libera/##covid-19/ Monday, 2021-09-06

nixonixfisman is the man behind that canadian delta vs alpha study. come on dude, l-theanine00:00
nixonixthis one https://www.medrxiv.org/content/10.1101/2021.07.05.21260050v2.full00:02
nixonixwho resigned after leaking some doomsday model supposedly made by ontarios rona modellers00:02
LjLuuh think i missed that drama00:03
nixonix.title https://twitter.com/DFisman/status/142976166367118541300:03
Brainstormnixonix: From twitter.com: David Fisman (@DFisman): "It is with mixed emotions that I have decided to resign from Ontario’s science and modeling tables. I wish every success to the colleagues who remain on these tables. Ontario [...]00:03
nixonix.title https://twitter.com/DFisman/status/142903745899019059600:04
Brainstormnixonix: From twitter.com: David Fisman (@DFisman): "The Ontario science table has important modeling work that projects a grim fall. I don't understand why they're not releasing that. It's important for people to understand [...]00:04
twomoonlol rona modellers00:09
twomoonsuddenly it seems like you're not a John Campbell clone00:10
LjLnixonix, with some fear i ask, what doomsday scenario did he leak?00:10
twomoongood, nixonix is giving us the angles that John Campbell won't touch00:13
LjLCampbell is boring00:13
twomoonhe's just a windbag. he wouldn't be so boring if he talked a lot less00:15
twomoonwe just got tired of getting his spiel in 40 minutes instead of 1000:15
nixonixafaik he didnt leak the model or pictures, just told about it and it seems he disagrees their with their recommendations that he sees as political, while their models showed something like this:00:18
BrainstormNew from r/Coronavirus: Coronavirus: A Colorado COVID-19 test center denied service to Candace Owens, accused her of making 'this pandemic worse' → https://is.gd/Woy89q00:18
nixonix.title https://mobile.twitter.com/DFisman/status/142507761764075520100:19
Brainstormnixonix: From mobile.twitter.com: David Fisman (@DFisman): "Important for people to understand the numbers: there's currently credible modeling in Ontario projecting a 70% covid attack rate in schools this fall. And why wouldn't there [...]00:19
imihi00:20
imiwhich vaccine(s) were used in Columbia?00:21
imimaybe you've already heard of the mu variant00:22
nixonixbut those models show pretty much anything depending on parameters used, since they are very sensitive to small changes. what ive seen, they usually just pick three curves that were made with different parameters, and show them to politicians or media, showing lower, higher, and middle estimate. but really low and high estimates are not shown,00:22
nixonixsince they are very far from the middle estimate (ive seen some examples)00:22
nixonixbasically meaning, its just bullshit, their models00:22
LjLook, gave that article a skim (really just a skim), it seems to say some pretty reasonable things but it looks like when it eventually estimates risk, "a few percents" is really not consistent with what we have from various studies - which, sure, don't look into the *very* long term, but00:22
LjLimi, you mean Colombia, or the District of Columbia, or what? (i might not know the answer anyway)00:23
imiI mean Columbia the south-american country00:25
LjLyeah it's called Colombia in English, not Columbia00:25
LjLanyway it appears its government websites don't open up for me00:26
LjLthey've authorized a bit of everything: Moderna, Pfizer, AZ, J&J, Sinovac00:26
LjLbut what they've actually used, i'm not really sure00:26
imiapparently there's a new mu variant there allegedly 100% resistant to vaccines00:27
LjLhttp://eps.coomeva.com.co/publicaciones.php?id=156885 has some veeeery basic info on what vaccines they're using00:27
LjLimi, it's not the first time i hear of Mu, and admittedly i haven't been following it closely, but it *is* the first time i hear it's "100%" resistant to vaccines00:28
nixonixballoux is a go-to guy for things like that. see if he thinks mu is concerning. if not, just forgettabout it for now (unless interested in some mutation effect study or speculation)00:28
BrainstormNew from Shane Crotty: @profshanecrotty: [sigh]Hospitals in crisis in least vaccinated state: Mississippi (from @AP) https://apnews.com/article/cbc4d9aa87d4f74991f9bea959bf0939https://is.gd/WX4ztW00:29
imi"The Mu variant has a constellation of mutations that indicate potential properties of immune escape."00:30
imihttps://www.who.int/docs/default-source/coronaviruse/situation-reports/20210831_weekly_epi_update_55.pdf00:30
imiapparently I've been clickbaited :(00:30
de-factohttps://www.elpais.com.co/colombia/llegaron-al-pais-244-800-dosis-de-vacuna-de-astrazeneca-y-774-320-de-la-de-sinovac.html00:31
de-facto.title00:31
Brainstormde-facto: From www.elpais.com.co: Llegaron al país 244.800 dosis de vacuna de AstraZeneca y 774.320 de la de Sinovac00:31
LjLoh, i can certainly believe something will evade *sinovac* by 100% :P00:31
de-factohttps://en.wikipedia.org/wiki/COVID-19_vaccination_in_Colombia00:31
ookLjL: well the author isn't an idiot00:31
de-factohttps://en.wikipedia.org/wiki/SARS-CoV-2_Mu_variant00:33
nixonix.title https://www.cnet.com/news/why-you-shouldnt-panic-about-coronavirus-doomsday-variant-headlines/00:33
Brainstormnixonix: From www.cnet.com: Why you shouldn't panic about coronavirus 'doomsday variant' headlines - CNET00:33
twomoonoh gawd what's this Mu now00:34
de-factowhat is R346K?00:34
imiok so they have 50 million people with less than 15mil fully vaccinated00:35
nixonixrbd substitution that affects some mabs like this: R346K/S could evade targeting by the Rockefeller University antibody C13500:36
imianyhow as far as we know the mrna vaccines would be easy to update and get authorized00:37
twomoonyeah but it is easy to accidentally create mrna that can produce weird side effects00:38
twomoonso it needs testing00:38
imias we're already at the subject: have you heard of any weird side effects of the sputnik vaccine?00:39
nixonixit has no side effects. just like those chinese either00:39
imiwas that supposed to be a joke?00:40
nixonixno, i see if i can see the list where i saw it...00:40
nixonixdamn, anyone remembers a list where side effects were listed, and there was none for sputnik and the chinese? i just saw it couple days ago, but cant remember where00:41
nixonixit might have been "None known" or something00:43
twomoonthe cells manufacture proteins based on the mRNA vaccine contents. and those proteins can do weird things sometimes00:43
imime and one of my friends had strange things happened to us between the two doses00:43
twomoonso we need at least basic FDA trials with enough participants to make sure there aren't any major side effects00:44
twomoonlike for example narcolepsy with the Pandemrix vaccine00:44
nixonixsince i found some mild side effects listed in that infamous lancet paper for sputnik, the list probably had "severe adverse effects" or something only (and for az and mrna vaccines those that you know about)00:46
nixonixfrom sputnik? what kind?00:46
nixonix.title https://www.medicalnewstoday.com/articles/sputnik-v-covid-19-vaccine-how-much-do-we-know-about-its-side-effects00:47
Brainstormnixonix: From www.medicalnewstoday.com: What are the side effects of the Sputnik V COVID-19 vaccine?00:47
nixonixfor jnj that list had GBS mentioned (not sure if thats confirmed yet though, but it was in the list)00:48
BrainstormNew from BBC Health: (news): NHS to receive extra £5.5bn to help Covid recovery, says government source → https://is.gd/1yP6jf00:50
imiboth me and one of my friends were vaccinated with sputnik almost at the same time, and we experienced some sore muscles, my friend in the arm vaccinated, me in my right leg00:55
twomoonwhich countries are using the sputnik vax now?00:56
imiI got some someting like nettle rash00:57
imiI don't know the comprehensive list but there are plenty00:57
twomoondamn nettle rash?00:57
twomoonthat's not good00:57
LjLhttps://covid19.trackvaccines.org/vaccines/12/ says00:57
LjLor at least it says where it's approved, usually it won't be approved if it's not in active use though, except, i did hear there have been supply issues, so it might not always be used *much*00:58
LjLCovidVax (which i get the impression is not always up to date) lists, distribution (started in December 2020):00:59
LjLAlbania, Algeria, Argentina, Armenia, Azerbaijan, Bahrain, Belarus, Bolivia, Bosnia and Herzegovina, Congo, Djibouti, Egypt, Ghana, Guinea, Guyana, Honduras, Hungary, India, Iran, Iraq, Jordan, Kazakhstan, Kenya, Kyrgyzstan, Laos, Lebanon, Libya, Mexico, Moldova, Mongolia, Montenegro, Nicaragua, North Macedonia, Oman, Pakistan, Palestine, Paraguay, Philippines, Russia, San Marino, Serbia, Sri Lanka, Syria, Tunisia, Turkmenistan, United Arab Emirates, Uzbekistan,00:59
LjLVenezuela, Vietnam, Zimbabwe00:59
nixonixif you google about az side effects, those from sputnik are probably mostly similar01:03
twomoonjust remember the Pandemrix story01:03
twomoondon't ever forget it01:03
nixonixbut how knows about possibly damaged s-proteins, which can vary. like possibly more damaged in az than jnj, according to some researcher01:04
twomoonyep01:05
twomoonheat can damage the mRNA and cause all sorts of weirdness01:05
nixonix.title https://www.ft.com/content/f76eb802-ec05-4461-9956-b250115d0577   https://archive.is/4KCoL01:06
Brainstormnixonix: From www.ft.com: Scientists claim to have solved Covid vaccine blood-clot puzzle | Financial Times01:06
LjLtwomoon, those vaccines don't contain mRNA though ;(01:07
twomoonyeah i know01:07
twomooni was just blabbering on and on after nixonix said mRNA is totally safe01:08
twomoonit kinda irked me01:08
twomoonPandemrix isn't mRNA either01:08
twomoonbut it just shows us that random proteins can do weird unexpected shit01:08
nixonix.title https://www.nejm.org/doi/full/10.1056/NEJMc211130501:09
Brainstormnixonix: From www.nejm.org: No Correlation between Anti-PF4 and Anti–SARS-CoV-2 Antibodies after ChAdOx1 nCoV-19 Vaccination | NEJM01:09
nixonixCovidVax? i like that. is RonaVax also in use?01:12
LjLlol, doubt it01:13
twomoonlol01:13
twomoonRonaVax would be funny as hell01:13
LjLronavax.com and .org are taken, but .net is not, go get it01:14
twomoonnixonix should slowly try to displace Campbell01:16
twomoonnix has more levity than Campbell01:16
twomoonand maybe Finns are not as stiff as I thought01:16
nixonixwhat are you talking about01:20
nixonixi meant vaccine names, not site names01:21
nixonix.title https://trialstat.com/2020/09/ufovax-announces-its-self-assembling-nanoparticles-as-the-next-generation-vaccine-solution-for-covid-19/01:21
Brainstormnixonix: From trialstat.com: Ufovax Announces Its Self-Assembling NanoParticles as the Next-Generation Vaccine Solution for COVID-19 – TrialStat Solutions Inc.01:21
twomooni hope ljl isn't a domain squatter type01:26
twomoonwow UFOVax is gonna sit really well with anti-vaxxers01:26
nixonixNanoVax still free? There is PicoVacc01:27
nixonix.title https://twitter.com/MackayIM/status/1434343974379028481  at least he has childhood vax program in the pic (apparently he supports flu-like covid future hypothesis, what i read from some tweeters)01:35
Brainstormnixonix: From twitter.com: ɪᴀɴ ᴍ. ᴍᴀᴄᴋᴀʏ, ᴘʜᴅ 🦠🤧🧬🥼🦟🧻🧙‍♂️ (@MackayIM): "How life might look as we adapt to "living protected" from SARS-CoV-2, via immune-moderated encounters throughout life. Any major flaws or improvements [...]01:35
nixonix.title https://twitter.com/ChristosArgyrop/status/143465558805140684801:38
Brainstormnixonix: From twitter.com: ChristosArgyropoulos MD, PhD (Green Chili Check) (@ChristosArgyrop): "Here is an ivermectin doll for you to comment about" | El Pajarito de NoGAFAM01:38
nixonix.title https://www.ft.com/content/b67e2368-fbae-4035-9119-c8de6d6b4915?segmentid=acee4131-99c2-09d3-a635-873e61754ec6    https://archive.is/ff4hg01:44
Brainstormnixonix: From www.ft.com: Subscribe to read | Financial Times01:44
nixonix* A generation of young people is at risk from the UK’s latest Covid experiment01:45
twomoonthe UK prob wants to kill off some older folks ?01:49
twomoontheir policies seem to suggest they want the virus to spread around01:49
dTalI think it's more that the government is more scared of economic fallout than of covid01:53
dTaldeaths are scary stats that can be held against them, but no one gives a toss about long covid01:53
nixonix"let them bodies pile high"01:53
twomoonwell they accomplish two things01:54
twomoonbetter economy and boomer remover01:55
twomoonboth help their finances01:55
twomoontheir health system is oversubscribed according to what I saw recently on Campbell's channel01:56
nixonixtheres also a scenario with endemic rona that keeps changing and reinfecting depleting naive t-cell reserves, like with old people, but with non-old01:56
twomoonso getting rid of some older folks is probably high on their priority list01:56
nixonixso keep em titers high, so they wont be needed. preferably with IgA nasal vaccines every couple months01:57
twomoonlol what the hell are you talking about01:57
nixonixgoogle about it or something01:58
twomoon"Intranasally administered influenza vaccines could be more effective than injected vaccines, because intranasal vaccination can induce virus-specific immunoglobulin A (IgA) antibodies in the upper respiratory tract, which is the initial site of infection."01:59
twomooninteresting nixonix01:59
BrainstormNew from r/WorldNews: worldnews: For scientists, path to covid endgame remains uncertain → https://is.gd/dTsTsp02:04
LjLnot only for scientists02:05
twomoonthe covid endgame is stop vaccinations that put massive evolutionary pressure on the virus to be extremely transmissible02:05
twomoonthe only way to get rid of the virus is to put evolutionary pressure on it to become less transmissible (and even possibly more lethal)02:06
twomoonbut at high transmissibility it will never go away02:06
twomoonalthough right now i'm not sure exactly how strong the selective pressure from the vaccines is02:06
nixonix.title https://www.medrxiv.org/content/10.1101/2021.08.08.21261768v1.full02:07
Brainstormnixonix: From www.medrxiv.org: Full vaccination suppresses SARS-CoV-2 delta variant mutation frequency | medRxiv02:07
pwr22Even without vaccines - rising human immune resistance would lead it the same pressures02:07
pwr22So I don't buy that logic02:07
twomoontrue social distancing would also be a very strong pressure02:07
twomoongood thing we don't really social distance when we all go back home every day02:07
twomoon(with a bunch of relatives/roommates)02:08
nixonixfirst vaccines where protection doesnt wane that fast, then sometimes later pan-rona vaccines possibly, or more probably pan rona variant vax02:09
de-factohow would you have any scenario with negative selection for a more fit and more contagious variant?02:10
de-factothat just does not work like this02:10
twomoonif you want to get rid of a virus that mutates as quickly as flu and rona you had better use extreme science to predict every possible "constellation" ahead of time (science isn't quite there yet, though)02:11
de-factoin any real world scenario without 100.00% infection rates there will be positive selection for more contagious variants, regardless of any of the other conditions02:11
twomoonand then create a pan-rona vaccine that gives epic coverage02:11
nixonixsure, but more efficient vaccines, less changes for new variants to emerge and then start spreading02:12
twomoonso is de-facto saying that the high transmissibility is the natural end-stage of a virus about to exit-stage-left?02:13
nixonixwith leaking vaccines and high coverage, after couple of months when the protection is waned, more evading variants will spread faster than those that are faster among non-immune population02:13
de-factoevery pathogen has a reproduction advantage from becoming more infectious02:14
nixonixor non-immune, those that are almost non-immune (waned several months or longer)02:14
twomooni think we aren't even seeing selective pressure yet02:15
twomoonit's just short term random-walking02:15
de-factothe more similarity in the immunity induced by vaccines based on Wuhan-Hu-1 spike the higher the probability the mutations able to break through vaccination immunity on one host can exploit the same vulnerability in the next vaccinated, hence continue the trajectory to resistance02:17
de-factoimho pretty similar to monoculture being more susceptible to a parasite02:19
pwr22<twomoon> "if you want to get rid of a..." <- That seems combinatorically infeasible02:21
nixonixbetter lasting protection would come from longer affinity maturation of GC b-cells, so they are more likely to bind to epitopes with mutations, and less chances to escape by mutating02:21
de-factomaybe vaccines that induce a type of immunity that got a more broad spectrum of antigenic affinity could prevent that selection in one break through allows it to continue to evolve in the next breakthrough on the same side of the antigenic affinity distribution02:22
LjLde-facto, but so far, vaccines that use the whole virus seem less effective, and i think nixonix is concerned the N-protein may be somewhat harmful02:22
twomoonpwr22 i'm full of crap comparex to the other guys. i will stop talking now02:23
pwr22😛02:23
twomoonwhen de-fact talks it's over my head sometimes02:23
pwr22Me too02:23
pwr22I think a very simple thing we could do that would help is to actually iterate vaccines to target newer variants of the virus that gain prevalence02:24
de-factoLjL i am not sure how to cook such a vaccine, i just think that the current gen induces too "narrow" immunity in terms of being much too specific to only the Wuhan-Hu-1 spike that almost is two years old by now02:24
pwr22Right now our vaccines are kind of the lowest bar02:24
pwr22At some point fairly soonish I suspect they'll be not particularly useful anymore02:24
twomoonlol "cook a vaccine"02:24
pwr22And waiting until that point before taking action is not great for a few different reasons02:25
LjLpwr22, getting, literally, them *all* is probably unfeasible, but i am sort of hopeful that we can figure out ways to predict "mutations of interest". of course there are infinite possible viruses, but at least as long as we assume this virus needs to bind to ACE2 (there are already hints it can bind to other things too, but, whatever, i will ignore that for now), then there may only be a finite (big? small? i'm not the one to say) set of conspicuous mutations it02:25
LjLcan acquire that give it advantages *while* not ruining its ability to bind to ACE2. at the same time, even if you don't predict every possible variant, just predicting important mutations could be enough to produce the right antibodies, you don't really need to predict *every* change the virus will undergo02:25
BrainstormNew from Reddit (test): Covid2019: Nigeria - Forcing people to take COVID-19 vaccination violates human rights, it’s political – Akinyemi, Chairman, COVID-19 response alliance → https://is.gd/jn6SZf02:25
pwr22LjL: I'd settle for any number more than 1 variant at this point 😛02:26
pwr22Worry about more of them later02:26
pwr222 years is just ancient history in terms of the mutations going on here02:26
pwr22Even flu vaccines we iterate faster than this02:26
LjLpwr22, i fear that just iterating them will be too slow and cause a lot of anxiety in all of us, which it's already doing... as someone said a bit earlier, we *do* need to run trials even for new mRNA vaccines, as there *could* be serious issues with a new vaccine even if you're "just rearranging the mRNA". we're seeing now we've had Alpha, Beta, Gamma, Delta, and no variant-specific vaccine is anywhere near mass production. it's too slow02:27
twomoonwe need PanRonaVax1 and then PanRonaVax2 (updated for even more spread-spectrum effect)02:27
pwr22Protein folding is something we're only starting to get more feasible stuff out of nowadays so I'm not sure we can really do that sort of modelling02:27
de-factoLjL, yes interestingly some of the evasive mutations cost the pathogen replication fitness (in naive hosts) but give them an advantage in hosts with outdated immunity, yet have to be compensated (or even made possible) by some other pure fitness mutations02:27
pwr22LjL: trials and stuff is exactly one of the reasons we need to get ahead on these things02:28
* archpc peeks in02:28
de-factoe.g. E484K may cost fitness, but can be afforded together with N501Y or such02:28
LjLpwr22, i think it may be theoretically feasible, we might not be there yet, but i don't think it's outright hopeless just because of combinatorial explosion02:28
twomooni don't think we've witnessed true selective-pressure evolution yet. it's just random walking imo02:28
LjLarchpc, hi02:28
pwr22archpc: is it time for dr de-facto  to take your vitals?02:28
LjLtwomoon, all evolution is technically "random walking", but we've already seen convergent evolution02:29
* archpc bends over, unbuckles his belt02:29
LjLmany of the variants end up with the same (or similar) mutations, acquired independently02:29
twomoonconvergent evolution isn't necessarily due to selection02:29
archpcStill tested positive on the 3rd02:29
LjLarchpc, argh :(02:29
pwr22LjL: yeah me either. I kind of worry we might make something though that stops even our own stuff binding ace 2 (well we already have these drugs...) and then bad things could happen02:29
LjLpwr22, and ADE. i think while ADE is not *currently* a concern, it doesn't mean it won't *ever* be a concern.02:30
archpcI feel good except for the post covid effects02:30
* archpc shrugs, goes back to email02:30
LjLwhen we test a new vaccine, we need to make sure it isn't02:30
LjLarchpc, sat?02:30
archpcwhat02:30
nixonixi just saw a tweet where somebody said, ADE found in sars1 vacc animal tests, caused by N epitopes (which are mostly conserved and similar). hard to say if those chinese whole virus vaccines cause it, but apparently nothing very severe. unless they modified some concerning epitopes, hard to say02:30
LjLarchpc, what's your oxygen saturation lately02:30
pwr22Find an animal with ACE2 equivalents the virus doesn't work on and gene modify the entire human race to use that instead 😛02:31
pwr22Also furin and such things02:31
archpcOh, last time I checked it was 9002:31
pwr22😛02:31
LjLnixonix, but i've seen it pointed out multiple times that ADE findings in animals often don't translate to humans02:31
LjLarchpc, hmm, still not stellar02:31
pwr22LjL: mine was only 95 earlier 😛02:31
LjLpwr22, mine is usually around that ballpark too, sometimes lower :( but i'm currently at about 1000m altitude fwiw02:32
LjLstill, 90 is low02:32
pwr22I thought 90-100 is normal range?02:32
LjLit's certainly good that it got up from 8302:32
pwr22Ah, 95-10002:32
LjLpwr22, nominally 94 tends to be considered the cutoff for "put him under oxygen"02:32
pwr22misremembered02:32
nixonixyeah. but using N doesnt seem to help. maybe because killer t-cells are affected by orf8 then02:32
LjLpwr22, it's similar to 37.5°C or whatever being the threshold for "fever" though, we had a nitpicking discussion about all that with ecks, i think02:33
nixonixand not relevant fc mediated effector functions with sars202:33
LjLif you happen have 94% or 93% you probably shouldn't rush to the hospital :P02:33
twomoonljl's focus on making sure the PanRonaVax caters to the ACE2 receptor is a good idea02:33
LjLbut we *know* that archpc has [had] COVID and is still not feeling good and the saturation reflects that02:34
pwr22I started getting sick at the stag party I was at yesterday so eventually had to leave fairly early02:34
LjLtwomoon, i was more saying that the *virus* probably has limited wiggling-around potential with the RBD, because, hey, whatever it does, it needs to bind.02:34
archpcI feel fine except for the long post covid shit02:35
pwr22I think I got a minor concussion in a bad go karting collision earlier in the day02:35
LjLlol02:35
pwr22So not sure how much of it was down to that tbh02:35
LjLarchpc, so you're feeling fine except for not feeling fine? :P02:35
pwr22The entire front pack crashed out into me so I was almost ejected from the cart02:36
twomooni feel fine except for long term maladies02:36
BrainstormNew from r/WorldNews: worldnews: Global warming is already affecting people's health so much that emergency action on climate change cannot be put on hold while the world deals with the Covid-19 pandemic, medical journals across the globe warned on Monday → https://is.gd/QaBWgV02:36
pwr22It knackered my left leg, back and neck02:36
pwr22Oh yeah, and my arms too but not sure how much of that is just from the steering02:36
pwr22Was fun though02:36
twomoonreal life mario kart =)02:36
pwr22Yeah I mean I could have done with a blue shell at points02:37
LjLpwr22, i'm not familiar except for the movies, is this kind of thing intended to give yourselves a last chance to die of natural causes before the tragedy of getting married? :P02:37
pwr22Possibly02:37
pwr22It's a form of sexist gender restricted party that grooms have before their marriage yeah02:37
pwr22Women have an equivalent hen party02:37
LjL"hen party", that also sounds sexists tbf02:39
pwr22Yeah, it's all men in stag parties and all women at hen parties02:39
pwr22I have no idea how these things work in the more gender fluid world that exists now02:39
archpcWell, I don’t feel ill, except for the post effects02:39
archpcIdk, I refer to everyone in the 3rd person, always works fine02:40
LjLwhy, how else would archpc refer to them?02:40
archpchuh02:40
twomoonhow is archpc doing?02:41
twomoonbetter than that German guy?02:41
archpcMerely vibing02:41
archpcWhat German02:41
LjLi thought everyone was either german or finnish here02:41
twomoonthat trbp kid02:42
* archpc hears a bald eagle scream in the distance 02:42
twomoonwhere are all the Italians02:42
archpc…in Italy02:42
LjLhopefully far, far away02:42
twomoonI figured what happened in Lombardy would have brought them out of the woodwork and into IRC02:43
twomoonturned them all into armchair virologists02:43
LjLthey're probably all on IRCNet though02:43
archpc Dual satellite, what happened02:43
LjLheh02:44
twomoonwhat are u talkin about archpc02:45
archpcIdk02:45
twomoondual sat? huh?02:45
archpcIt was a joke on your nixk02:46
archpcNick02:46
twomooni see02:46
LjLtwomoon, you're going very often "what are you on about" lately, when i think you could just think for a minute and figure it out just as i did with my "heh"02:46
BrainstormNew from Reddit (test): Covid2019: Brazil v Argentina abandoned five minutes after kick-off after visiting players accused of Covid violation → https://is.gd/irB89B02:46
twomooni blame it on long coronavirus (but not covid) brain fog02:46
archpcMy brains been off somewhere else02:47
twomoonremember i also had anosmia several times in my life, as well as tinnitus02:47
archpcAlso, insomnia, and some drinking02:47
archpcI’m thoroughly dumb02:47
LjLarchpc, anyway, Lombardy was the first place after China where a COVID outbreak was identified, and basically pioneered lockdowns in the west. lots of deaths, although now Italy is second in number of deaths after the UK within Europe i think02:47
archpcHeh, amateurs02:48
twomoonoh...jesus. i just realized archpc didn't realize that02:48
twomoonwake up man02:48
archpc:|02:48
LjLtwomoon, did you even know Lombardy was a thing before the pandemic?02:48
twomoonno02:49
twomoonI just knew Milan02:49
twomoonI had never heard of Lombardy, the region that contains Milan02:49
LjLi bet i have no idea what county archpc, or you, live in, even if you tell me the city/town02:50
twomoonwhen Lombardy got hit by the virus I recall being in a state of shock02:50
archpcLjL, Old Fort :D02:51
archpcWhich one? Who knows!02:51
LjLi was in a state of rabid frustration with others' unwillingness to see we were in deep shit02:51
nixonixsounds texas02:51
archpcNo, oh god no02:51
LjLarchpc, the old one, duh02:51
archpcHeh02:51
twomoonljl I always imagine italians not wanting to take things too seriously. like shrugging off dire shit just like the dutch often do02:52
twomoonand I can imagine you believing that about your fellow countrymen too and having it really annoy you02:53
archpcMy Dutch lady friend had some family members pass, it’s apparently been bad there02:53
twomoonit's been rough in many countries, yeah. it's been pretty bad in Indonesia too02:54
pwr22<LjL> "i thought everyone was either..." <- I have been told I have a German look to me02:56
LjLpwr22, kyllä02:56
de-factoI wonder what is going on in Vietnam right now02:57
de-facto.title https://www.reuters.com/world/asia-pacific/vietnam-pay-recovered-covid-19-patients-help-hospitals-2021-08-25/02:57
Brainstormde-facto: From www.reuters.com: Vietnam to pay recovered COVID-19 patients to help in hospitals | Reuters02:57
LjLuh, easier than vaccinating nurses?02:57
nixonixthey have bad vaccines, cases and deaths rocketing02:58
LjL%cases vietnam02:58
BrainstormLjL: Vietnam has had 501649 confirmed cases (0.5% of all people) and 12446 deaths (2.5% of cases) as of 2 days ago. 16.9 million tests were done (3.0% positive). 17.5 million were vaccinated (18.2%). +14922 cases, +308 deaths since a day ago. See https://offloop.net/covid19/?default=Vietnam02:58
LjLhmm, 15000 in one day versus 500k total, that's a substantial amount02:58
twomoonwhen did vietnam go from 35 to 12000 ?02:58
twomoonwhat the hell ?? they were like the biggest winner of the pandemic the last time i checked02:59
de-factojust very recently they are having an exponential huge Delta wave02:59
twomoonfor a long time their death count sat at 3502:59
archpcI thought they were untouched almost02:59
de-factobefore yeah02:59
nixonixdeaths been stable just lately tho, but who knows that the real numbers are02:59
twomoonman, i have totally not been paying attention. my bad02:59
LjLsomeone was ranting on twitter yesterday about how those who call themselves winners in this pandemic pay for it later...02:59
LjL(it was about Australia)02:59
archpcI wonder how Pitcairn island is doing02:59
LjLhttps://offloop.net/covid19/?default=Italy;Vietnam&byPopulation=yes&cumulative=no&smooth=yes03:00
LjLcase growth is... not really similar, but not wildly dissimilar03:00
LjLbut deaths certainly differ03:00
LjL(since July, i mean)03:00
archpcApparently Pitcairn has had 0 cases, wow, new plague inc challenge03:01
de-factook according to that graph cases are similar, but i bet they do more testing in Italy than in Vietnam03:02
nixonixi wonder how much delta will spread in south america. a few countries have cases going up. many not sequencing much. there is some delta in chile, which is among the most vaccinated03:03
LjLhmm yeah i guess. Brainstorm says the total amount of tests but we should have a graph (i do for italy, i don't for vietnam, although covidly does)03:04
LjL%cases italy03:04
de-factopositivity rate italy 2.4% Vietnam 7.1%03:04
BrainstormLjL: Italy has had 4.6 million confirmed cases (7.6% of all people) and 129352 deaths (2.8% of cases) as of 3 days ago. 84.9 million tests were done (5.4% positive). 42.9 million were vaccinated (71.2%). See https://www.epicentro.iss.it/en/coronavirus/sars-cov-2-dashboard or https://lab24.ilsole24ore.com/coronavirus/en/03:04
LjLde-facto, okay, that's... definitely an indication they test less03:04
de-factoThailand 33.9%03:04
LjL-.-03:04
LjLbut we did have something like 30% at some point03:04
LjLalso, we currently do between 250k and 300k tests per day, but only about 100k of those are PCR, the rest are antigen03:05
LjLand the positivity ratio for those is very different03:05
de-facto.title https://ourworldindata.org/coronavirus-testing03:05
Brainstormde-facto: From ourworldindata.org: Coronavirus (COVID-19) Testing - Statistics and Research - Our World in Data03:05
LjLbut they all get counted as "tests"03:05
nixonixcounted in owid stats?03:05
de-factogood question03:06
LjLcounted in the government's official stats, dunno about owid03:06
LjLi look at Il Sole 24 Ore which has separate graphs for them03:06
LjLso i can see they definitely have different trends03:06
de-factoi guess owid gets it from the official dashboards03:06
LjLyeah my assumption is they count them both03:07
LjLand, yeah, it's both03:07
nixonixwhen did they notice significant breakthroughs in israel? a bit over 4 months since around 25% was double vaccinated with pfizer and 3w interval?03:07
LjL(based on the "How many tests are performed each day?" map)03:07
LjLde-facto, here are the separate graph https://lab24.ilsole24ore.com/coronavirus/#box_6a i don't know if the # thing will work for you, maybe after a refresh03:08
nixonixlook for other countries reaching 25-30% among the first, and count 4 months. chile, usa soon...03:08
LjLsensitivity of antigen tests to the second wave looks pretty "meh" to me from those graphs03:09
LjL(second wave i mean delta)03:09
de-factoLjL, so PCR tests are also 6-8% positive in Italy after pre-selection by rapid antigen tests?03:10
nixonixuruguay, qatar, singapore, serbia. uk but with long intervals03:10
twomoonwhat do you mean by "sensitivity of antigen tests"?03:10
LjLde-facto, if you mean after censoring antigen tests... yes03:11
twomoonoh, sensitivty, right03:11
nixonixso those countries should see lots of breakthroughs soon, unless started 3rd doses03:11
LjLtwomoon, i mean that from the PCR tests you can see an obvious second wave almost as tall as the previous one, while the antigen tests barely register it03:11
twomoonyeah...i get it now. my lag is bad03:11
nixonixmaybe sooner if some chinese vaxes etc used03:11
LjLmaybe the chinese ones wane slower, who knows, sort of like AZ03:12
LjLthey suck but they keep sucking for longer03:12
de-factoi still would like to see antibody half-life as function of booster delay after priming and that per age group03:13
nixonixit takes longer than 4 months for pfizers and az's curves converge, if those were accurate with reality03:13
de-factoall i know they are around 70-ish days for Moderna 4 weeks apart for averaging over big age ranges03:14
nixonixneut ab half life for moderna 70 days?03:14
nixonixyou have a link?03:14
de-factoyes03:14
de-factoyes03:15
twomoonLOL they suck but they keep sucking for longer.03:15
de-facto.title https://www.nejm.org/doi/full/10.1056/nejmc210391603:15
Brainstormde-facto: From www.nejm.org: Antibody Persistence through 6 Months after the Second Dose of mRNA-1273 Vaccine for Covid-19 | NEJM03:15
nixonixits shorter for pfizer, i saw around 50 or so. for actual abs. the titers half-life was 68 days in that study, because more are produced (and possibly maturation affecting too)03:16
nixonixah, its the same with moderna then, at least in that paper: "The estimated half-life of binding antibodies after day 43 for all the participants was 52 days03:17
de-facto.title https://papers.ssrn.com/sol3/papers.cfm?abstract_id=389106503:19
Brainstormde-facto: From papers.ssrn.com: Sustained T Cell Immunity, Protection and Boosting Using Extended Dosing Intervals of BNT162b2 mRNA Vaccine by Rebecca P. Payne, Stephanie Longet, James A. Austin, Donal Skelly, Wanwisa Dejnirattisai, [...]03:19
de-factonixonix, nope 69-ish days for neutralizing ab in the Moderna paper03:20
de-factohttps://www.pitch-study.org/PITCH_Dosing_Interval_23072021.pdf03:20
nixonixalmost the same. what are those 200 days results03:21
nixonixmodeled, not measured?03:22
nixonixand wide differencies between the two models, hmm03:22
de-factofigures at https://www.pitch-study.org/Figures_Appendix_PITCH_Dosing_interval_23072021.pdf03:23
nixonixexponential and power-law model. so which one is the right for protection?03:27
de-factonixonix, where did you find 50 days for BNT?03:27
de-factonixonix, as long as those titers look like straight lines in log plots i guess the exponential model03:28
nixonix"By computation, the predicted average half-life of all the NT 50 values turned out to be 67.8 days and those of S1-binding-IgG and IgM levels were 53.5 days and 43.6 days, respectively03:30
nixonix.title https://www.researchsquare.com/article/rs-847396/v103:30
Brainstormnixonix: From www.researchsquare.com: Correlates of Neutralizing/SARS-CoV-2-S1-binding Antibody Response with Adverse Effects and Immune Kinetics in BNT162b2-Vaccinated Individuals | Research Square03:30
nixonixk next time, lets compare them then03:31
de-factonice thanks03:32
twomoonwhen is nix gonna get burnt out?03:36
twomoondude is going too hard these days03:37
BrainstormNew from Reddit (test): CoronaVirus_2019_nCoV: Covid medical bills are about to get bigger as U.S. insurance companies change policies. → https://is.gd/4TCSWp03:38
de-facto.title https://www.science.org/doi/10.1126/science.abf406303:40
Brainstormde-facto: From www.science.org: Immunological memory to SARS-CoV-2 assessed for up to 8 months after infection03:40
twomoonde-facto, is there any evidence so far that *more severe infection* leads to improved immunological memory?03:44
de-factointeresting, at quick glance it looks like convalescent individuals have almost double the half-life for antibodies03:44
de-factotwomoon, i think that is the case, but the antigenic drift of the pathogen takes place independently since its outside of the individual03:46
de-factoe.g. how fast evasive mutants emerge in breeding the pathogen in a society03:47
twomoonyeah, but if we could somehow fix for antigenic drift...03:47
de-factowe cant, its naturally occurring by copy errors03:47
twomooni suspect that more severe infection creates a larger variety of immunological memory cells03:47
de-factoyes that indeed could be the case03:48
twomoonbut i just don't have the data all organized in front of me03:48
twomoonit's like i've read enough papers now to get that sense but i don't have all those papers nicely organized in Zotero lol03:48
de-factothat the immunity by severe infections may be "broader" but on the other hand, maybe the reason for the infection to become severe may be an individual property of that unlucky individual that also could persist03:48
twomoondo you have a paper that demonstrates this effect?03:49
twomooni need to start organizing some papers03:49
de-factoi dont have any links, i just remember some and grep them out of backscroll :D03:50
twomoonlol03:50
de-factoi wish i had a zotero setup or such03:50
de-factotwomoon, afaik there were papers about SARS-CoV-1 survivors vaccinated with BNT162b2 developing such broad immunity that they could neutralize all variants03:51
de-facto.title https://www.nejm.org/doi/full/10.1056/NEJMoa210845303:52
Brainstormde-facto: From www.nejm.org: Pan-Sarbecovirus Neutralizing Antibodies in BNT162b2-Immunized SARS-CoV-1 Survivors | NEJM03:52
twomooni'm looking for a paper that looks at non-vaccinated survivors03:52
twomoonthat just demonstrates clearly that harsher infection creates a larger variety of imm. memory cells03:52
twomoonthanks for the paper, worth a look03:53
de-factoso maybe that is also related, SARS-CoV-1 having a s-protein that also docks on ACE2 and the infection is much more severe, 10% fatality rate03:53
de-factoi wonder if it has something to do with their immune system now knowing about similarities in both SARS-CoV-1/2 or being more on alarm due to the more pronounced severity of prior SARS-CoV-1 infection03:55
de-factodefinitely something relevant, e.g. if mixing mRNA sequences of many similar CoVs possibly could broaden antibody affinity spectrum to be broad enough to cover the spreading phylogenetic tree of SARs-CoV-203:56
LjLi think that paper may prove extremely important04:09
twomoonwhat's the main point of that paper ?04:10
BrainstormNew from Politico: Boris Johnson’s care funding fix spooks his party: Tax hikes, vaccine passports and the fallout from Afghanistan mean MPs start the new term in a tetchy mood. → https://is.gd/9yNaXF04:10
LjLtwomoon, it finds that people who had SARS and later got vaccinated against COVID with BNT develop some antibodies that are active against *all* types of sarbecovirus which is a (large, i think) type of coronaviruses04:13
LjLit means that if we could elicit those same antibodies without giving people SARS, we'd have a vaccine that would potentially work against all variants of COVID, as well as SARS, and maybe MERS or other things that may pop up from bats04:14
twomoonoh wow04:21
twomooni suspect more severe infection creates more variety04:24
twomoonand we have antibodies to select from04:25
de-factoSARS-CoV-1/2 are quite similar, but MERS-CoV uses a different receptor04:26
LjLthis to me seems to be about two different but related pathogens ending up with our immune system recognizing that they can be targeted with some common antibodies04:26
LjLde-facto, fair enough, MERS was just a guess04:27
LjLbut taking out SARS1 and 2, with all their variants, in one shot would be pretty great04:28
de-factobut yeah it would make sense that similarities between SARS-1/2 are selecting the more conserved regions on their genome, hence some that the virus can to change easily without much fitness costs or such04:29
twomoongenus betacoronavirus04:29
LjL<Brainstorm> New from Reddit (test): CoronaVirus_2019_nCoV: Covid medical bills are about to get bigger as U.S. insurance companies change policies. → https://is.gd/4TCSWp04:29
twomoonwhy are you sending this article again04:30
LjLi didn't notice it had been already sent. i grabbed it from ##covid-ticker04:30
BrainstormNew from r/WorldNews: worldnews: Climate action cannot wait for pandemic to end, medical journals warn. Global warming is already affecting people's health so much that emergency action on climate change cannot be put on hold while the world deals with the Covid-19 pandemic, 220 leading medical journals across the globe are warning → https://is.gd/FT969b04:32
LjLi do fear COVID is just the beginning of a pretty sharp decline we're going to experience for other reasons too, like climate :(04:33
LjLand experience in the pretty short term, i'll add, even though we've all been conditioned to think this is about "the future"04:33
de-factoLjL, maybe its a bit like AI, its accuracy strongly depends on training with a wide variety of different data for it to be able to recognize the preserved patterns, hence providing the immune system with many versions of spikes targeting the same receptor teach it to recognize the more abstracted or generic patterns occuring in such spikes04:35
de-facto(wild speculation)04:35
LjLyeah, i don't know, it's enough to know that it can work04:35
LjLwe do have some tentative SARS1 vaccine, right?04:36
LjLi think we should trial giving it to people together with a SARS2 vaccine, and see what happens04:36
de-factowhy not just put in the sequence for its spike in the mRNA platforms04:37
de-factoas broad of a variety as possible, all known variants for spikes of SARS-CoV-1 and SARS-CoV-2 VoCs04:37
LjLbecause first you need to see if it works? :P04:38
de-factoyes i mean as trial04:38
de-factothen measure neutralization of the serum04:38
de-factoif it works it would be fantastic, if not it really could have something to do with severe disease of SARS-CoV-1 or such04:38
LjLwell it's the same thing as what i said basically isn't it04:38
de-factoyes04:39
de-factoi think this will turn out to be one very important point in vaccinations: the magnitude of variety in antibody affinity covering all variants and more04:41
de-factoas well as inducing IgA and resident B-cells in the nasal and pharyngeal mucus04:42
BrainstormNew from The Indian Express: World: Australia takes delivery of Pfizer Covid-19 vaccine from Britain → https://is.gd/o1THbG05:03
BrainstormNew from The Indian Express: World: No cash, only soft incentives for taking Covid-19 vaccines: S African Health Minister → https://is.gd/72pDC705:46
twomoonljl why did you originally want to get involved in creating a channel to talk about the virus? this doesn't seem "up your alley" given what we know about you05:51
twomoonfrom what we know you are interested in linguistics and earthquakes mainly (and old computers/ odd computing devices)05:52
BrainstormNew from The Indian Express: World: Covid deaths surge across a weary America as a once-hopeful summer ends → https://is.gd/eEwAbI06:38
BrainstormNew from The Indian Express: World: The best birthday present in 2021? A COVID vaccine → https://is.gd/tsx2q708:03
BrainstormNew from The Indian Express: World: Thai protesters are back, and angrier, as government fumbles on Covid → https://is.gd/1YIKih08:46
BrainstormNew from r/Coronavirus: Daily Discussion Thread | September 06, 2021: Please refer to our Wiki for more information on COVID-19 and our sub. You can find answers to frequently asked questions in our FAQ , where there is valuable information such as our: → https://is.gd/v60Iv209:07
BrainstormNew from r/WorldNews: worldnews: COVID-19: Anti-Vaxxers Are Targeting Pregnant Women Leading to Tragedy → https://is.gd/2x3F2y11:04
BrainstormNew from BBC Health: Covid: Which children are being vaccinated and why?: Millions of children, including 16- to 17-year-olds, are now being offered a Covid vaccine. → https://is.gd/iJlbhj11:15
BrainstormNew from r/WorldNews: worldnews: Brazil vs. Argentina World Cup qualifier suspended, as four Argentinian players accused of breaking Covid travel protocols → https://is.gd/KW5Thx11:37
BrainstormNew from BMJ: Why I . . . volunteer as a Royal Parks ranger: For years, Ramai Santhirapala has lived near Richmond Park in London, enjoying its beauty. But she found that the solace of nature was never more needed than during the pandemic when she faced the... → https://is.gd/jXPWp911:47
BrainstormNew from PubMed: Ahmad Shamabadi: Medical Biotechnology in the Service of Coronavirus Vaccine Discovery and Production → https://is.gd/dBf3es13:01
BrainstormNew from StatNews: Visualizing how fast the pandemic is getting better or worse, state by state: STAT is making available real-time data that shows how fast Covid-19 is accelerating in every state and territory. → https://is.gd/ln8hpx13:12
de-facto.title https://www.biorxiv.org/content/10.1101/2021.03.12.435191v213:36
Brainstormde-facto: From www.biorxiv.org: A novel soluble ACE2 protein totally protects from lethal disease caused by SARS-CoV-2 infection | bioRxiv13:36
pwr22In transgenic mice designed to die from covid13:40
pwr22Hmm13:40
pwr22Given I take ACE inhibitors, presumably flooding me with a bunch of long lasting super ACE binding things wouldn't be great for me?13:41
pwr22Specifically ACE 2 inhibitors13:41
BrainstormNew from Science-Based Medicine: The Vaccine Versus the Virus:  An Update: The virus is more dangerous than the vaccine for adolescents and young adults.  Pro-vaccine doctors will share this fact. The post  first appeared on Science-Based Medicine . → https://is.gd/5A5vSn14:05
BrainstormNew from r/WorldNews: worldnews: Not getting vaccinated puts lives at risk - Mattarella → https://is.gd/js864R14:48
BrainstormNew from EMA: Human medicine assessment reports: (news): Human medicines European public assessment report (EPAR): ProQuad, measles, mumps, rubella and varicella vaccine (live), Chickenpox;Rubella;Measles;Mumps;Immunization, Date of authorisation: 05/04/2006, Revision: 28, Status: Authorised → https://is.gd/1i1qKM15:32
BrainstormNew from BMJ: What is driving the pandemic related surge in disordered eating?: As Feinmann points out, the effect of the covid-19 pandemic on disordered eating is striking and seems to be international.1 Reports from North America and Europe accord with our observations in New... → https://is.gd/ei5wPc15:43
BrainstormNew from BioNTech: Pfizer and BioNTech Submit a Variation to EMA with the Data in Support of a Booster Dose of COMIRNATY®: NEW YORK, USA and MAINZ, GERMANY, September 6, 2021 — Pfizer Inc. (NYSE: PFE) and BioNTech SE (Nasdaq: BNTX) today announced that they submitted a variation to the European Medicines Agency (EMA) requesting to update the [... want %more?] → https://is.gd/OleU9z15:53
BrainstormNew from Virological.org: Latest posts: Tackling Rumors of a Suspicious Origin of nCoV2019: profbillg1901: All around the globe, those of us who have studied emerging viral pathogens at the molecular level for decades are united in our judgment, based on protein and RNA sequence analysis, that SARS-CoV-2 evolved by a series of recombination events in [... want %more?] → https://is.gd/wtsb5h16:04
BrainstormNew from EMA: Human medicine assessment reports: (news): Human medicines European public assessment report (EPAR): COVID-19 Vaccine Janssen, COVID-19 vaccine (Ad26.COV2-S [recombinant]), COVID-19 virus infection, Date of authorisation: 11/03/2021, Revision: 7, Status: Authorised → https://is.gd/leysw616:25
BrainstormNew from EMA: What's new: Medicine: Veterinary medicines European public assessment report (EPAR): Vectormune ND, Newcastle disease and Marek’s disease vaccine (live recombinant), Date of authorisation: 08/09/2015, Revision: 7, Status: Authorised → https://is.gd/QSIU3L16:36
BrainstormNew from EMA: What's new: Medicine: Veterinary medicines European public assessment report (EPAR): Porcilis PCV, adjuvanted inactivated vaccine against porcine circovirus, Date of authorisation: 12/01/2009, Revision: 7, Status: Authorised → https://is.gd/kSAd2l16:57
BrainstormNew from Reddit (test): Monday 06 September 2021 Update: submitted by /u/HippolasCage to r/CoronavirusUK → https://is.gd/yH2aFp17:08
BrainstormNew from Eric Topol: @EricTopol: Just published @Nature Characterization of the marked fitness of the Delta variant: higher replication, cell entry, ability to evade our natural and vaccine-induced immune response relative to other🦠strains and lineageshttps://www.nature.com/articles/s41586-021-03944-y@GuptaR_lab and collaborators → https://is.gd/E3InNA18:03
-RSSBot[LjLmatrix- Zotero / COVID links Group / Top-Level Items: Pfizer and BioNTech Submit a Variation to EMA with the Data in Support of a Booster Dose of COMIRNATY® ( https://www.zotero.org/groups/covid_links/items/M4XIPE76 )18:15
-RSSBot[LjLmatrix- Zotero / COVID links Group / Top-Level Items: SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion ( https://www.zotero.org/groups/covid_links/items/E5PW36VV )18:20
BrainstormNew from r/WorldNews: worldnews: WHO approved first Chinese ‘SinoPharm’ vaccine for alternative use around the globe : COVID-19 vaccine → https://is.gd/Mg7xxk18:34
LjLwhy would WHO do that when it's just been shown to be marginally better than nothing?18:35
BrainstormNew from Eric Topol: @EricTopol: Tomorrow's @AmerAcadPeds @hospitals4kidsreport will inevitably show the highest number of pediatric cases in the pandemic, with ~1% of this large number of kids requiring hospitalization https://downloads.aap.org/AAP/PDF/AAP%20and%20CHA%20-%20Children%20and%20COVID-19%20State%20Data%20Report%208.26%20FINAL-update.pdf [... want %more?] → https://is.gd/NbHoVt19:07
inxoinxwhat do we have on hospitalization rates with delta? or with uk variant? cdc had something by age group, but i think its mixed variants19:48
inxoinx.title https://www.smh.com.au/politics/nsw/more-than-one-in-10-people-in-nsw-with-covid-now-end-up-in-hospital-20210905-p58oyv.html19:48
Brainstorminxoinx: From www.smh.com.au: NSW COVID: More than one in 10 people now end up in hospital19:48
inxoinx.title https://twitter.com/MThallinger/status/143484022891372953819:49
Brainstorminxoinx: From twitter.com: Monica Thallinger MD PhD (@MThallinger): "Data was collected just after arrival of Delta in Norway and after our 3rd wave. In a period with very little community transmission. See graphs. We now see a [...]19:49
inxoinxyeah, those 6+1 studies mentioned in topol's thread. prob better than raw datas, while not perfect. canada, denmark, singapore, uk, england or scotland, what was it again?, israel, michigan raw data, ...19:51
inxoinxanyone knows how to check if SARS-CoV-2/human/Liverpool/REMRQ0001/2020 has D or G at 614? googling doesnt seem to help, so maybe looking at the sequence then20:11
BrainstormNew from Eric Topol: @EricTopol: Just published @NatureBiotech A unique single cell multiomic study in ~200 people with Covid-19 and assessment of over 1,000 metaboliteshttps://www.nature.com/articles/s41587-021-01020-4@jihoonwlee @UW @MCBSeattle @fredhutch @isbsci @LabHeath @SuYapeng @Swedish → https://is.gd/UjHfBv20:11
inxoinxhas turbo been here lately? i dont remember his whole nick. he could prob comment this, the monocyte dysregulation part:20:37
inxoinx.title https://www.nature.com/articles/s41587-021-01020-420:37
Brainstorminxoinx: From www.nature.com: Integrated analysis of plasma and single immune cells uncovers metabolic changes in individuals with COVID-19 | Nature Biotechnology20:37
LjLno i think i've seen him in other channels though20:38
LjLinxoinx, do you know https://cov2tree.org/ ? i have no idea about SARS-CoV-2/human/Liverpool/REMRQ0001/2020 (it seems to be the first British patient's virus?) and i intended to try cov2tree in case it could help, but the site loads so much stuff it just crashes my browser now20:39
inxoinxyeah, from diamond princess. i couldnt find pango name for it20:40
inxoinxthey use it in neutralization comparisons. i was wondering if it was 614d or g. i found the paper on it, but it doesnt mention, suggesting perhaps that it didnt20:41
inxoinxwhile in a recent paper publ in nature "wild type (WT) Wuhan-1 bearing D614G" and "WT (SARS-CoV-2/human/Liverpool/REMRQ0001/2020)"20:41
LjLi've only figured out it's part of the B pango lineage20:42
inxoinxsuggesting that it didnt have g, i meant20:42
inxoinx.title https://www.nature.com/articles/s41586-021-03944-y20:43
Brainstorminxoinx: From www.nature.com: SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion | Nature20:43
inxoinx.title https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7602519/  this has something about that diamond princess sample20:45
Brainstorminxoinx: From www.ncbi.nlm.nih.gov: Amplicon-Based Detection and Sequencing of SARS-CoV-2 in Nasopharyngeal Swabs from Patients With COVID-19 and Identification of Deletions in the Viral Genome That Encode Proteins Involved in [...]20:45
inxoinx.title https://biology.stackexchange.com/questions/101065/virus-lineage-strain-and-relation-to-spike-protein-variants  and somebody wondering the same here20:46
Brainstorminxoinx: From biology.stackexchange.com: virology - Virus lineage, strain, and relation to spike protein variants - Biology Stack Exchange20:46
nixonixmaybe defacto is handy with those lineages and can find out20:47
nixonixwas it in march, when vaccinatios became available for 20 yo in usa? so many got the 2nd shot by the end of april. over 4 moons for them now:21:11
nixonix.title https://old.reddit.com/r/UBC/comments/pirwd2/anyone_who_went_to_the_frat_parties_you_likely/21:11
Brainstormnixonix: From old.reddit.com: Anyone who went to the frat parties: you likely have COVID. : UBC21:11
nixonixnah, bc aka canada. so not that long, and they increased the interval too21:15
lastshellIs true that vegetarians have more resistance to get covid ?21:28
lastshellhttps://nutrition.bmj.com/content/early/2021/05/18/bmjnph-2021-00027221:30
lastshellsadly I starting to eat more protein :(21:30
nixonixpossibly those that eat a lot of fish (norway, iceland). prob omega-3, but it has been greatly reduced in norwegian water broilers, though, since apparently they feed them with chicken shit or something nowdays21:45
nixonixturbo could help, but he is awol21:46
nixonixtheres been talks here and there, that sars2 infection turns naive t-cells to non-naive at way higher frequency than eg flu infection. and increase in that pool leads to decrease in naive t-cell pool, since there are limits to how large pools can be maintained (not sure if its about thymus or just some energy conservation or something)21:50
nixonixso the effect of repeated reinfections, when we have turned rona flu-like, would lead to the situation where naive t-cell reservoir is like old people have21:51
nixonixnot sure how is it with b-cells, are their naive reserve depleted faster than eg with flu too, but leads to more class-switching anyway, and similar results (possibly not as fast but i dont know)21:52
de-factonixonix, erm but was that for naive immune systems first training its naive t-cells or for reinfections?21:52
de-factobecause it probably is not the same for each contamination, as in the flu the immune system is not naive for it after the first exposure21:52
nixonixi dont know, but this is another betacoronavirus, and most of us get betarona infections quite often, especially as a kid (while reserve depleting might not affect similarly pre-puberty, but i dont know  how it is)21:53
de-factofirst exposure: train a lot of naive t-cells, repeated exposure: they already should know the epitopes, so i would assume less amount of naive t-cells consumed for reinfections21:54
de-factonixonix, well good point, but how much t-cell overlap to the other beta coronaviruses that were in circulation before 2020?21:55
de-facto*how much t-cell epitope overlap21:55
nixonixnot for conserved sites, but those sites that keep changing with variants. and apparently sars2 uses naive t-cell reserve a lot more than influenza21:55
nixonixif i recall i read something similar with hiv, but not sure21:56
de-factoor sure some, since there were t-cells reacting to SARS-CoV-2 that were sampled prior to 202021:56
nixonixyeah, lots of cross-reactivity, also with animal coronaviruses21:56
de-factowhat i mean is that first exposure to sars-cov-2 should not be comparable to repeated exposure to influenza21:57
de-factoit probably consumes less amount of naive t-cells each re-exposure21:57
de-facto(i dont know that though, its just a guess)21:57
nixonixstill if true, it uses naive reserve at high rate (compared to flu etc). i try to find something about the topic (already googled) but since is mostly new topic for me, it will require some time to dig deeper21:57
LjLi find this extremely simplistic thinking https://old.reddit.com/r/worldnews/comments/pj2g1a/who_approved_first_chinese_sinopharm_vaccine_for/hbuherp/ when it comes to vaccines with possibly very low efficacy21:57
nixonixalso i read couple of a few years older papers, there was a lot of uncertainties, things not known yet21:58
nixonixbut good point, would a reinfection with the same variant use new naive t-cells, and how much (compared to eg flu). yet the concern seems to be the repeated reinfections, so maybe they do22:00
nixonixbut severe cases apparently use way more, so good protection from recent vaccinations (preferably with IgA from nasal vax), and naive reservoir is conserved, better anyway22:01
nixonixnot sure what happens in body with mild upper respiratory infections, do cellular immune memory develop, while IgG doesnt (whether killer t-cells protect or damage more)22:03
de-factoif severity decreases with each reinfection (or breakthrough) maybe also consumption of naive t-cells decreases with each iteration22:03
nixonixhow about if the protection, from vax or previous infection, has waned for severe symptoms too? (how fast compared to protection for infection, which is mostly IgG at least from current im vaxes, does that happen anyways)22:05
de-factoprobably a lot different to the immune system if it sees a multi-organ system wide infection or if it sees a infection of the mucus local to nasal and pharyngeal regions22:05
nixonixbut accumulating protection for severe, when repeated... i dont know, you can only hope22:05
nixonixthat danish study on reinfections, i think it didnt hint much about reinfections being milder22:06
nixonixshould check22:06
nixonixbut there might be bias. while danish test anybody that want to be tested, those that have had it and then have mild symptoms, might be less apt to get tested when they get some mildish symptoms22:07
nixonixsince the naive t-cell reserve depleting seems to be associated to symptom severity (i saw in some study), probably less cellular memory develop too with mild symptoms. but does it still happen with mild symptoms in upper respiratory only. at least some of them will get lc and stuff22:10
nixonixbut do those, that dont produce IgG22:11
nixonixbtw, last year when it looked like pretty much everybody, excluding immunocompromised, would get antibodies, and if not found, then it was about assay sensitivity. the difference to what we are discussing now is, it was for purpose of recognizing the share of those getting infected (for IFR etc), and also if the share of nonsymptomatic22:12
nixonixnow its about protection. so if there is some minimal amount of IgG, it doesnt matter for protection22:13
nixonixand some of those assays only looked at IgM i think22:13
nixonixso, have you had rona? the answer depends, in what sense. protection wise, or tracking infection chains or something else22:14
de-factoit would be helpful to have a fast decaying marker for contamination to get a representative estimate for current incidence to calculate IFR as metric for how successful our strategies really are22:17
nixonixprotection-wise, it looks like maybe 25-30% infections wont produce IgG protection with levels that matter. cellular protection or perhaps some modified innate immune response, who knows22:17
nixonixbut identifying-wise, its prob close to 100% if right antibodies (perhaps IgM) and sensitive enough assay is used within maybe couple months or so22:18
de-factofor incidence estimation we would need something really fast decaying22:19
de-factopreferably already decaying during the raise of IgG or such22:19
nixonixhc officials are prob not interested. they want to let it burn through when not too many people die22:20
de-factobut also something that is global, so easily testable via blood sample22:20
nixonixand then to be endemic, new flu-like-rona era. who cares about things like permanent organ damage, depleted t-cell reserve, telomeres etc as long as the hospitals dont get filled up. they can worry about later, if it materializes. then say, look, we didnt know. or more likely not commenting22:21
lastshellbut a what cost nixonix22:22
lastshell(human cost)22:22
nixonixhard to say, but its a risky game, using other peoples health22:22
ecksi am willing to sacrifice a few nucleotides of telomeres if it means i can go to the pub and have a beer22:25
nixonixyeah, but you dont even own a thermometer22:25
ecksand still going strong!22:26
nixonixbtw, what do you think about that depleting naive t-cell reserve, and reinfections etc above?22:26
eckscan't really say i'm well-versed enough in these subjects to comment22:27
ecksimmunology is hard22:27
nixonixsince we are just bunch of nerds, give us some opinion22:27
ecksi tend to not open my immunology book if i can avoid it22:27
nixonixis it the same with most md's?22:27
ecksprobably22:29
ecksit's a difficult subject (from my experience) so many tend to shy away from it22:30
nixonixthey offer NLP at HUS long covid clinic. and their guidance slides say that no more lab tests should be made for patients, because it would lead to nocebo loop22:34
nixonixaccepting placebo as a treatment is quackery. thats what they are doing anyway22:35
ecksfinally someone who understands the no-labs method22:38
nixonixbtw, i agree with those your points not testing too much, just send them home (they will come back if something is still wrong). i heard in usa they do so many unnecessary lab test because court cases would be expensive. if true, maybe the main reason why healthcare is so expensive there22:40
ecksit has its own name, "defensive medicine"22:42
nixonix.title https://twitter.com/EricTopol/status/143492977781979955422:42
Brainstormnixonix: From twitter.com: Eric Topol (@EricTopol): "Is the annual physical headed towards obsolescence? https://www.wsj.com/articles/tech-advances-put-the-annual-doctor-visit-on-the-critical-list-11630933201 by @ronwinslow" | [...]22:42
de-factofor me a test that finds the cause of something is extremely valuable, almost more as the actual treatment as i know what i deal with22:43
de-factoso if a doctor tells me "its this and that" i am satisfied and go away as its determined22:43
nixonixi think ecks is more in the "if you dont feel too bad, you are prob ok" bandwagon22:44
de-factoyeah22:44
de-factonot knowing literally makes me sick, if i have the impression i understand something it cant really worry me anymore22:46
ecksno more blood tests for you22:54
ecksthey should do some clinical trial where half of the patients in the ER triage are seen by doctors and the other half by monkeys22:55
ecksi bet the monkeys would be more cost-efficient22:55
nixonixthere was this fake doctor Laiho. i thought he seemed to do his job pretty well, based on what i read which might not be accurate with the reality, and wouldnt have mind seeing him probably23:03
nixonixhe had some studies ofc. and when he didnt understand something well enough, he asked from somebody else23:04
nixonixhe got 5 years prison (half of it reduced automatically)23:06
nixonixso he was no monkey. but probably more expensive23:10
de-factofor me a proper diagnostic is the best thing a MD can possibly give to me23:21
BrainstormNew from Eric Topol: @EricTopol: Good new way to #dataviz cases, daily, by state @statnews https://www.statnews.com/2021/09/06/visualizing-fast-the-pandemic-is-getting-better-or-worse-state-by-state/ by @jaspar → https://is.gd/2p1hRR23:23
nixonix.title https://twitter.com/ChristosArgyrop/status/143497811065126093123:23
Brainstormnixonix: From twitter.com: ChristosArgyropoulos MD, PhD (Green Chili Check) (@ChristosArgyrop): "I am somewhat surprised that not many epidemiologists who tweet about the analysis of VE from RWD over time have noticed that [...]23:23
BrainstormNew from r/WorldNews: worldnews: Vietnamese man jailed for 5 years for spreading coronavirus → https://is.gd/ri2UmX23:34
nixonix.title https://twitter.com/VirusesImmunity/status/143357004871576371423:34
Brainstormnixonix: From twitter.com: Prof. Akiko Iwasaki (@VirusesImmunity): "Excited to share our work by @BenIsraelow et al published today. We asked what are the roles of antibodies vs. T cells in controlling primary infection, [...]23:34
nixonix.title https://www.science.org/doi/10.1126/sciimmunol.abl4509#.YTFPFaWpCph.twitter23:41
Brainstormnixonix: From www.science.org: Adaptive immune determinants of viral clearance and protection in mouse models of SARS-CoV-223:41
nixonix.title https://www.jimmunol.org/content/207/2/376.long23:41
Brainstormnixonix: From www.jimmunol.org: Cutting Edge: Nucleocapsid Vaccine Elicits Spike-Independent SARS-CoV-2 Protective Immunity | The Journal of Immunology23:41
nixonix.title https://jacobinmag.com/2021/02/finland-vaccine-covid-patent-ip  old article23:56
Brainstormnixonix: From jacobinmag.com: Finland Had a Patent-Free COVID-19 Vaccine Nine Months Ago — But Still Went With Big Pharma23:56

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