:51
DocScrutinizer05or do you share your implementation? I certainly will need sth like this sooner or later18:52
BrainstormNew from BBC Health: (news): Covid-19: Vaccine minister 'confident' of supplies amid production delays → https://is.gd/w4p9Xq18:53
ubLIX[m]LjL | anyway i found the bug with the ID matching i think  << oh phew18:54
LjLDocScrutinizer05, from difflib import SequenceMatcher18:55
LjLit's part of Python18:55
LjLubLIX[m], get on IRC though18:56
Jigsy%cases UK18:57
BrainstormJigsy: In United Kingdom, there have been 3.7 million confirmed cases (5.6% of the population) and 100162 deaths (2.7% of cases) as of 16 minutes ago. 69.4 million tests were performed (5.3% positive). See https://offloop.net/covid19/?default=United%20Kingdom for time series data.18:57
LjLanyway, it's all good, it should be fixed now, at least until some RSS feed finds a novel and unexpected way to break it19:03
LjLit's like with virus variants19:04
BrainstormNew from The Guardian: Politics: UK Covid live: Johnson 'sorry for every life lost' and takes 'full responsibility' as death toll passes 100,000 → https://is.gd/JdpcbH19:05
LjL"[Boris Johnson] expressed sorrow after the total UK death toll exceeded 100,000 on nearly every metric"19:16
LjL100,000 dead, and 100,000 deceased, also 100,000 passed away, as well as 100,000 gone forever?19:16
DocScrutinizer05LjL: many thanks! :-)19:16
DocScrutinizer05(2 up) yeah indeed, >>nearly every metric<< what the hell?19:19
bin_bashlol l19:45
bin_bashLjL**19:45
raccoon_dogI think it's bad, bad phrasing. Like it was maybe the highest percentage of people infected that ended up dying, the highest percentage per population density, etc.19:53
raccoon_dogI'm guessing that's what's meant with "nearly every metric" here.19:53
LjLthey probably had two different things in mind and they got mangled into one19:58
LjLde-facto, oh you'll love this comment, "The government’s proposed mandatory hotel quarantine measures for travellers arriving from high-risk countries could wipe out nearly £548m a day from the UK economy in lost travel, according to the World Travel and Tourism Council (WTTC)."20:00
raccoon_dog> £548m a day 20:02
raccoon_dogwat20:02
DocScrutinizer05I call BS20:03
DocScrutinizer05Arsanerit: de-facto: https://i.imgur.com/Uzp4Cld.png suggests R_eff=0.7 from a week ago to today20:14
LjLi don't know, it's just a random and unimportant number to me20:26
LjLit seems pretty obvious you should stop flights or at *least* quarantine people from countries at high risk20:26
LjLtourism industry can start blabbering about billions and trillions, it doesn't matter20:26
CoronaBot04/r/coronavirus: Dr. Anthony Fauci applauds Moderna's program to create COVID-19 booster for South African variant (10101 votes) | https://www.newsweek.com/dr-anthony-fauci-applauds-modernas-program-create-covid-19-booster-south-african-variant-1564215 | https://redd.it/l5cynm20:34
BrainstormUpdates for Spain: +33072 cases (now 2.6 million), +591 deaths (now 56799) since a day ago — Italy: +10584 cases (now 2.5 million), +541 deaths (now 86422) since a day ago — France: +556 deaths (now 73949) since 18 hours ago20:43
BrainstormUpdates for Mozambique: +1274 cases (now 34055) since 21 hours ago21:20
BrainstormNew from BBC Health: Covid-19: UK deaths likely to come down slowly, Whitty warns: There will be "a lot more deaths" before the effect of vaccines is felt, England's chief medical officer says. → https://is.gd/FmflNv21:34
BrainstormNew from FDA Press Releases: FDA: Coronavirus (COVID-19) Update: January 26, 2021 → https://is.gd/pSwvEa21:59
BrainstormNew from Medical Xpress: Johnson & Johnson Covid vaccine results 'next week': CFO: Johnson & Johnson expects to report results from the eagerly-anticipated clinical trial of its COVID-19 vaccine next week, the US pharmaceutical's chief financial officer told CNBC Tuesday. → https://is.gd/3we1ku22:12
DocScrutinizer05yes, I heard in TV news today that JJ is about to "deliver"22:20
BrainstormUpdates for Netherlands: +3955 cases (now 959979) since 22 hours ago22:22
mjensen[m]My question regarding the duplicate post situation is this, is there a benefit to re-posting the same article if it has changes or a modified timestamp?  Personally, I won't go back and read it again but maybe some here do.22:23
mjensen[m]It seems like de-duplicating based solely on URL would be enough.  (at least for me)22:25
LjLPlease just read the backscroll22:26
DocScrutinizer05megakenny[m]: no benefit. And it's fixed22:27
mjensen[m]sorry, I skimmed through the history..  I'll go read it more carefully22:27
DocScrutinizer05oops sorry, wrong nick22:28
LjLI deduplicate based on URL, ID, string, as well as other thing. The code is, or hopefully was, buggy, and remains ugly, but I don't need to be repeatedly told to compare something against something else, I can figure that easily enough on my own... It's not like it's *meant* to post duplicates22:30
ArsaneritDocScrutinizer05: Can we trust those numbers?22:36
ArsaneritWhy are people still allowed to quarantaine at home?  Hotels are empty.  Is it too much to ask people who insist on travelling under the present conditions to spend their two week quarantaine in a hotel where they pay regular market rates for full-board lodging including room service for all meals?22:38
BrainstormNew from r/WorldNews: worldnews: Pandemic Earnings of World's 10 Wealthiest Men Could Buy COVID-19 Vaccines for All: Oxfam → https://is.gd/eiOztJ22:46
DocScrutinizer05Arsanerit: they are not completely implausible22:49
DocScrutinizer05the numbers that is22:50
DocScrutinizer05though this edge in R_eff from two days ago (~0.9) to today (0.7) is a bit less plausible22:52
ArsaneritLet's hope it's true.22:53
DocScrutinizer05actually yesterday the 7d-reference R_edd was = 122:53
DocScrutinizer05s.dd.ff.22:53
DocScrutinizer05oh, btw. happy first birthday, german covid, may you die before you're 222:55
DocScrutinizer05Arsanerit: we really shouldn't look at daily changes, noise and jitter is too high in that. You could read the numbers like "a few thousand reported one day early, and so the previous R_eff was too high and today's R_eff is too low.23:01
ArsaneritDocScrutinizer05: Yes.23:01
DocScrutinizer05sorry I nevertheless did, I'm also eagerly hoping for any good signs23:01
ArsaneritGerman covid will not die before it's 2, but hopefully it will be under control before then.23:01
ArsaneritThe news outlets also report numbers daily, even if they sometimes say "numbers not meaningful" then still report them.23:02
DocScrutinizer05today was particularly bad - they claimed "we're down from a max of >33k to 6k now" which is BS23:03
LjLHere it's "slight decrease in infection today" followed by explaining that there were fewer tests and so the ratio is actually higher, meaning no decrease at all. But they start by saying that Anyway23:03
DocScrutinizer05yeah, news are more and more silly and BS23:04
DocScrutinizer05I been aware of this quite a while ago already, that's when I started my own stats on http://reisenweber.net/et_al/covid/covid19_statistics.htm23:05
ArsaneritDocScrutinizer05: Thanks23:09
DocScrutinizer05yw23:09
ArsaneritIs there somewhere where the test positive rate is nicely visualised, rather than hidden in an XLS file on the RKI website?23:09
BrainstormNew from StatNews: U.S. will have enough Covid-19 vaccines for 300 million Americans by end of summer, Biden says: Biden plans to purchase enough vaccines from Pfizer and Moderna to fully vaccinate 300 million Americans by the end of summer 2021, the administration said Tuesday. → https://is.gd/VFT4QP23:10
DocScrutinizer05Arsanerit: I didn't see any yet23:10
de-facto.title https://imgur.com/a/SqrbY44 https://i.imgur.com/2NUxZkr.png source: https://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Projekte_RKI/Nowcasting.html23:16
Brainstormde-facto: From imgur.com: Germany COVID-19: Daily Incidence and Reproduction - Album on Imgur23:16
de-facto.title https://imgur.com/a/D0MKmsi https://i.imgur.com/dqA6Vgd.png source: https://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Projekte_RKI/Nowcasting.html23:17
Brainstormde-facto: From imgur.com: Germany COVID-19: Zoomed Daily Incidence and Reproduction - Album on Imgur23:17
ArsaneritDocScrutinizer05: is that from the spreadsheets?23:19
BrainstormUpdates for Switzerland: +58 deaths (now 9204) since 19 hours ago23:25
de-facto.title https://imgur.com/a/xYRlzzc https://i.imgur.com/mR8zJEO.png source: https://www.intensivregister.de/#/aktuelle-lage/zeitreihen23:32
Brainstormde-facto: From imgur.com: Germany COVID-19: Occupied ICU beds and daily change - Album on Imgur23:32
DocScrutinizer05Arsanerit: hm, what exactly? or was that a nick-expand-fail?23:33
BrainstormNew from NPR: California Health Secretary On Lifting Stay-At-Home Orders And Vaccinations: California Health and Human Services Secretary Dr. Mark Ghaly talked with NPR about why the state eased some COVID-19 restrictions and addressed the relatively slow vaccine rollout. → https://is.gd/znW1M623:35
ArsaneritDocScrutinizer05: Yes.23:36
Arsaneritde-facto: Are those plots from the spreadsheets?23:36
de-factoyes23:39
de-factofrom the source i linked 23:39
CoronaBot04/r/covid19: Moderna Provides U.S. COVID-19 Vaccine Supply Update (82 votes) | https://investors.modernatx.com/news-releases/news-release-details/moderna-provides-us-covid-19-vaccine-supply-update/ | https://redd.it/l5fabg23:42
ArsaneritI tried to open those spreadsheets but failed.23:46
Arsaneritgoodnight23:46
de-factohuh? its just xlsx23:51
de-factoyou need LibreOffice or MS Office for that23:51

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