libera/##covid-19/ Saturday, 2021-06-26

LjLde-facto, they just said here on TV that some 10 countries that have used Sinovac and Sinopharm (both inactivated) are among the countries with the most new cases and the most hospitalizations00:22
LjLthey said it's probably because these vaccines aren't great against variants and they also said that Sputnik as well doesn't guarantee much against Delta00:22
LjLbut isn't that counterintuitive?00:22
LjLinactivated vaccines should be able to have an "all-around" efficacy on the virus even if the S-protein changes a bit00:23
LjLand why is Sputnik any different from AZ or J&J00:23
BrainstormUpdates for Switzerland: +109 cases (now 702507), +2 deaths (now 10882) since 9 hours ago00:32
BrainstormUpdates for India: +434 deaths (now 393310) since 16 hours ago01:10
BrainstormNew from FDA Press Releases: FDA: Coronavirus (COVID-19) Update: June 25, 2021 → https://is.gd/OhUeYc01:55
TimvdeLjL: vaccine effectivenes against hospitalisation is higher for the delta variant even, according to your last image?02:02
LjLTimvde, it's a bit strange isn't it?02:02
LjLTimvde, but i guess it could be explained by the fact that Delta leads to more hospitalizations than Alpha in unvaccinated people (that's nearly certain by now, unfortunately), but maybe in vaccinated people they become similar again02:03
TimvdeThat, or the delta variant leads to more breakthrough infections, but not much more hospitalisations, so the total number compared against is higher02:04
TimvdeBut we would need raw numbers to get to a conclusion, not just percentages02:04
de-factoLjL, i dont know that, i just have seen that Sputnik was doing big PR tamtam about being able to take delta into account, what i did not really understood (since they actually provided ZERO real info) was if they are working on an update, or if they were blabering about a third update shot with the original02:08
de-factoi guess their twitter account is not run by people who know such things02:09
LjLSputkin has been good at PR for sure02:10
LjLi don't think they're necessarily above a bit of bullshitting if they think it helps them02:10
de-factountil i see some data in form of a trial i assume Sputnik is just like all the other vaccines with Wuhan spike02:10
LjLTimvde, agreed about numbers but when i talk to that particular person it's like a surgical extraction to know where he's getting data from exactly02:11
de-factoi dont say they lied or anything like that, to me its just completely unclear what they actually are talking about when referring to efficacy against delta02:11
LjL"the internet" was the answer last time i wanted to know where he was getting the tweets he commented on ;(02:11
de-factobut heh maybe that is just stupid old me :P02:11
de-factoi do hope Sputnik in its current form is somewhat efficant against Delta given the Moscow spike02:13
Timvdede-facto: isn't the vaccination rate in Russia very low?02:14
TimvdeThey're at 14% according to Our World in Data02:15
de-factoyes i have seen that too02:15
de-factomeans not even their risk groups are vaccinated fully yet02:16
de-factoless than India even02:16
de-factohttps://ourworldindata.org/covid-vaccinations02:16
de-factosince begin of June the cases in Russia seem to be on steep rise02:18
de-facto.title  https://www.medrxiv.org/content/10.1101/2021.05.22.21257658v102:22
Brainstormde-facto: From www.medrxiv.org: Effectiveness of COVID-19 vaccines against the B.1.617.2 variant | medRxiv02:22
de-facto.title https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(21)01358-1/fulltext02:22
Brainstormde-facto: From www.thelancet.com: SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness - The Lancet02:22
TimvdeI wonder if J&J will at some point revise their strategy and suggest taking a second dose anyway02:26
de-factofrom first paper02:26
de-facto"Effectiveness was notably lower after 1 dose of vaccine with B.1.617.2 cases 33.5% (95%CI: 20.6 to 44.3) compared to B.1.1.7 cases 51.1% (95%CI: 47.3 to 54.7) with similar results for both vaccines. "02:26
de-facto"With BNT162b2 2 dose effectiveness reduced from 93.4% (95%CI: 90.4 to 95.5) with B.1.1.7 to 87.9% (95%CI: 78.2 to 93.2) with B.1.617.2. With ChAdOx1 2 dose effectiveness reduced from 66.1% (95% CI: 54.0 to 75.0) with B.1.1.7 to 59.8% (95%CI: 28.9 to 77.3) with B.1.617.2."02:26
de-facto"Sequenced cases detected after 1 or 2 doses of vaccination had a higher odds of infection with B.1.617.2 compared to unvaccinated cases (OR 1.40; 95%CI: 1.13-1.75)."02:27
de-factofrom second paper02:28
de-facto"The Cox regression analysis for time to hospital admission found that S gene-positive cases were associated with an increased risk of COVID-19 hospital admission: hazard ratio (HR) 1·85 (95% CI 1·39–2·47) when compared to S gene-negative cases, after adjusting for age, sex, deprivation, temporal trend, and comorbidities."02:28
de-factoso apparently delta is worse than alpha in every aspect02:30
TimvdeYea, that's not surprising02:31
TimvdeThe question is: should we be worried even when we have decent vaccination coverage?02:31
de-factobut yeah that was to be expected since the pathogen optimized itself for being more infectious and reproductive (on cellular level)02:32
de-factoyes of course, there is only ONE metric: incidence02:32
de-factothe hope would be that vaccinations not only lower the ratio between infections and severe progressions, but also lower epidemiological reproduction by 1) decreasing infection risk 2) decreasing viral shedding 3) decreasing duration of infectiousness02:33
de-factoTimvde, i am pretty sure that vaccinations alone are not able to control delta in a naive and unaware population, rates must go way over 95% vaccinated for achieving endemic (R=1), that simply is not realistic02:35
Timvde95% is crazy high indeed, wtf?02:35
de-factohence vaccinations only can be seen as one additional tool that helps with maintaining ontrol02:35
TimvdeWe may reach 90+ for the adult population here, but with all the minors who aren't getting a vaccine, it's pretty much impossible to get that high02:36
Timvdede-facto: but people won't accept other measures for much longer02:37
BrainstormUpdates for Palestine: +505 cases (now 313520), +1 deaths (now 3556) since 2 days ago — France: +19 deaths (now 110983) since 21 hours ago — Netherlands: +346 cases (now 1.7 million), +3 deaths (now 17876) since 21 hours ago — United Kingdom: +11825 cases (now 4.7 million), +14 deaths (now 128189) since 21 hours ago02:37
de-factoTimvde, assuming Rt = R0 (1 - v e) == 1 (endemic) we would need to vaccinate v = (R0 - Rt) / ( e R0 ) part of the population when everything is averaged and the vaccine would have an efficacy of preventing transmission of e02:37
de-factoso putting in numbers v = (R0 -Rt) / ( e R0 ) = ( 6 - 1 ) / ( 0.88 6) = 0.946902:39
de-factobut that is even unrealistic the efficacy against symptomatic endpoints with B.1.617.2 is 0.879 according to above paper with two shots of BNT162b2, hence efficacy against transmission is even lower (as there is such quite common thing like asymptomatic transmission)02:41
LjLTimvde, minors (12 and above) are getting vaccinated here02:41
LjLbut yeah 95% seems unrealistic02:42
LjLthat's kinda why we need vaccines that are a bit better than 60%02:42
de-factodoes not matter anyhow, the conclusion is: vaccinations can help with controlling B.1.617.2 but they cant keep its reproduction dynamics under control by themselves (alone), we always need additional measures02:42
LjLsuch as for example not AZ or J&J ;(02:42
TimvdeLjL: Only patients at risk here02:42
LjLde-facto, my friend of few words insists that the most important metric is hospitalization and death, if we just manage to make this stop being a healthcare emergency, everything will be good or something02:43
LjLexcept that i bet your immediate objection will be that we'll still be breeding variants02:43
de-factoyes that is the obvious one02:43
LjLTimvde, well, that may change soon as you get more vaccines. the EU is all getting the same amounts anyway02:43
TimvdeLjL: we'd be breeding variants at a much lower rate, though02:44
LjLbut de-facto what can we do? maybe you can accept living a life of perennial social distancing, masks, quarantine after flights... but seriously, you are in the minority02:44
TimvdeLjL: I think they may be aiming to send more vaccines to COVAX02:44
de-factobut also: reproduction dynamics become more difficult to control the wider the prevalence is spread: even if hospitalizations are not a problem (yet) if we allow hundreds of thousands of infections per day and have an exponential runaway also the hospitalizations will run away exponentially (hence reach a threshold at some point)02:45
LjLTimvde, not necessarily *much* lower imo, if the vaccine only has something resembling 50% or 60% efficacy, even if the efficacy against severe forms is better... it means the pathogen has a fighting chance to mutate against the vaccine (it reproduces, it makes you sick, it doesn't make you dead or needing oxygen, but it can play with its own genes in the meanwhile to see what works best)02:45
de-factobut then we got a gigantic incidence to control (not even to begin to speak of that in the middle of all of that a new variant could emerge and make hospitalizations skyrocket very fast)02:46
LjLwell what's your suggestion, apart from things that realistically people won't do02:46
LjLmy suggestion is, develop a variant-enhanced mRNA vaccine very fast, forget about adenoviruses, and deploy the new vaccine asap02:46
LjLif it's true that by now we know what the key mutations are / are gonna be, just make this mRNA vaccine02:47
de-factovaccinations as fast as possible everywhere, contact reduction enforced to keep R<1 at all costs (absolutely no compromises with that one), and yeah you know me: no traveling.02:47
BrainstormNew from r/WorldNews: worldnews: WHO urges fully vaccinated people to continue to wear masks as delta Covid variant spreads → https://is.gd/KdPwVK02:47
Win7ineLjL I agree, mRNA is the only fast adaptable vaccine so far02:47
TimvdeLjL: mRNA isn't magically super good either, see CureVac02:47
TimvdeBut it is likely that Pfizer or Moderna can quickly make an adapted mRNA vaccine that is highly efficient, yes02:48
de-factoLjL, yes we do need updated vaccines indeed, but there will be more and more variants02:48
LjLTimvde, true, but we know some mRNA vaccines that *are* pretty good, so we need to tweak them for variants02:48
LjLTimvde, well, that's where Pfizer disappoints me, because Moderna is already trialling such a vaccine, but Pfizer got a "good result" with 75% efficacy on Delta, so they're saying their third booster will just be the original vaccine02:48
TimvdeLol, literally today we stopped requiring people to wear masks here02:49
LjLand at the same time there is the possibility that we can't take too many mRNA vaccines before the side effects become too strong, so it would be nice to have one that is good for a long time and for many variants02:49
LjLTimvde, we're dropping it in Italy as well but only outdoors, still mandatory indoors02:49
de-factoi think the problem CureVac had is that they did not use nucleoside modified mRNA but natural mRNA that induced a strong innate immune reaction so that the reactogenicity did not allow more than 12µg doses (otherwise side effects would have been too much) and therefore those 12µg did not produce enough antibody response to be effective enough02:49
TimvdeIt's still mandatory indoors in busy public places, but not at home02:50
LjLwell i'd hope it's not mandatory at home :P02:50
LjL(how could that be enforced even if it were?)02:50
TimvdeLjL: I mean, when people come over02:50
LjLwell it's unenforceable anyway, so in practice it's just a recommendation02:50
LjLsome people will still be worried and wear masks, and others won't02:50
TimvdeWe may invite up to 8 people at home at the same time starting from Sunday02:51
de-factoi hoped they would have more effective translation from mRNA to s-protein (more times translated, hence more s-protein molecules per one mRNA molecule) but obviously that did not compensate for their 12µg enough02:51
LjLand mostly it will be the same people as before02:51
Win7ineda-facto are you active in the reserach field?02:51
LjLTimvde, when they removed the mask mandate here last summer, i didn't really see a change in the amount of people who were wearing a mask02:51
TimvdeI think many people do try to follow the recommendation02:51
de-factoWin7ine, nope02:51
TimvdeI must say that I saw about 80% still wearing a mask today02:51
TimvdeNot sure if that's because they're still being careful, or just don't know that the mandate was removed today02:51
Timvde(I'm in the first group, just being careful)02:52
LjLyou'll see the new few days, but my guess is that you'll only see a moderate reduction02:52
de-factobtw a legitimate question to ask could be: with mRNA if booster got more side effects than primer, what is the actual cause of those increased side effects? would that increase even more with every shot of the same platform? would that also occur with protein based vaccine platforms ?02:52
LjLanyway good lord can we please have a winter not like last winter or the spring before that one02:52
Win7inede-facto so how abaout the particulars you pick, is it regurgiating publication or self reflected?02:53
Timvdede-facto: I think that's still to be investigated02:53
LjLde-facto, those questions were raised in the italian article i linked a few days ago, you saw that?02:53
de-factoyes02:53
LjLTimvde, maybe you'd like to read this too, it's just a newspaper article but written by two presumed experts, it's an automatic translation but it's fairly understandable https://paste.ee/r/qu8h3/002:54
de-factoWin7ine, about CureVac? partly what i read in some articles (non-nucleoside modified mRNA, other promoter sequences etc), partly my thoughts (why would they not have gone the safe path and saturated their dose on the metric of side effects, when they would have to assume the virus will optimize?)02:55
LjLde-facto, i can see another reason for hoping a small dose will work: production capability02:55
LjLi assume CureVac's company isn't huge02:55
TimvdeLjL: is that the same paste you sent earlier?02:55
TimvdeBecause I read that already02:56
LjLTimvde, i did send it earlier, yeah, wasn't sure if you'd seen that one, i remember nixonix saw it02:56
LjLi have some memory issues02:56
TimvdeI may have nto confirmed that I've read it02:57
LjLwell no issue anyway, i just quickly grep'd it back02:57
de-factoTimvde, i mean they surely thought about that when designing their vaccination platforms as they were advertising their fast update capabilities, so hopefully they tried to avoid including immunogenic epitope in either their LNP surfaces or their disassembly molecules and pathways (when those get trashed)02:57
Timvdede-facto: I fear tat you are getting to technical for me to really follow what you are saying02:58
Timvde(sorry for the typos, I'm getting kinda tired and I'm typing from an awkward position in bed, not a great combination :p)02:59
de-factowhat i mean that i guess they have thought about how to avoid that the immune system reacts to the lipid nano particles that encapsulate the mRNA (to protect it against ribonuclease destruction and transport it into the cells)03:00
LjLTimvde, we all just nod and pretend to understand when he gets maths-y03:00
LjLexcept nixonix i guess03:00
LjLalthough i guess it's not mathsy in this case03:00
de-factoif they achieved that though, i guess we will see after more shots with the same platform03:00
LjLi'm just kidding03:00
LjLde-facto, is it possible they just didn't have access to the modRNA patent, and hoped it would just work anyway?03:01
Timvdede-facto: but given the stronger reactions on the seconde dose, did they succeed?03:01
TimvdeOh03:03
TimvdeYou said the same thing already :D03:03
de-factoit would have been a good experiment to encode a different vaccine antigen in the mRNA each time (to avoid adjuvant effect from the same antigen for the LNPs) and try to employ some metric for side effects with series of injections to see if some reactogenicity would build up against the platform itself (the common denominator between those different encoded antigens then)03:03
Timvdede-facto: "a different vaccine antigen" = getting your immune system to attack the virus in a different way?03:03
LjLde-facto, do you mean encoding something other than the S-protein?03:04
de-factoTimvde, if the stronger reactions after the 2nd dose is against the s-protein itself, yes they succeeded then, but what if it also would be against the lipid nano particles? or against the pseudo-uridine?03:04
LjLi think the S-protein is targeted because it's very likely that antibodies against it will be neutralizing antibodies...03:04
de-factoor other parts of the platform itself rather than the s-protein?03:05
de-factoi mean do we know the exact origin of the (increased booster) reactogenicity yet? i doubt we do know that yet03:05
* de-facto has to go to sleep, has to got up in 6 hours again03:07
TimvdeI should go to sleep too, but mostly in order not to mess up my biorhythm too much :)03:07
TimvdeBtw, we did have 12 deaths in a nursing home after an outbreak last week. All of them were fully vaccinated.03:12
Timvde(I *think* with the Pfizer vaccine, but I'm not 100% sure)03:13
Win7ineTimvde what is your location03:15
TimvdeBelgium03:15
de-factojust had another idea for increased reactogenicity, maybe killer cells go berserk about the s-protein producing cells after booster (and update) shots much faster, hence they release the cellular interior into the plasma at much higher rates thereby producing higher concentrations of s-protein, mRNA, pseudo-uridine, lipids etc that cause reactogenicity03:16
de-factojust a crazy speculation though03:16
Win7ineTimvde do you know what strain caused death?03:16
Timvdede-facto: and again speculation that is above my level of understanding :)03:16
TimvdeWin7ine: Do you mean which variant it was?03:16
Win7ineyep03:17
TimvdeThe article mentions both the Alfa and Delta variants, but points more specifically to the Delta variant as being dangerous, so I'd think that at least the majority of them was Delta03:18
TimvdeIt doesn't mention any numbers though03:18
TimvdeThere were about 60 infections in total, so 12 deaths is already 20%... That's incredibly high, and even crazier considering the vaccination03:20
de-factoi think its pretty clear now that we cant rely on vaccinations "to end" the pandemic, as i was saying a year ago already incidence must be brought down with NPIs, vaccinations help us with keeping it under control at low rates then03:20
Win7ineTimvde somehow not surprising if a the variant Delta, ther is now also a Delta PLUS identified and 1 in 10 hospitalisations 2 weeks ago were fully vaccinated individuals with DELTA03:21
de-factobtw was was that delta plus thingy?03:22
de-factodelta with some more mutations included? which ones woudl that be?03:22
Win7ineTimvde the olnly way vaccine can work is if it is deployed synchronized around the globe or no peoples movement is taking place. As long as there are infections ther will be new variants that circumvent immune response03:23
de-factomaybe delta could improve on vaccine evasion with aquiring some immune escape capabilities in addition to its fitness advantages?03:24
de-facto(hopefully not, but potentially I guess it could do that)03:24
Win7ineIt has03:24
TimvdeWin7ine: Not necessarily. We see that the current vaccines work great against most of the variants, it's only Delta that is troublesome03:25
Win7ineNow we have Delta Plus as well03:25
Timvdede-facto: https://edition.cnn.com/2021/06/25/health/delta-plus-variant-explainer-intl-hnk-scn/index.html03:25
de-factosuch a mutant would be selected in a population where vaccine breakthrough is a significant part of incidence03:25
LjLTimvde, the South African variant is pretty damned troublesome vaccine-wise, the only good thing about it is it hasn't seemed to thrive in Europe, perhaps because by the time it got here, the UK variant was there and more infectious than it, so it prevailed03:25
TimvdeAll variants carry clusters of mutations. Delta Plus has an extra mutation called K417N, which distinguishes it from the regular Delta variant. This mutation affects the spike protein, the part of the virus that attaches to the cells it infects. [...] "The mutation may contribute to immune escape, though its impact on transmissibility is not clear-cut," he added.03:26
LjLTimvde, AZ has about zero efficacy on the South African variant, although it may still have some efficacy in preventing hospitalizations and deaths (but it's not really known)03:26
TimvdeLjL: True, AZ has been pretty bad against it. I'm actually not sure about the other vaccines, I thought the mRNA vaccines were still good enough.03:27
TimvdeBut the "Delta Plus" is apparently a very similar mutation to the Beta variant, so that sounds kinda dangerous03:27
Win7ineAfter Delta comes Epsilon and Zeta/ETA  ...03:28
LjLTimvde, the mRNA vaccines, in vitro, are about 10 to 12 times less effective at killing the virus. how that translates to actual immunity for people i'm not sure, i *think* they're still somewhat efficacious03:28
LjL(i mean with the SA variant)03:28
de-facto"Delta Plus has an extra mutation called K417N, which distinguishes it from the regular Delta variant. "03:28
TimvdeLjL: What is actually the reason that other variants die out when a more transmittable variant arises?03:28
TimvdeI would think that the virus doesn't really care about what else is circulating, it just keeps on reproducing...03:29
de-facto.title https://covariants.org/variants/S.K41703:29
Brainstormde-facto: From covariants.org: CoVariants03:30
LjLTimvde, i'm not entirely sure... if the new variant actually saturated the population, then you could explain it: there's just not enough people to infect anymore. but when we're still at 20% prevalence in the *worst* places (like here), i'm not really sure. but maybe there is a natural tendency for people to take more drastic measures (whether or not the government tells them to) when it becomes clear there is a worse threat... i think that's also a possible03:30
LjLexplanation to the way the Indian peak rose at a crazy speed, but then also went down at a similar speed03:30
Win7ineTHere were reporte sof the P2 brazilian V at some point and that it ejected the spike protein all together some time ago, never read of it again.03:30
LjLand if you take measures drastic enough to *somewhat* keep the worst variant at bay, then the less infectious variants will die out03:30
LjLjust like the flu didn't happen this year03:31
TimvdeLjL: it is also not clear that being infected by one variant makes you immune to other variants, so even with higher prevalence, that reasoning doesn't fully work03:31
de-factohmm so potentially more immune escape but less efficient ACE2 binding, may be a trade off for the virus that may improve overall reproduction in a vaccinated population, but maybe not so much in a immuno-naive population03:31
LjLTimvde, that definitely depends on the variants involved03:31
Win7ineLjL the flu probably did not happen because of social distancing measures03:32
TimvdeYes, of course.03:32
LjLTimvde, but anyway i've seen saying for a while that i don't think the way spikes "go down" can be fully explained by our half-assed lockdowns. i'm not really sure what is going on.03:32
de-factoi guess we will see the dynamics of that B.1.617.2.1 or AY.1 "Delta Plus"03:32
LjLTimvde, sometimes spikes have gone down slowly, but the worst spikes have gone down about as quickly as they went up. and that is a bit peculiar03:33
TimvdeLjL: according to the conspiracy theorists here, it's because of one of our virologists :) Apparently he has the power to manipulate numbers world-wide, or something03:34
Win7ineHaha03:35
LjLTimvde, well some people in mediterranean countries do say that the numbers somewhat magically go down when the government wants to open the tourism season :P and as much of a joke that sounds, i *know* that some regions in italy have tampered with the numbers for similar reasons03:36
TimvdeLjL: tampering is bad :( But if there was any, I'd expect it to happen in the other direction: make it seem less bad in order to open up more quickly03:37
LjLTimvde, well, yeah, that's what they've done. consider that a study was posted here yesterday indicating a moderate-to-high seasonality effect (less transmission in the summer). i'm sure most of it is a real effect, but eh, i've also seen spikes happen in the middle of the summer, like in Arizona...03:38
LjLthis particular study was only on European countries03:38
BrainstormUpdates for Zimbabwe: +911 cases (now 45217), +12 deaths (now 1721) since 22 hours ago — Bermuda: +6 cases (now 2510) since 7 days ago03:39
TimvdeLjL: yes, we had a really good summer last year, but the cases already started to rise mid-August when the weather still was really good03:40
TimvdeI expect there to be a low seasonal effect at best03:40
LjLTimvde, this study placed the low peak at the start of July, so August would already be starting to get worse03:42
TimvdeYes, but what is causing a seasonal effect if not the weather?03:42
LjLTimvde, https://www.medrxiv.org/content/10.1101/2021.06.10.21258647v1.full03:43
LjLTimvde, the weather with maybe some added "ignoring the real numbers and not testing people" to get better tourism? :P03:43
LjLanyway, i'm concerned that we'll feel like "it's gone" again, just like last summer, except this time we attribute it to the vaccines, but then it'll hit us like a hurricane again in the fall03:44
LjLwhile we are utterly unprepared because we're assuming the vaccine will prevent further bad spikes like last winter03:44
Win7ineLjL did you have any Jab yet?03:45
LjLWin7ine, yes, one Pfizer03:45
LjLsecond will be on 8 July03:45
TimvdeLjL: we do have graphs about the positivity rate, and it was also a lot lower during July03:46
LjLit was supposed to be on 10 July but i could move it03:46
TimvdeLjL: How many weeks are there in between two shots?03:46
LjLTimvde, true, i'm not saying the "frauds" are a significant contributor, but i'm still scared that the seasonality effect will make us, again, overconfident, just like last summer03:46
TimvdeIt seems to be different in each country...03:46
LjLTimvde, in Italy, it's 12 weeks for AZ, and between 21 and 48 days for Pfizer03:47
LjLi think Moderna is the same as Pfizer but not sure, and then J&J of course is just one shot, but it's mainly used on people who had COVID previously03:47
TimvdeHere, AZ has been recently shortened from 12 to 8 weeks, Pfizer is 5 weeks, Moderna is 4 weeks03:47
Win7ineModera is mRNA but not the same as BionTech/Pfizer03:48
TimvdeWin7ine: that's not what he meant03:48
TimvdeHe meant "the time in between vaccines is probably the same as for Pfizer"03:49
Win7ineALso has slightly different side effects03:49
Win7ineOk03:49
TimvdeDefinitely going to bed now though03:54
Timvdegn!03:54
Win7ineHave good rest, bye03:57
BrainstormUpdates for Channel Islands: +68 cases (now 4218) since 2 days ago04:04
BrainstormNew from r/WorldNews: worldnews: Covid-19 Patients Who Experience Loss Of Smell Could Take Up To One Year To Recover: Study → https://is.gd/SlVyXr04:31
BrainstormUpdates for Thailand: +4161 cases (now 240452), +51 deaths (now 1870) since 23 hours ago — United Kingdom: +15649 cases (now 4.7 million), +19 deaths (now 128194) since 23 hours ago — France: +28 deaths (now 110992) since 23 hours ago — Netherlands: +506 cases (now 1.7 million), +4 deaths (now 17877) since 23 hours ago04:41
BrainstormNew from r/WorldNews: worldnews: Indonesia doctors fell sick, many died after taking Chinese-made Sinovac vaccine → https://is.gd/AdTR8K04:41
LjLasking again although now everyone's asleep... anyone has a study handy on AZ+Pfizer being more effective than either AZ+AZ or Pfizer+Pfizer?05:17
BrainstormNew from The Indian Express: World: US FDA adds warning about rare heart inflammation to Pfizer, Moderna Covid vaccines → https://is.gd/DTFL5v05:33
BrainstormNew from The Indian Express (Health): Health: Foods that will help maximise the effect of Covid-19 vaccine → https://is.gd/OjZACG05:43
BrainstormUpdates for Belgium: +568 cases (now 1.1 million), +8 deaths (now 25160) since 23 hours ago06:08
BrainstormNew from This Week In Virology: TWiV 772: COVID-19 clinical update #68 with Dr. Daniel Griffin: In COVID-19 clinical update #68, Daniel Griffin discusses children acquiring infection at birthday parties, immunogenicity of vaccines in solid organ transplant patients, reinfection rates in recovered patients, lack of efficacy of azithromycin, bacterial [... want %more?] → https://is.gd/ooJPLU06:14
BrainstormNew from The Indian Express: World: Just give us the vaccines, WHO pleads, as poor countries go wanting → https://is.gd/2N2fH406:25
BrainstormUpdates for Honduras: +1531 cases (now 258349), +23 deaths (now 6902) since a day ago06:33
BrainstormNew from The Indian Express: World: Delta the ‘most transmissible’ of variants, spreading rapidly among unvaccinated populations: WHO chief → https://is.gd/6BwFAM06:56
BrainstormNew from The Indian Express: World: Sydney’s COVID-19 cases grow, more restrictions loom → https://is.gd/3FOqdG07:27
BrainstormUpdates for Moscow Oblast, Russia: +2436 cases (now 301291), +19 deaths (now 6419) since a day ago — Mexico City, Mexico: +1500 cases (now 678996), +43 deaths (now 34607) since a day ago — Saint Petersburg, Russia: +1194 cases (now 462895), +98 deaths (now 15793) since a day ago — C. Valenciana, Spain: +821 cases (now 399794) since a day ago07:35
BrainstormNew from BBC Health: Covid-19: 'Grab a jab' for all over-18s opens in England: Any adult will be able to get a vaccine without an appointment this weekend at hundreds of walk-in sites. → https://is.gd/d5BIWE08:09
BrainstormUpdates for India: +48698 cases (now 30.2 million), +1176 deaths (now 394109) since 15 hours ago08:37
BrainstormNew from The Indian Express: World: Brazilian lawmaker denouncing vaccine deal wears bullet-proof vest to hearing → https://is.gd/XsVz0t09:00
BrainstormNew from r/Coronavirus: Daily Discussion Thread | June 26, 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/bkQNit09:11
BrainstormUpdates for Uzbekistan: +546 cases (now 108730), +2 deaths (now 727) since a day ago — Germany: +442 cases (now 3.7 million) since 22 hours ago09:39
TimvdeLjL: https://www.medrxiv.org/content/10.1101/2021.06.13.21258859v110:07
TimvdeIt's still a preprint though10:08
TimvdeBut afaik that's the original source10:09
TimvdeHere's the accompanying press release (it links to the article): https://www.uni-saarland.de/fileadmin/upload/aktuell/pdf/2021/PM_111a_Impfstoffvergleich_Sester.pdf10:10
BrainstormNew from r/WorldNews: worldnews: Just give us the vaccines, WHO pleads, as poor countries go wanting → https://is.gd/nEozmF10:22
BrainstormNew from The Indian Express: World: UK PM Boris Johnson stands by health secretary who broke Covid rules kissing aide → https://is.gd/NBJ7X810:43
BrainstormUpdates for Russia: +21665 cases (now 5.4 million), +619 deaths (now 132683) since 23 hours ago11:06
de-facto.title https://www.researchsquare.com/article/rs-634590/v1 <-- i wonder if that is what was happening in India11:25
Brainstormde-facto: From www.researchsquare.com: Overuse of Steroid Drugs Methylprednisolone and Dexamethasone (Oral) Causes a Diabetic Patient to Become Infected with the Black Fungus in the Corona Virus. | Research Square11:26
de-factoat least in some of their cases11:26
zutt%cases sweden12:51
Brainstormzutt: In Sweden, there have been 1.1 million confirmed cases (10.5% of the population) and 14619 deaths (1.3% of cases) as of a day ago. 10.6 million tests were performed (10.3% positive). Fatality can be broadly expected to lie between 1.4% (assuming prevalence as in tests) and less than 1.4% (considering only deaths and recoveries). See https://offloop.net/covid19/?default=Sweden for time series data.12:51
zutt%cases finland12:51
Brainstormzutt: In Finland, there have been 94719 confirmed cases (1.7% of the population) and 969 deaths (1.0% of cases) as of a day ago. 5.4 million tests were performed (1.8% positive). Fatality can be broadly expected to lie between 1.0% (assuming prevalence as in tests) and less than 2.1% (considering only deaths and recoveries). See https://offloop.net/covid19/?default=Finland for time series data.12:51
BrainstormUpdates for UAE: +2282 cases (now 624814), +10 deaths (now 1792) since 21 hours ago13:10
BrainstormNew from r/WorldNews: worldnews: Brazil sets single-day record for coronavirus cases → https://is.gd/SFDKOm13:19
BrainstormNew from Gazzetta Ufficiale italiana: MINISTERO DELLA SALUTE - ORDINANZA 25 giugno 2021: Ulteriori misure  urgenti  in  materia  di  contenimento  e  gestionedell'emergenza  epidemiologica  da  COVID-19  nella   Regione   Valled'Aosta. (21A03927) → https://is.gd/qv4wUY13:29
BrainstormUpdates for Indonesia: +21095 cases (now 2.1 million), +358 deaths (now 56729) since a day ago — Romania: +62 cases (now 1.1 million), +309 deaths (now 33177) since 23 hours ago — Canada: +22 deaths (now 26197) since 16 hours ago — Germany: +433 cases (now 3.7 million) since 23 hours ago14:00
BrainstormUpdates for Brunei: +3 cases (now 259) since 3 days ago14:37
LjLthanks Timvde, i want to try to convince my parents to get an antibody test and in case it's low, they might be able to get Pfizer instead of another AZ14:48
BrainstormNew from r/WorldNews: worldnews: Australia's largest city enters hard two-week Covid-19 lockdown → https://is.gd/NxwHxb15:23
TimvdeLjL: can you do that?15:28
TimvdeI don't think we have an actual choice15:28
BrainstormUpdates for Nepal: +1174 cases (now 632326), +30 deaths (now 8975) since 22 hours ago15:40
BrainstormNew from The Indian Express (Health): Health: COVID vaccine for pregnant women: What you need to know before the jab → https://is.gd/7cFMpO15:44
BrainstormUpdates for Finland: +270 cases (now 94989) since 2 days ago16:04
de-factohmm hmm do we have *any* data about reduction of transmission likelihood by vaccinations?16:46
BrainstormNew from r/WorldNews: worldnews: Sri Lanka zoo lion contracts COVID-19 as reports of animal infections rise → https://is.gd/ashGOH16:46
de-factoi need this for a model16:46
BrainstormNew from Reddit (test): Saturday 26 June 2021 Update: submitted by /u/HippolasCage to r/CoronavirusUK → https://is.gd/p6OHzi17:27
BrainstormUpdates for Bangladesh: +4334 cases (now 883138), +77 deaths (now 14053) since a day ago17:31
xrogaanSo, Peter Daszak was forced to step down from the investigation team?17:47
xrogaan%title https://www.dailymail.co.uk/news/article-9710875/Peter-Daszak-removed-COVID-commission-following-bombshell-conflict-report.html17:48
Brainstormxrogaan: From www.dailymail.co.uk: Peter Daszak removed from UN commission investigating COVID after being exposed for Lancet letter | Daily Mail Online17:48
BrainstormNew from r/WorldNews: worldnews: COVID-19: UK reports 18,270 new coronavirus cases - the highest since 5 February → https://is.gd/U10lmQ18:09
BrainstormUpdates for United Kingdom: +17668 cases (now 4.7 million) since 22 hours ago18:09
BrainstormNew from The Indian Express (Health): Health: Covid-19 pandemic leads to 80% drop in routine cancer screening, limits research → https://is.gd/sDuSdP18:19
BrainstormNew from r/WorldNews: worldnews: Tens of thousands of anti-lockdown protesters march on London in biggest demo yet → https://is.gd/bDmzY918:40
BrainstormNew from Shane Crotty: @profshanecrotty: Of the more than 18,000 COVID-19 deaths in May in America, only about 150 were fully vaccinated people. 150! I.e., less than 1% of the COVID-19 fatalities were in vaccinated people.Vaccines [... want %more?] → https://is.gd/mpST5U18:51
BrainstormNew from Reddit (test): nCoV: Delta Variant Forces New Lockdowns As Europe Lifts Covid Restrictions | 26JUN21 → https://is.gd/ruYBF019:12
Krey[m]LjL: bcs the repo is pain to navigate in~19:20
BrainstormUpdates for Italy: +838 cases (now 4.3 million), +40 deaths (now 127458) since 22 hours ago19:30
BrainstormNew from r/WorldNews: worldnews: WHO urges fully vaccinated people to continue to wear masks as delta Covid variant spreads → https://is.gd/DsQeXW19:33
BrainstormNew from BBC Health: (news): Hancock quits as health secretary after breaching Covid guidance → https://is.gd/oM7ybF19:54
BrainstormNew from The Indian Express: World: UK Health Secretary Matt Hancock resigns after Covid breach → https://is.gd/TYCeJn20:14
LjLKrey[m], well it's a pain for me as well, it's not like i know all the things in it or i wouldn't need it in the first place. if you have a better idea on how to arrange it, suggestions are welcome20:37
Krey[m]hmmm~20:38
de-factoits a really neat collection of the finest resources collected and refined for more than a year now though21:20
operationalhey so i got pfizer for my first dose but if i go to the same place for my 2nd i'll be getting moderna. is this ok? good, bad?21:31
BrainstormNew from Derek Lowe: @Dereklowe: R to @Dereklowe: And if we had a real ADE problem, you could expect proportionally *more* deaths among the vaccinated, because ADE makes subsequent infections worse - the “enhancement” part. (3/5) → https://is.gd/Uu9tOU21:38
de-factooperational, its not known by trial results, but i *guess* it will be just fine, because the immune system builds immunity against the spike protein blooming form the cells where the vaccine gave the instruction for its production and that is exactly the same version of s-protein for both Pfizer and MOderna21:47
de-factoin doubt ask your MD about that21:47
ArsaneritTomorrow morning I get my second dose with Comirnaty®22:05
de-factonice, got something important the day after tomorrow? :D22:09
de-factowell then you are just in time before the raise of delta to be fully immunized22:10
de-factothat good22:10
LjLwho does Pfizer+Moderna? O.o22:15
LjLat least there is a *reason* to do AZ+Pfizer, be it good or bad22:15
LjLbut Pfizer+Moderna, while probably fine, sounds just silly22:16
de-factoi would try to stick to something that will later be "supported" as with the existence of trial results so expectation values can be given etc22:19
LjLde-facto, i made a bit of a scene with my parents because they just wouldn't listen, although now i am unsure whether it's a good idea anyway - they booked an S-protein RBD IgG antibody test (supposedly quite specific for vaccine-elicited antibodies, €35) so that if they turn out to have few antibodies, they can show it and hopefully get Pfizer as second shot instead of another AZ22:19
LjLbut now i wonder 1) what if Pfizer makes them feel quite bad, especially my mom who's always feeling sick anyway, and 2) will the place where they get the antibody test be a needless COVID risk too22:19
LjL(the scene was because i've been saying this for days and of course the slots for these tests are now limited and the vaccine is shortly)22:20
de-factohmm i am not sure such results are "normalized" as in comparable, do they provide comparison values for their analytic pipeline for both Pfizer and AZ?22:21
de-factoalso they can just pick out "one" type of antibody, the one that binds to their artificial antigen22:21
de-factoso they only can measure exactly the one that they "ask for"22:22
de-factothey dont know about how "broad" the antibody spectrum is and how well it would bind to another antigen (if they dont have it in their assay)22:22
de-factoalso i am not sure if its already established how well such results actually correlate with neutralization assays with live pathogen in cell cultures22:23
de-factodo we have papers about that?22:23
Arsaneritde-facto: the day after tomorrow... just a working day22:27
de-factoLjL, but for sure if ELISA was negative it would mean vaccination did not work, if above a certain level (which one for that specific analytic pipeline though?) it may indicate there should (potentially?) be a certain level of immunity associated with that22:28
de-factoArsanerit, i am curious to hear from people about their second injection experiences, so far i have heard the full spectrum from no side effects to flu like symptoms for a day22:29
Arsaneritde-facto: ok, I'll let you know, assuming I survive to come back to IRC ;)22:30
de-factoall ended up to just be fine though, yet i wonder on what it depends22:30
de-factoyeah probably the majority of people dont have much side effects and we only hear from the ones that experienced some side effects because then they have something to report22:31
de-factohence i always ask people about that22:31
ArsaneritI had mild side effects after the first dose22:31
de-factoyeah thats for most it seems22:31
de-factolike a bit of sore arm and fatigue for primer22:32
Arsanerityes22:41
ArsaneritI was a bit dizzy too.22:41
LjLde-facto, it's not specific to any vaccine. it will give a value with a scale and points that say "below this it's probably too low". i realize it's far from perfect, but really it's just a way to try to obtain Pfizer as a second dose... which i'm a bit conflicted about (i know the studies aren't big), but i don't want to spend another winter scared that they get COVID22:45
LjLif AZ+Pfizer really gives the highest immunity i just find it attractive for my parents22:45
LjLi hope my judgment isn't biased too much by... now wanting to be scared another winter22:46
BrainstormNew from r/WorldNews: worldnews: Scientists at Wuhan lab admit being bitten by bats in cave which is home to Covid-infected bats → https://is.gd/ck1OZR22:46
de-factoLjL,  i hear you, i am also worried about my parents in their 70s, but when being honest we both know there will be no 100% protection especially not for them as being elderly, ofc one would desire the best possible protection for them22:47
de-factoi guess we also could look at UK hospital data for such questions22:48
LjLde-facto, well, i don't know the details of the data (and the person who knows doesn't like to give me URLs but only tweets with pictures of graphs), but in general, 1/3 of the deaths in the UK are currently among vaccinated people, and 50% of new cases in Israel are among vaccinated people22:49
LjLi know, ages, biases, etc22:49
LjLbut still22:49
de-factothe important thing is that they get their second shot prior to delta rise22:49
LjLde-facto, unfortunately my dad moved it from june 29 to july 3, maybe that wasn't the best idea, but he wanted to get it at a place closer to home22:50
LjLnow my parents both have it on july 322:50
LjL(and i have it on july 8)22:50
de-factoyeah thats fine22:50
LjLi think it will be just around delta becoming dominant according to your calculations22:50
LjLwell, your calculations were for germany, i just assume they mostly apply22:50
de-factowell dominant but with low incidence22:50
LjLi heard delta is 17% here now (just from tv, so i don't know if it's just the unadjusted sequencing ratio, probably is)22:51
de-factoi want to integrate seasonality and vaccinations22:51
LjLyes, right22:51
LjLde-facto, seasonality + vaccinations + NPI = zero covid22:51
LjLbut instead, we'll be doing the opposite of the NPI part ;(22:51
de-factoseasonality with sinus (from that paper with 42.1% amplitude factor) and vaccinations i thought i would just employ a logistic function for that22:51
de-factofor Germany  i wanted to assume vaccinations(t) = 0.835/(1 + 359 Exp[-t/32.3434]);22:52
de-factojust because 16.5% of population would be below 18 (hence 1-0.165 = 0.835 saturation point)22:52
LjLalthough to be fair, say all you want about masks, but with ~30°C or even less, it DRIPS inside the mask, it's pretty awful22:52
de-factoand from eyeballing on OWID those vaccination curves look to me like logistic functions, S-shape gaining some initial speed, then having a linear part and going into saturation at some point when most demand is satisfied22:54
de-factoso in an "ideal world" everyone would get their shot, except those young ( i took 18 years old because i did not find any demographics for younger)22:55
de-factoLjL,  do we have any estimated on the likelihood for a fully vaccinated to *transmit* delta (compared to someone not vaccinated) in the same environment?22:58
LjLde-facto, do we even have that for Alpha? :P23:00
LjLi think i still don't have a paper to shove in the face of people who say "vaccine only stops symptoms, not transmission"23:00
LjLit's pretty obvious it also helps lower transmission, but it's hard to measure23:01
LjLwell actually i think there was some Scottish paper perhaps about lowered transmission in households23:01
BrainstormUpdates for India: +48858 cases (now 30.2 million), +1218 deaths (now 394528) since 21 hours ago23:01
de-factoprotection from symptomatic infection with delta is ~88% with BNT but i assume transmission including asymptomatic events would therefore have to be <88% then23:01
LjLbut definitely just about the UK variant, well before Delta23:01
LjLde-facto, maybe, not necessarily. but i just don't know23:01
de-factooh yeah you are right there was something about secondary attack rates in households23:02
de-factobut it was after 1st shot only afaik23:02
LjLdunno about that, but it was definitely not about Delta23:02
de-factogood remark i almost forgot about those, we would need a study about Delta with fully vaccinated on secondary attack rates in households23:03
de-facto.title https://www.nejm.org/doi/full/10.1056/NEJMc210771723:09
Brainstormde-facto: From www.nejm.org: Effect of Vaccination on Household Transmission of SARS-CoV-2 in England | NEJM23:09
de-facto"Overall, the likelihood of household transmission was approximately 40 to 50% lower in households of index patients who had been vaccinated 21 days or more before testing positive than in households of unvaccinated index patients; the findings were similar for the two vaccines. Most of the vaccinated index patients in our data set (93%) had received only the first dose of vaccine."23:11
de-factoso hmm ~50% for both BNT and AZ against B.1.1.7 afer primer23:12
de-factoso second shot would increase that protection > 50% for B.1.1.7 but then comes B.1.617.2 and puts it down again, where would it land though?23:15
BrainstormNew from Shane Crotty: @DrPatSoonShiong: RT by @profshanecrotty: The role of NK cells in Covid is key to recovery . NK and T cells matter #SARSCoV2 https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(21)00251-6/fulltext → https://is.gd/H1yUqm23:27
de-factohah23:29
LjLde-facto, i think 50% is also about the protection you get from symptomatic disease with one dose on Pfizer23:56
LjLso maybe whatever the efficacy number is for two doses, that's also the reduction in household transmission?23:57
LjL(bit of a stretched guess)23:57
de-factohmm is that Delta?23:57
de-factohmm above study also is ALpha though23:59
de-facto"Between January 4 and February 28, 2021, there were 960,765 household contacts of unvaccinated index patients, and there were 96,898 secondary cases of Covid-19 (10.1%). "23:59

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