nixonix | fisman is the man behind that canadian delta vs alpha study. come on dude, l-theanine | 00:00 |
---|---|---|
nixonix | this one https://www.medrxiv.org/content/10.1101/2021.07.05.21260050v2.full | 00:02 |
nixonix | who resigned after leaking some doomsday model supposedly made by ontarios rona modellers | 00:02 |
LjL | uuh think i missed that drama | 00:03 |
nixonix | .title https://twitter.com/DFisman/status/1429761663671185413 | 00:03 |
Brainstorm | nixonix: 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/1429037458990190596 | 00:04 |
Brainstorm | nixonix: 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 |
twomoon | lol rona modellers | 00:09 |
twomoon | suddenly it seems like you're not a John Campbell clone | 00:10 |
LjL | nixonix, with some fear i ask, what doomsday scenario did he leak? | 00:10 |
twomoon | good, nixonix is giving us the angles that John Campbell won't touch | 00:13 |
LjL | Campbell is boring | 00:13 |
twomoon | he's just a windbag. he wouldn't be so boring if he talked a lot less | 00:15 |
twomoon | we just got tired of getting his spiel in 40 minutes instead of 10 | 00:15 |
nixonix | afaik 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 |
Brainstorm | New 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/Woy89q | 00:18 |
nixonix | .title https://mobile.twitter.com/DFisman/status/1425077617640755201 | 00:19 |
Brainstorm | nixonix: 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 |
imi | hi | 00:20 |
imi | which vaccine(s) were used in Columbia? | 00:21 |
imi | maybe you've already heard of the mu variant | 00:22 |
nixonix | but 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 |
nixonix | since they are very far from the middle estimate (ive seen some examples) | 00:22 |
nixonix | basically meaning, its just bullshit, their models | 00:22 |
LjL | ook, 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, but | 00:22 |
LjL | imi, you mean Colombia, or the District of Columbia, or what? (i might not know the answer anyway) | 00:23 |
imi | I mean Columbia the south-american country | 00:25 |
LjL | yeah it's called Colombia in English, not Columbia | 00:25 |
LjL | anyway it appears its government websites don't open up for me | 00:26 |
LjL | they've authorized a bit of everything: Moderna, Pfizer, AZ, J&J, Sinovac | 00:26 |
LjL | but what they've actually used, i'm not really sure | 00:26 |
imi | apparently there's a new mu variant there allegedly 100% resistant to vaccines | 00:27 |
LjL | http://eps.coomeva.com.co/publicaciones.php?id=156885 has some veeeery basic info on what vaccines they're using | 00:27 |
LjL | imi, 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 vaccines | 00:28 |
nixonix | balloux 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 |
Brainstorm | New from Shane Crotty: @profshanecrotty: [sigh]Hospitals in crisis in least vaccinated state: Mississippi (from @AP) https://apnews.com/article/cbc4d9aa87d4f74991f9bea959bf0939 → https://is.gd/WX4ztW | 00:29 |
imi | "The Mu variant has a constellation of mutations that indicate potential properties of immune escape." | 00:30 |
imi | https://www.who.int/docs/default-source/coronaviruse/situation-reports/20210831_weekly_epi_update_55.pdf | 00:30 |
imi | apparently I've been clickbaited :( | 00:30 |
de-facto | https://www.elpais.com.co/colombia/llegaron-al-pais-244-800-dosis-de-vacuna-de-astrazeneca-y-774-320-de-la-de-sinovac.html | 00:31 |
de-facto | .title | 00:31 |
Brainstorm | de-facto: From www.elpais.com.co: Llegaron al país 244.800 dosis de vacuna de AstraZeneca y 774.320 de la de Sinovac | 00:31 |
LjL | oh, i can certainly believe something will evade *sinovac* by 100% :P | 00:31 |
de-facto | https://en.wikipedia.org/wiki/COVID-19_vaccination_in_Colombia | 00:31 |
ook | LjL: well the author isn't an idiot | 00:31 |
de-facto | https://en.wikipedia.org/wiki/SARS-CoV-2_Mu_variant | 00:33 |
nixonix | .title https://www.cnet.com/news/why-you-shouldnt-panic-about-coronavirus-doomsday-variant-headlines/ | 00:33 |
Brainstorm | nixonix: From www.cnet.com: Why you shouldn't panic about coronavirus 'doomsday variant' headlines - CNET | 00:33 |
twomoon | oh gawd what's this Mu now | 00:34 |
de-facto | what is R346K? | 00:34 |
imi | ok so they have 50 million people with less than 15mil fully vaccinated | 00:35 |
nixonix | rbd substitution that affects some mabs like this: R346K/S could evade targeting by the Rockefeller University antibody C135 | 00:36 |
imi | anyhow as far as we know the mrna vaccines would be easy to update and get authorized | 00:37 |
twomoon | yeah but it is easy to accidentally create mrna that can produce weird side effects | 00:38 |
twomoon | so it needs testing | 00:38 |
imi | as we're already at the subject: have you heard of any weird side effects of the sputnik vaccine? | 00:39 |
nixonix | it has no side effects. just like those chinese either | 00:39 |
imi | was that supposed to be a joke? | 00:40 |
nixonix | no, i see if i can see the list where i saw it... | 00:40 |
nixonix | damn, 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 where | 00:41 |
nixonix | it might have been "None known" or something | 00:43 |
twomoon | the cells manufacture proteins based on the mRNA vaccine contents. and those proteins can do weird things sometimes | 00:43 |
imi | me and one of my friends had strange things happened to us between the two doses | 00:43 |
twomoon | so we need at least basic FDA trials with enough participants to make sure there aren't any major side effects | 00:44 |
twomoon | like for example narcolepsy with the Pandemrix vaccine | 00:44 |
nixonix | since 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 |
nixonix | from 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-effects | 00:47 |
Brainstorm | nixonix: From www.medicalnewstoday.com: What are the side effects of the Sputnik V COVID-19 vaccine? | 00:47 |
nixonix | for jnj that list had GBS mentioned (not sure if thats confirmed yet though, but it was in the list) | 00:48 |
Brainstorm | New from BBC Health: (news): NHS to receive extra £5.5bn to help Covid recovery, says government source → https://is.gd/1yP6jf | 00:50 |
imi | both 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 leg | 00:55 |
twomoon | which countries are using the sputnik vax now? | 00:56 |
imi | I got some someting like nettle rash | 00:57 |
imi | I don't know the comprehensive list but there are plenty | 00:57 |
twomoon | damn nettle rash? | 00:57 |
twomoon | that's not good | 00:57 |
LjL | https://covid19.trackvaccines.org/vaccines/12/ says | 00:57 |
LjL | or 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 |
LjL | CovidVax (which i get the impression is not always up to date) lists, distribution (started in December 2020): | 00:59 |
LjL | Albania, 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 |
LjL | Venezuela, Vietnam, Zimbabwe | 00:59 |
nixonix | if you google about az side effects, those from sputnik are probably mostly similar | 01:03 |
twomoon | just remember the Pandemrix story | 01:03 |
twomoon | don't ever forget it | 01:03 |
nixonix | but how knows about possibly damaged s-proteins, which can vary. like possibly more damaged in az than jnj, according to some researcher | 01:04 |
twomoon | yep | 01:05 |
twomoon | heat can damage the mRNA and cause all sorts of weirdness | 01:05 |
nixonix | .title https://www.ft.com/content/f76eb802-ec05-4461-9956-b250115d0577 https://archive.is/4KCoL | 01:06 |
Brainstorm | nixonix: From www.ft.com: Scientists claim to have solved Covid vaccine blood-clot puzzle | Financial Times | 01:06 |
LjL | twomoon, those vaccines don't contain mRNA though ;( | 01:07 |
twomoon | yeah i know | 01:07 |
twomoon | i was just blabbering on and on after nixonix said mRNA is totally safe | 01:08 |
twomoon | it kinda irked me | 01:08 |
twomoon | Pandemrix isn't mRNA either | 01:08 |
twomoon | but it just shows us that random proteins can do weird unexpected shit | 01:08 |
nixonix | .title https://www.nejm.org/doi/full/10.1056/NEJMc2111305 | 01:09 |
Brainstorm | nixonix: From www.nejm.org: No Correlation between Anti-PF4 and Anti–SARS-CoV-2 Antibodies after ChAdOx1 nCoV-19 Vaccination | NEJM | 01:09 |
nixonix | CovidVax? i like that. is RonaVax also in use? | 01:12 |
LjL | lol, doubt it | 01:13 |
twomoon | lol | 01:13 |
twomoon | RonaVax would be funny as hell | 01:13 |
LjL | ronavax.com and .org are taken, but .net is not, go get it | 01:14 |
twomoon | nixonix should slowly try to displace Campbell | 01:16 |
twomoon | nix has more levity than Campbell | 01:16 |
twomoon | and maybe Finns are not as stiff as I thought | 01:16 |
nixonix | what are you talking about | 01:20 |
nixonix | i meant vaccine names, not site names | 01:21 |
nixonix | .title https://trialstat.com/2020/09/ufovax-announces-its-self-assembling-nanoparticles-as-the-next-generation-vaccine-solution-for-covid-19/ | 01:21 |
Brainstorm | nixonix: From trialstat.com: Ufovax Announces Its Self-Assembling NanoParticles as the Next-Generation Vaccine Solution for COVID-19 – TrialStat Solutions Inc. | 01:21 |
twomoon | i hope ljl isn't a domain squatter type | 01:26 |
twomoon | wow UFOVax is gonna sit really well with anti-vaxxers | 01:26 |
nixonix | NanoVax still free? There is PicoVacc | 01:27 |
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 |
Brainstorm | nixonix: 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/1434655588051406848 | 01:38 |
Brainstorm | nixonix: From twitter.com: ChristosArgyropoulos MD, PhD (Green Chili Check) (@ChristosArgyrop): "Here is an ivermectin doll for you to comment about" | El Pajarito de NoGAFAM | 01:38 |
nixonix | .title https://www.ft.com/content/b67e2368-fbae-4035-9119-c8de6d6b4915?segmentid=acee4131-99c2-09d3-a635-873e61754ec6 https://archive.is/ff4hg | 01:44 |
Brainstorm | nixonix: From www.ft.com: Subscribe to read | Financial Times | 01:44 |
nixonix | * A generation of young people is at risk from the UK’s latest Covid experiment | 01:45 |
twomoon | the UK prob wants to kill off some older folks ? | 01:49 |
twomoon | their policies seem to suggest they want the virus to spread around | 01:49 |
dTal | I think it's more that the government is more scared of economic fallout than of covid | 01:53 |
dTal | deaths are scary stats that can be held against them, but no one gives a toss about long covid | 01:53 |
nixonix | "let them bodies pile high" | 01:53 |
twomoon | well they accomplish two things | 01:54 |
twomoon | better economy and boomer remover | 01:55 |
twomoon | both help their finances | 01:55 |
twomoon | their health system is oversubscribed according to what I saw recently on Campbell's channel | 01:56 |
nixonix | theres also a scenario with endemic rona that keeps changing and reinfecting depleting naive t-cell reserves, like with old people, but with non-old | 01:56 |
twomoon | so getting rid of some older folks is probably high on their priority list | 01:56 |
nixonix | so keep em titers high, so they wont be needed. preferably with IgA nasal vaccines every couple months | 01:57 |
twomoon | lol what the hell are you talking about | 01:57 |
nixonix | google about it or something | 01:58 |
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 |
twomoon | interesting nixonix | 01:59 |
Brainstorm | New from r/WorldNews: worldnews: For scientists, path to covid endgame remains uncertain → https://is.gd/dTsTsp | 02:04 |
LjL | not only for scientists | 02:05 |
twomoon | the covid endgame is stop vaccinations that put massive evolutionary pressure on the virus to be extremely transmissible | 02:05 |
twomoon | the 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 |
twomoon | but at high transmissibility it will never go away | 02:06 |
twomoon | although right now i'm not sure exactly how strong the selective pressure from the vaccines is | 02:06 |
nixonix | .title https://www.medrxiv.org/content/10.1101/2021.08.08.21261768v1.full | 02:07 |
Brainstorm | nixonix: From www.medrxiv.org: Full vaccination suppresses SARS-CoV-2 delta variant mutation frequency | medRxiv | 02:07 |
pwr22 | Even without vaccines - rising human immune resistance would lead it the same pressures | 02:07 |
pwr22 | So I don't buy that logic | 02:07 |
twomoon | true social distancing would also be a very strong pressure | 02:07 |
twomoon | good thing we don't really social distance when we all go back home every day | 02:07 |
twomoon | (with a bunch of relatives/roommates) | 02:08 |
nixonix | first vaccines where protection doesnt wane that fast, then sometimes later pan-rona vaccines possibly, or more probably pan rona variant vax | 02:09 |
de-facto | how would you have any scenario with negative selection for a more fit and more contagious variant? | 02:10 |
de-facto | that just does not work like this | 02:10 |
twomoon | if 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-facto | in any real world scenario without 100.00% infection rates there will be positive selection for more contagious variants, regardless of any of the other conditions | 02:11 |
twomoon | and then create a pan-rona vaccine that gives epic coverage | 02:11 |
nixonix | sure, but more efficient vaccines, less changes for new variants to emerge and then start spreading | 02:12 |
twomoon | so is de-facto saying that the high transmissibility is the natural end-stage of a virus about to exit-stage-left? | 02:13 |
nixonix | with 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 population | 02:13 |
de-facto | every pathogen has a reproduction advantage from becoming more infectious | 02:14 |
nixonix | or non-immune, those that are almost non-immune (waned several months or longer) | 02:14 |
twomoon | i think we aren't even seeing selective pressure yet | 02:15 |
twomoon | it's just short term random-walking | 02:15 |
de-facto | the 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 resistance | 02:17 |
de-facto | imho pretty similar to monoculture being more susceptible to a parasite | 02:19 |
pwr22 | <twomoon> "if you want to get rid of a..." <- That seems combinatorically infeasible | 02:21 |
nixonix | better 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 mutating | 02:21 |
de-facto | maybe 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 distribution | 02:22 |
LjL | de-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 harmful | 02:22 |
twomoon | pwr22 i'm full of crap comparex to the other guys. i will stop talking now | 02:23 |
pwr22 | 😛 | 02:23 |
twomoon | when de-fact talks it's over my head sometimes | 02:23 |
pwr22 | Me too | 02:23 |
pwr22 | I 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 prevalence | 02:24 |
de-facto | LjL 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 now | 02:24 |
pwr22 | Right now our vaccines are kind of the lowest bar | 02:24 |
pwr22 | At some point fairly soonish I suspect they'll be not particularly useful anymore | 02:24 |
twomoon | lol "cook a vaccine" | 02:24 |
pwr22 | And waiting until that point before taking action is not great for a few different reasons | 02:25 |
LjL | pwr22, 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 it | 02:25 |
LjL | can 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 undergo | 02:25 |
Brainstorm | New 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/jn6SZf | 02:25 |
pwr22 | LjL: I'd settle for any number more than 1 variant at this point 😛 | 02:26 |
pwr22 | Worry about more of them later | 02:26 |
pwr22 | 2 years is just ancient history in terms of the mutations going on here | 02:26 |
pwr22 | Even flu vaccines we iterate faster than this | 02:26 |
LjL | pwr22, 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 slow | 02:27 |
twomoon | we need PanRonaVax1 and then PanRonaVax2 (updated for even more spread-spectrum effect) | 02:27 |
pwr22 | Protein 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 modelling | 02:27 |
de-facto | LjL, 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 mutations | 02:27 |
pwr22 | LjL: trials and stuff is exactly one of the reasons we need to get ahead on these things | 02:28 |
* archpc peeks in | 02:28 | |
de-facto | e.g. E484K may cost fitness, but can be afforded together with N501Y or such | 02:28 |
LjL | pwr22, 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 explosion | 02:28 |
twomoon | i don't think we've witnessed true selective-pressure evolution yet. it's just random walking imo | 02:28 |
LjL | archpc, hi | 02:28 |
pwr22 | archpc: is it time for dr de-facto to take your vitals? | 02:28 |
LjL | twomoon, all evolution is technically "random walking", but we've already seen convergent evolution | 02:29 |
* archpc bends over, unbuckles his belt | 02:29 | |
LjL | many of the variants end up with the same (or similar) mutations, acquired independently | 02:29 |
twomoon | convergent evolution isn't necessarily due to selection | 02:29 |
archpc | Still tested positive on the 3rd | 02:29 |
LjL | archpc, argh :( | 02:29 |
pwr22 | LjL: 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 happen | 02:29 |
LjL | pwr22, and ADE. i think while ADE is not *currently* a concern, it doesn't mean it won't *ever* be a concern. | 02:30 |
archpc | I feel good except for the post covid effects | 02:30 |
* archpc shrugs, goes back to email | 02:30 | |
LjL | when we test a new vaccine, we need to make sure it isn't | 02:30 |
LjL | archpc, sat? | 02:30 |
archpc | what | 02:30 |
nixonix | i 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 say | 02:30 |
LjL | archpc, what's your oxygen saturation lately | 02:30 |
pwr22 | Find an animal with ACE2 equivalents the virus doesn't work on and gene modify the entire human race to use that instead 😛 | 02:31 |
pwr22 | Also furin and such things | 02:31 |
archpc | Oh, last time I checked it was 90 | 02:31 |
pwr22 | 😛 | 02:31 |
LjL | nixonix, but i've seen it pointed out multiple times that ADE findings in animals often don't translate to humans | 02:31 |
LjL | archpc, hmm, still not stellar | 02:31 |
pwr22 | LjL: mine was only 95 earlier 😛 | 02:31 |
LjL | pwr22, mine is usually around that ballpark too, sometimes lower :( but i'm currently at about 1000m altitude fwiw | 02:32 |
LjL | still, 90 is low | 02:32 |
pwr22 | I thought 90-100 is normal range? | 02:32 |
LjL | it's certainly good that it got up from 83 | 02:32 |
pwr22 | Ah, 95-100 | 02:32 |
LjL | pwr22, nominally 94 tends to be considered the cutoff for "put him under oxygen" | 02:32 |
pwr22 | misremembered | 02:32 |
nixonix | yeah. but using N doesnt seem to help. maybe because killer t-cells are affected by orf8 then | 02:32 |
LjL | pwr22, 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 think | 02:33 |
nixonix | and not relevant fc mediated effector functions with sars2 | 02:33 |
LjL | if you happen have 94% or 93% you probably shouldn't rush to the hospital :P | 02:33 |
twomoon | ljl's focus on making sure the PanRonaVax caters to the ACE2 receptor is a good idea | 02:33 |
LjL | but we *know* that archpc has [had] COVID and is still not feeling good and the saturation reflects that | 02:34 |
pwr22 | I started getting sick at the stag party I was at yesterday so eventually had to leave fairly early | 02:34 |
LjL | twomoon, 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 |
archpc | I feel fine except for the long post covid shit | 02:35 |
pwr22 | I think I got a minor concussion in a bad go karting collision earlier in the day | 02:35 |
LjL | lol | 02:35 |
pwr22 | So not sure how much of it was down to that tbh | 02:35 |
LjL | archpc, so you're feeling fine except for not feeling fine? :P | 02:35 |
pwr22 | The entire front pack crashed out into me so I was almost ejected from the cart | 02:36 |
twomoon | i feel fine except for long term maladies | 02:36 |
Brainstorm | New 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/QaBWgV | 02:36 |
pwr22 | It knackered my left leg, back and neck | 02:36 |
pwr22 | Oh yeah, and my arms too but not sure how much of that is just from the steering | 02:36 |
pwr22 | Was fun though | 02:36 |
twomoon | real life mario kart =) | 02:36 |
pwr22 | Yeah I mean I could have done with a blue shell at points | 02:37 |
LjL | pwr22, 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? :P | 02:37 |
pwr22 | Possibly | 02:37 |
pwr22 | It's a form of sexist gender restricted party that grooms have before their marriage yeah | 02:37 |
pwr22 | Women have an equivalent hen party | 02:37 |
LjL | "hen party", that also sounds sexists tbf | 02:39 |
pwr22 | Yeah, it's all men in stag parties and all women at hen parties | 02:39 |
pwr22 | I have no idea how these things work in the more gender fluid world that exists now | 02:39 |
archpc | Well, I don’t feel ill, except for the post effects | 02:39 |
archpc | Idk, I refer to everyone in the 3rd person, always works fine | 02:40 |
LjL | why, how else would archpc refer to them? | 02:40 |
archpc | huh | 02:40 |
twomoon | how is archpc doing? | 02:41 |
twomoon | better than that German guy? | 02:41 |
archpc | Merely vibing | 02:41 |
archpc | What German | 02:41 |
LjL | i thought everyone was either german or finnish here | 02:41 |
twomoon | that trbp kid | 02:42 |
* archpc hears a bald eagle scream in the distance | 02:42 | |
twomoon | where are all the Italians | 02:42 |
archpc | …in Italy | 02:42 |
LjL | hopefully far, far away | 02:42 |
twomoon | I figured what happened in Lombardy would have brought them out of the woodwork and into IRC | 02:43 |
twomoon | turned them all into armchair virologists | 02:43 |
LjL | they're probably all on IRCNet though | 02:43 |
archpc | Dual satellite, what happened | 02:43 |
LjL | heh | 02:44 |
twomoon | what are u talkin about archpc | 02:45 |
archpc | Idk | 02:45 |
twomoon | dual sat? huh? | 02:45 |
archpc | It was a joke on your nixk | 02:46 |
archpc | Nick | 02:46 |
twomoon | i see | 02:46 |
LjL | twomoon, 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 |
Brainstorm | New from Reddit (test): Covid2019: Brazil v Argentina abandoned five minutes after kick-off after visiting players accused of Covid violation → https://is.gd/irB89B | 02:46 |
twomoon | i blame it on long coronavirus (but not covid) brain fog | 02:46 |
archpc | My brains been off somewhere else | 02:47 |
twomoon | remember i also had anosmia several times in my life, as well as tinnitus | 02:47 |
archpc | Also, insomnia, and some drinking | 02:47 |
archpc | I’m thoroughly dumb | 02:47 |
LjL | archpc, 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 think | 02:47 |
archpc | Heh, amateurs | 02:48 |
twomoon | oh...jesus. i just realized archpc didn't realize that | 02:48 |
twomoon | wake up man | 02:48 |
archpc | :| | 02:48 |
LjL | twomoon, did you even know Lombardy was a thing before the pandemic? | 02:48 |
twomoon | no | 02:49 |
twomoon | I just knew Milan | 02:49 |
twomoon | I had never heard of Lombardy, the region that contains Milan | 02:49 |
LjL | i bet i have no idea what county archpc, or you, live in, even if you tell me the city/town | 02:50 |
twomoon | when Lombardy got hit by the virus I recall being in a state of shock | 02:50 |
archpc | LjL, Old Fort :D | 02:51 |
archpc | Which one? Who knows! | 02:51 |
LjL | i was in a state of rabid frustration with others' unwillingness to see we were in deep shit | 02:51 |
nixonix | sounds texas | 02:51 |
archpc | No, oh god no | 02:51 |
LjL | archpc, the old one, duh | 02:51 |
archpc | Heh | 02:51 |
twomoon | ljl I always imagine italians not wanting to take things too seriously. like shrugging off dire shit just like the dutch often do | 02:52 |
twomoon | and I can imagine you believing that about your fellow countrymen too and having it really annoy you | 02:53 |
archpc | My Dutch lady friend had some family members pass, it’s apparently been bad there | 02:53 |
twomoon | it's been rough in many countries, yeah. it's been pretty bad in Indonesia too | 02:54 |
pwr22 | <LjL> "i thought everyone was either..." <- I have been told I have a German look to me | 02:56 |
LjL | pwr22, kyllä | 02:56 |
de-facto | I wonder what is going on in Vietnam right now | 02:57 |
de-facto | .title https://www.reuters.com/world/asia-pacific/vietnam-pay-recovered-covid-19-patients-help-hospitals-2021-08-25/ | 02:57 |
Brainstorm | de-facto: From www.reuters.com: Vietnam to pay recovered COVID-19 patients to help in hospitals | Reuters | 02:57 |
LjL | uh, easier than vaccinating nurses? | 02:57 |
nixonix | they have bad vaccines, cases and deaths rocketing | 02:58 |
LjL | %cases vietnam | 02:58 |
Brainstorm | LjL: 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=Vietnam | 02:58 |
LjL | hmm, 15000 in one day versus 500k total, that's a substantial amount | 02:58 |
twomoon | when did vietnam go from 35 to 12000 ? | 02:58 |
twomoon | what the hell ?? they were like the biggest winner of the pandemic the last time i checked | 02:59 |
de-facto | just very recently they are having an exponential huge Delta wave | 02:59 |
twomoon | for a long time their death count sat at 35 | 02:59 |
archpc | I thought they were untouched almost | 02:59 |
de-facto | before yeah | 02:59 |
nixonix | deaths been stable just lately tho, but who knows that the real numbers are | 02:59 |
twomoon | man, i have totally not been paying attention. my bad | 02:59 |
LjL | someone 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 |
archpc | I wonder how Pitcairn island is doing | 02:59 |
LjL | https://offloop.net/covid19/?default=Italy;Vietnam&byPopulation=yes&cumulative=no&smooth=yes | 03:00 |
LjL | case growth is... not really similar, but not wildly dissimilar | 03:00 |
LjL | but deaths certainly differ | 03:00 |
LjL | (since July, i mean) | 03:00 |
archpc | Apparently Pitcairn has had 0 cases, wow, new plague inc challenge | 03:01 |
de-facto | ok according to that graph cases are similar, but i bet they do more testing in Italy than in Vietnam | 03:02 |
nixonix | i 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 vaccinated | 03:03 |
LjL | hmm 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 italy | 03:04 |
de-facto | positivity rate italy 2.4% Vietnam 7.1% | 03:04 |
Brainstorm | LjL: 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 |
LjL | de-facto, okay, that's... definitely an indication they test less | 03:04 |
de-facto | Thailand 33.9% | 03:04 |
LjL | -.- | 03:04 |
LjL | but we did have something like 30% at some point | 03:04 |
LjL | also, we currently do between 250k and 300k tests per day, but only about 100k of those are PCR, the rest are antigen | 03:05 |
LjL | and the positivity ratio for those is very different | 03:05 |
de-facto | .title https://ourworldindata.org/coronavirus-testing | 03:05 |
Brainstorm | de-facto: From ourworldindata.org: Coronavirus (COVID-19) Testing - Statistics and Research - Our World in Data | 03:05 |
LjL | but they all get counted as "tests" | 03:05 |
nixonix | counted in owid stats? | 03:05 |
de-facto | good question | 03:06 |
LjL | counted in the government's official stats, dunno about owid | 03:06 |
LjL | i look at Il Sole 24 Ore which has separate graphs for them | 03:06 |
LjL | so i can see they definitely have different trends | 03:06 |
de-facto | i guess owid gets it from the official dashboards | 03:06 |
LjL | yeah my assumption is they count them both | 03:07 |
LjL | and, yeah, it's both | 03:07 |
nixonix | when 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 |
LjL | de-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 refresh | 03:08 |
nixonix | look for other countries reaching 25-30% among the first, and count 4 months. chile, usa soon... | 03:08 |
LjL | sensitivity of antigen tests to the second wave looks pretty "meh" to me from those graphs | 03:09 |
LjL | (second wave i mean delta) | 03:09 |
de-facto | LjL, so PCR tests are also 6-8% positive in Italy after pre-selection by rapid antigen tests? | 03:10 |
nixonix | uruguay, qatar, singapore, serbia. uk but with long intervals | 03:10 |
twomoon | what do you mean by "sensitivity of antigen tests"? | 03:10 |
LjL | de-facto, if you mean after censoring antigen tests... yes | 03:11 |
twomoon | oh, sensitivty, right | 03:11 |
nixonix | so those countries should see lots of breakthroughs soon, unless started 3rd doses | 03:11 |
LjL | twomoon, 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 it | 03:11 |
twomoon | yeah...i get it now. my lag is bad | 03:11 |
nixonix | maybe sooner if some chinese vaxes etc used | 03:11 |
LjL | maybe the chinese ones wane slower, who knows, sort of like AZ | 03:12 |
LjL | they suck but they keep sucking for longer | 03:12 |
de-facto | i still would like to see antibody half-life as function of booster delay after priming and that per age group | 03:13 |
nixonix | it takes longer than 4 months for pfizers and az's curves converge, if those were accurate with reality | 03:13 |
de-facto | all i know they are around 70-ish days for Moderna 4 weeks apart for averaging over big age ranges | 03:14 |
nixonix | neut ab half life for moderna 70 days? | 03:14 |
nixonix | you have a link? | 03:14 |
de-facto | yes | 03:14 |
de-facto | yes | 03:15 |
twomoon | LOL they suck but they keep sucking for longer. | 03:15 |
de-facto | .title https://www.nejm.org/doi/full/10.1056/nejmc2103916 | 03:15 |
Brainstorm | de-facto: From www.nejm.org: Antibody Persistence through 6 Months after the Second Dose of mRNA-1273 Vaccine for Covid-19 | NEJM | 03:15 |
nixonix | its 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 |
nixonix | ah, 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 days | 03:17 |
de-facto | .title https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3891065 | 03:19 |
Brainstorm | de-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-facto | nixonix, nope 69-ish days for neutralizing ab in the Moderna paper | 03:20 |
de-facto | https://www.pitch-study.org/PITCH_Dosing_Interval_23072021.pdf | 03:20 |
nixonix | almost the same. what are those 200 days results | 03:21 |
nixonix | modeled, not measured? | 03:22 |
nixonix | and wide differencies between the two models, hmm | 03:22 |
de-facto | figures at https://www.pitch-study.org/Figures_Appendix_PITCH_Dosing_interval_23072021.pdf | 03:23 |
nixonix | exponential and power-law model. so which one is the right for protection? | 03:27 |
de-facto | nixonix, where did you find 50 days for BNT? | 03:27 |
de-facto | nixonix, as long as those titers look like straight lines in log plots i guess the exponential model | 03:28 |
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, respectively | 03:30 |
nixonix | .title https://www.researchsquare.com/article/rs-847396/v1 | 03:30 |
Brainstorm | nixonix: 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 Square | 03:30 |
nixonix | k next time, lets compare them then | 03:31 |
de-facto | nice thanks | 03:32 |
twomoon | when is nix gonna get burnt out? | 03:36 |
twomoon | dude is going too hard these days | 03:37 |
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/4TCSWp | 03:38 |
de-facto | .title https://www.science.org/doi/10.1126/science.abf4063 | 03:40 |
Brainstorm | de-facto: From www.science.org: Immunological memory to SARS-CoV-2 assessed for up to 8 months after infection | 03:40 |
twomoon | de-facto, is there any evidence so far that *more severe infection* leads to improved immunological memory? | 03:44 |
de-facto | interesting, at quick glance it looks like convalescent individuals have almost double the half-life for antibodies | 03:44 |
de-facto | twomoon, i think that is the case, but the antigenic drift of the pathogen takes place independently since its outside of the individual | 03:46 |
de-facto | e.g. how fast evasive mutants emerge in breeding the pathogen in a society | 03:47 |
twomoon | yeah, but if we could somehow fix for antigenic drift... | 03:47 |
de-facto | we cant, its naturally occurring by copy errors | 03:47 |
twomoon | i suspect that more severe infection creates a larger variety of immunological memory cells | 03:47 |
de-facto | yes that indeed could be the case | 03:48 |
twomoon | but i just don't have the data all organized in front of me | 03:48 |
twomoon | it's like i've read enough papers now to get that sense but i don't have all those papers nicely organized in Zotero lol | 03:48 |
de-facto | that 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 persist | 03:48 |
twomoon | do you have a paper that demonstrates this effect? | 03:49 |
twomoon | i need to start organizing some papers | 03:49 |
de-facto | i dont have any links, i just remember some and grep them out of backscroll :D | 03:50 |
twomoon | lol | 03:50 |
de-facto | i wish i had a zotero setup or such | 03:50 |
de-facto | twomoon, afaik there were papers about SARS-CoV-1 survivors vaccinated with BNT162b2 developing such broad immunity that they could neutralize all variants | 03:51 |
de-facto | .title https://www.nejm.org/doi/full/10.1056/NEJMoa2108453 | 03:52 |
Brainstorm | de-facto: From www.nejm.org: Pan-Sarbecovirus Neutralizing Antibodies in BNT162b2-Immunized SARS-CoV-1 Survivors | NEJM | 03:52 |
twomoon | i'm looking for a paper that looks at non-vaccinated survivors | 03:52 |
twomoon | that just demonstrates clearly that harsher infection creates a larger variety of imm. memory cells | 03:52 |
twomoon | thanks for the paper, worth a look | 03:53 |
de-facto | so 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 rate | 03:53 |
de-facto | i 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 infection | 03:55 |
de-facto | definitely 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-2 | 03:56 |
LjL | i think that paper may prove extremely important | 04:09 |
twomoon | what's the main point of that paper ? | 04:10 |
Brainstorm | New 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/9yNaXF | 04:10 |
LjL | twomoon, 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 coronaviruses | 04:13 |
LjL | it 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 bats | 04:14 |
twomoon | oh wow | 04:21 |
twomoon | i suspect more severe infection creates more variety | 04:24 |
twomoon | and we have antibodies to select from | 04:25 |
de-facto | SARS-CoV-1/2 are quite similar, but MERS-CoV uses a different receptor | 04:26 |
LjL | this 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 antibodies | 04:26 |
LjL | de-facto, fair enough, MERS was just a guess | 04:27 |
LjL | but taking out SARS1 and 2, with all their variants, in one shot would be pretty great | 04:28 |
de-facto | but 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 such | 04:29 |
twomoon | genus betacoronavirus | 04:29 |
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/4TCSWp | 04:29 |
twomoon | why are you sending this article again | 04:30 |
LjL | i didn't notice it had been already sent. i grabbed it from ##covid-ticker | 04:30 |
Brainstorm | New 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/FT969b | 04:32 |
LjL | i 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 |
LjL | and 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-facto | LjL, 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 spikes | 04:35 |
de-facto | (wild speculation) | 04:35 |
LjL | yeah, i don't know, it's enough to know that it can work | 04:35 |
LjL | we do have some tentative SARS1 vaccine, right? | 04:36 |
LjL | i think we should trial giving it to people together with a SARS2 vaccine, and see what happens | 04:36 |
de-facto | why not just put in the sequence for its spike in the mRNA platforms | 04:37 |
de-facto | as broad of a variety as possible, all known variants for spikes of SARS-CoV-1 and SARS-CoV-2 VoCs | 04:37 |
LjL | because first you need to see if it works? :P | 04:38 |
de-facto | yes i mean as trial | 04:38 |
de-facto | then measure neutralization of the serum | 04:38 |
de-facto | if it works it would be fantastic, if not it really could have something to do with severe disease of SARS-CoV-1 or such | 04:38 |
LjL | well it's the same thing as what i said basically isn't it | 04:38 |
de-facto | yes | 04:39 |
de-facto | i think this will turn out to be one very important point in vaccinations: the magnitude of variety in antibody affinity covering all variants and more | 04:41 |
de-facto | as well as inducing IgA and resident B-cells in the nasal and pharyngeal mucus | 04:42 |
Brainstorm | New from The Indian Express: World: Australia takes delivery of Pfizer Covid-19 vaccine from Britain → https://is.gd/o1THbG | 05:03 |
Brainstorm | New from The Indian Express: World: No cash, only soft incentives for taking Covid-19 vaccines: S African Health Minister → https://is.gd/72pDC7 | 05:46 |
twomoon | ljl 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 you | 05:51 |
twomoon | from what we know you are interested in linguistics and earthquakes mainly (and old computers/ odd computing devices) | 05:52 |
Brainstorm | New from The Indian Express: World: Covid deaths surge across a weary America as a once-hopeful summer ends → https://is.gd/eEwAbI | 06:38 |
Brainstorm | New from The Indian Express: World: The best birthday present in 2021? A COVID vaccine → https://is.gd/tsx2q7 | 08:03 |
Brainstorm | New from The Indian Express: World: Thai protesters are back, and angrier, as government fumbles on Covid → https://is.gd/1YIKih | 08:46 |
Brainstorm | New 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/v60Iv2 | 09:07 |
Brainstorm | New from r/WorldNews: worldnews: COVID-19: Anti-Vaxxers Are Targeting Pregnant Women Leading to Tragedy → https://is.gd/2x3F2y | 11:04 |
Brainstorm | New 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/iJlbhj | 11:15 |
Brainstorm | New from r/WorldNews: worldnews: Brazil vs. Argentina World Cup qualifier suspended, as four Argentinian players accused of breaking Covid travel protocols → https://is.gd/KW5Thx | 11:37 |
Brainstorm | New 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/jXPWp9 | 11:47 |
Brainstorm | New from PubMed: Ahmad Shamabadi: Medical Biotechnology in the Service of Coronavirus Vaccine Discovery and Production → https://is.gd/dBf3es | 13:01 |
Brainstorm | New 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/ln8hpx | 13:12 |
de-facto | .title https://www.biorxiv.org/content/10.1101/2021.03.12.435191v2 | 13:36 |
Brainstorm | de-facto: From www.biorxiv.org: A novel soluble ACE2 protein totally protects from lethal disease caused by SARS-CoV-2 infection | bioRxiv | 13:36 |
pwr22 | In transgenic mice designed to die from covid | 13:40 |
pwr22 | Hmm | 13:40 |
pwr22 | Given 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 |
pwr22 | Specifically ACE 2 inhibitors | 13:41 |
Brainstorm | New 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/5A5vSn | 14:05 |
Brainstorm | New from r/WorldNews: worldnews: Not getting vaccinated puts lives at risk - Mattarella → https://is.gd/js864R | 14:48 |
Brainstorm | New 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/1i1qKM | 15:32 |
Brainstorm | New 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/ei5wPc | 15:43 |
Brainstorm | New 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/OleU9z | 15:53 |
Brainstorm | New 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/wtsb5h | 16:04 |
Brainstorm | New 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/leysw6 | 16:25 |
Brainstorm | New 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/QSIU3L | 16:36 |
Brainstorm | New 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/kSAd2l | 16:57 |
Brainstorm | New from Reddit (test): Monday 06 September 2021 Update: submitted by /u/HippolasCage to r/CoronavirusUK → https://is.gd/yH2aFp | 17:08 |
Brainstorm | New 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/E3InNA | 18:03 |
-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 | |
Brainstorm | New from r/WorldNews: worldnews: WHO approved first Chinese ‘SinoPharm’ vaccine for alternative use around the globe : COVID-19 vaccine → https://is.gd/Mg7xxk | 18:34 |
LjL | why would WHO do that when it's just been shown to be marginally better than nothing? | 18:35 |
Brainstorm | New 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/NbHoVt | 19:07 |
inxoinx | what do we have on hospitalization rates with delta? or with uk variant? cdc had something by age group, but i think its mixed variants | 19:48 |
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.html | 19:48 |
Brainstorm | inxoinx: From www.smh.com.au: NSW COVID: More than one in 10 people now end up in hospital | 19:48 |
inxoinx | .title https://twitter.com/MThallinger/status/1434840228913729538 | 19:49 |
Brainstorm | inxoinx: 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 |
inxoinx | yeah, 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 |
inxoinx | anyone 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 then | 20:11 |
Brainstorm | New 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/UjHfBv | 20:11 |
inxoinx | has 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/s41587-021-01020-4 | 20:37 |
Brainstorm | inxoinx: From www.nature.com: Integrated analysis of plasma and single immune cells uncovers metabolic changes in individuals with COVID-19 | Nature Biotechnology | 20:37 |
LjL | no i think i've seen him in other channels though | 20:38 |
LjL | inxoinx, 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 now | 20:39 |
inxoinx | yeah, from diamond princess. i couldnt find pango name for it | 20:40 |
inxoinx | they 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 didnt | 20:41 |
inxoinx | while 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 |
LjL | i've only figured out it's part of the B pango lineage | 20:42 |
inxoinx | suggesting that it didnt have g, i meant | 20:42 |
inxoinx | .title https://www.nature.com/articles/s41586-021-03944-y | 20:43 |
Brainstorm | inxoinx: From www.nature.com: SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion | Nature | 20:43 |
inxoinx | .title https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7602519/ this has something about that diamond princess sample | 20:45 |
Brainstorm | inxoinx: 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 here | 20:46 |
Brainstorm | inxoinx: From biology.stackexchange.com: virology - Virus lineage, strain, and relation to spike protein variants - Biology Stack Exchange | 20:46 |
nixonix | maybe defacto is handy with those lineages and can find out | 20:47 |
nixonix | was 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 |
Brainstorm | nixonix: From old.reddit.com: Anyone who went to the frat parties: you likely have COVID. : UBC | 21:11 |
nixonix | nah, bc aka canada. so not that long, and they increased the interval too | 21:15 |
lastshell | Is true that vegetarians have more resistance to get covid ? | 21:28 |
lastshell | https://nutrition.bmj.com/content/early/2021/05/18/bmjnph-2021-000272 | 21:30 |
lastshell | sadly I starting to eat more protein :( | 21:30 |
nixonix | possibly 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 nowdays | 21:45 |
nixonix | turbo could help, but he is awol | 21:46 |
nixonix | theres 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 |
nixonix | so 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 have | 21:51 |
nixonix | not 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-facto | nixonix, erm but was that for naive immune systems first training its naive t-cells or for reinfections? | 21:52 |
de-facto | because it probably is not the same for each contamination, as in the flu the immune system is not naive for it after the first exposure | 21:52 |
nixonix | i 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-facto | first 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 reinfections | 21:54 |
de-facto | nixonix, 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 overlap | 21:55 |
nixonix | not for conserved sites, but those sites that keep changing with variants. and apparently sars2 uses naive t-cell reserve a lot more than influenza | 21:55 |
nixonix | if i recall i read something similar with hiv, but not sure | 21:56 |
de-facto | or sure some, since there were t-cells reacting to SARS-CoV-2 that were sampled prior to 2020 | 21:56 |
nixonix | yeah, lots of cross-reactivity, also with animal coronaviruses | 21:56 |
de-facto | what i mean is that first exposure to sars-cov-2 should not be comparable to repeated exposure to influenza | 21:57 |
de-facto | it probably consumes less amount of naive t-cells each re-exposure | 21:57 |
de-facto | (i dont know that though, its just a guess) | 21:57 |
nixonix | still 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 deeper | 21:57 |
LjL | i 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 efficacy | 21:57 |
nixonix | also i read couple of a few years older papers, there was a lot of uncertainties, things not known yet | 21:58 |
nixonix | but 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 do | 22:00 |
nixonix | but severe cases apparently use way more, so good protection from recent vaccinations (preferably with IgA from nasal vax), and naive reservoir is conserved, better anyway | 22:01 |
nixonix | not 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-facto | if severity decreases with each reinfection (or breakthrough) maybe also consumption of naive t-cells decreases with each iteration | 22:03 |
nixonix | how 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-facto | probably 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 regions | 22:05 |
nixonix | but accumulating protection for severe, when repeated... i dont know, you can only hope | 22:05 |
nixonix | that danish study on reinfections, i think it didnt hint much about reinfections being milder | 22:06 |
nixonix | should check | 22:06 |
nixonix | but 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 symptoms | 22:07 |
nixonix | since 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 stuff | 22:10 |
nixonix | but do those, that dont produce IgG | 22:11 |
nixonix | btw, 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 nonsymptomatic | 22:12 |
nixonix | now its about protection. so if there is some minimal amount of IgG, it doesnt matter for protection | 22:13 |
nixonix | and some of those assays only looked at IgM i think | 22:13 |
nixonix | so, have you had rona? the answer depends, in what sense. protection wise, or tracking infection chains or something else | 22:14 |
de-facto | it 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 are | 22:17 |
nixonix | protection-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 knows | 22:17 |
nixonix | but identifying-wise, its prob close to 100% if right antibodies (perhaps IgM) and sensitive enough assay is used within maybe couple months or so | 22:18 |
de-facto | for incidence estimation we would need something really fast decaying | 22:19 |
de-facto | preferably already decaying during the raise of IgG or such | 22:19 |
nixonix | hc officials are prob not interested. they want to let it burn through when not too many people die | 22:20 |
de-facto | but also something that is global, so easily testable via blood sample | 22:20 |
nixonix | and 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 commenting | 22:21 |
lastshell | but a what cost nixonix | 22:22 |
lastshell | (human cost) | 22:22 |
nixonix | hard to say, but its a risky game, using other peoples health | 22:22 |
ecks | i am willing to sacrifice a few nucleotides of telomeres if it means i can go to the pub and have a beer | 22:25 |
nixonix | yeah, but you dont even own a thermometer | 22:25 |
ecks | and still going strong! | 22:26 |
nixonix | btw, what do you think about that depleting naive t-cell reserve, and reinfections etc above? | 22:26 |
ecks | can't really say i'm well-versed enough in these subjects to comment | 22:27 |
ecks | immunology is hard | 22:27 |
nixonix | since we are just bunch of nerds, give us some opinion | 22:27 |
ecks | i tend to not open my immunology book if i can avoid it | 22:27 |
nixonix | is it the same with most md's? | 22:27 |
ecks | probably | 22:29 |
ecks | it's a difficult subject (from my experience) so many tend to shy away from it | 22:30 |
nixonix | they 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 loop | 22:34 |
nixonix | accepting placebo as a treatment is quackery. thats what they are doing anyway | 22:35 |
ecks | finally someone who understands the no-labs method | 22:38 |
nixonix | btw, 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 there | 22:40 |
ecks | it has its own name, "defensive medicine" | 22:42 |
nixonix | .title https://twitter.com/EricTopol/status/1434929777819799554 | 22:42 |
Brainstorm | nixonix: 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-facto | for me a test that finds the cause of something is extremely valuable, almost more as the actual treatment as i know what i deal with | 22:43 |
de-facto | so if a doctor tells me "its this and that" i am satisfied and go away as its determined | 22:43 |
nixonix | i think ecks is more in the "if you dont feel too bad, you are prob ok" bandwagon | 22:44 |
de-facto | yeah | 22:44 |
de-facto | not knowing literally makes me sick, if i have the impression i understand something it cant really worry me anymore | 22:46 |
ecks | no more blood tests for you | 22:54 |
ecks | they should do some clinical trial where half of the patients in the ER triage are seen by doctors and the other half by monkeys | 22:55 |
ecks | i bet the monkeys would be more cost-efficient | 22:55 |
nixonix | there 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 probably | 23:03 |
nixonix | he had some studies ofc. and when he didnt understand something well enough, he asked from somebody else | 23:04 |
nixonix | he got 5 years prison (half of it reduced automatically) | 23:06 |
nixonix | so he was no monkey. but probably more expensive | 23:10 |
de-facto | for me a proper diagnostic is the best thing a MD can possibly give to me | 23:21 |
Brainstorm | New 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/2p1hRR | 23:23 |
nixonix | .title https://twitter.com/ChristosArgyrop/status/1434978110651260931 | 23:23 |
Brainstorm | nixonix: 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 |
Brainstorm | New from r/WorldNews: worldnews: Vietnamese man jailed for 5 years for spreading coronavirus → https://is.gd/ri2UmX | 23:34 |
nixonix | .title https://twitter.com/VirusesImmunity/status/1433570048715763714 | 23:34 |
Brainstorm | nixonix: 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.twitter | 23:41 |
Brainstorm | nixonix: From www.science.org: Adaptive immune determinants of viral clearance and protection in mouse models of SARS-CoV-2 | 23:41 |
nixonix | .title https://www.jimmunol.org/content/207/2/376.long | 23:41 |
Brainstorm | nixonix: From www.jimmunol.org: Cutting Edge: Nucleocapsid Vaccine Elicits Spike-Independent SARS-CoV-2 Protective Immunity | The Journal of Immunology | 23:41 |
nixonix | .title https://jacobinmag.com/2021/02/finland-vaccine-covid-patent-ip old article | 23:56 |
Brainstorm | nixonix: From jacobinmag.com: Finland Had a Patent-Free COVID-19 Vaccine Nine Months Ago — But Still Went With Big Pharma | 23:56 |
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