libera/##covid-19/ Monday, 2021-06-14

de-facto	so yeah indeed blasting it against hCoV-19/Wuhan/WIV04/2019 shows point mutations K986P and V987P aka the 2-proline prefusion stabilizing ones	00:01
de-facto	(btw that website is extremely cool it can generate a 3d view of the s-protein out of the sequence)	00:01
de-facto	LjL, maybe you could add that one to the %links	00:05
de-facto	%links mendel3	00:05
Brainstorm	de-facto, Sorry, nothing found. Try with broader keywords	00:05
de-facto	GISAID is using that tool to display the most frequent mutations at https://www.gisaid.org/hcov19-mutation-dashboard/	00:09
nixonix	anti-vaxer stuff seems to be on rise here. just when younger age groups, down to 16 at some areas, should go having their first shot	00:09
nixonix	with 12 weeks interval the the first dose percentage is high here	00:09
nixonix	check your twitters etc about vaccinations, the same stuff likely there	00:10
nixonix	so i recommend reading that derek lowe post about ivermectin and the comments too, for material to counter them	00:11
nixonix	unless ofc you are pro ivermectin for all instead of vaccine...	00:11
de-facto	indeed yeah vaccination should progress faster, also more evenly and synchronized opposed to how it currently is progressing worldwide https://ourworldindata.org/covid-vaccinations	00:13
nixonix	btw at least in that wiki article they dont have much 617.2 findings yet, but sequencing results may come several weeks late, and then they might not send them to gisaid and pangolin db	00:13
nixonix	we have a lot more than whats there. it says 0 in pangolin, date june 12th, and 1 in gisaid that is couple weeks old	00:14
de-facto	weah but what worries me is that i did not see a country where that VoC was introduced and then fizzled away, it seems to be on the rise once introduced regardless of the country	00:14
de-facto	B.1.617.2 i mean	00:15
nixonix	we used to have 15-20% s-gene positive, prob mostly south afican variant, then it jumped to 35% in two weeks. prob due to indian variant	00:15
LjL	de-facto, hm, that's a bit too specialist i think. i want links where regular people can at least understand my explanation of what the link is and why the information it has can be interesting. this is... i wouldn't know myself how to describe it in the list or where to place it	00:15
LjL	de-facto, can you write an explanation that fits similarly as the other ones in the list?	00:16
de-facto	ok its just a very handy tool for quickly pasting a sequence into and BLASTing it against the reference to see the mutations involved	00:16
de-facto	hmm let me see	00:16
LjL	when i added Sanger, by the way, i realized i'm not sure whether Sanger, Nextstrain, and all that should be under Genetics, or under Epidemiology. they are about virus variants but also about how the epidemic is changing in different places due to the variants	00:17
LjL	i'd be more motivated to moving everything to Zotero if it weren't, i guess, that Zotero is mainly for papers, but the list includes a lot of things that are not papers	00:18
LjL	but at least i could just tag them with things	00:18
nixonix	so if you can find information of the share of s-gene positive pcr tests (not having the deletions, so they are likely kent variant), and how those have increased, that will likely tell how 617.2 has spreaded	00:18
de-facto	id guess this link is genetics since its about sequence data, also nextstrain it is more genetics with a label attacked that localizes it on space and time	00:19
nixonix	* sorry, s-gene negatives are likely kent uk variant	00:20
nixonix	and the positive ones can be eg south-african, brazilian etc, but they dont spread as fast as the kent probably. a sudden increase of s-gene positive is then likely 617.2	00:21
Brainstorm	New from r/WorldNews: worldnews: Brazil reports 1,129 new COVID-19 deaths, nearly 40,000 cases → https://is.gd/NAB4Sa	00:23
nixonix	indo are you around?	00:24
nixonix	.seen palasso	00:24
Brainstorm	nixonix: I don't remember seeing palasso.	00:24
nixonix	who else did i know. the list looks like strangers to me...	00:25
nixonix	.seen yuri	00:25
Brainstorm	nixonix: I don't remember seeing yuri.	00:25
nixonix	.seen yuriwho	00:25
Brainstorm	nixonix: I last saw yuriwho at 2021-05-03 19:58:20 (41 days, 2:27:26 ago).	00:25
Brainstorm	Updates for Turks and Caicos: +2 cases (now 2423) since 4 days ago	00:29
de-facto	<a href="https://mendel3.bii.a-star.edu.sg/METHODS/corona/gamma/">CoVsurver - CoronaVirus Surveillance Server</a> provides a 3D structural visualization and lists variations for comparing a given protein or nucleotide sequences in FASTA format with appropriate reference sequences. <a href="https://www.gisaid.org/hcov19-mutation-dashboard/">hCoV-19 Spike Glycoprotein Mutation Surveillance Dashboard</a> summarizes the newest mutations submitted to the	00:33
de-facto	GISAID database.	00:33
de-facto	LjL, do you think something like that is readable?	00:33
LjL	nixonix, palasso is on freenode	00:34
LjL	yuriwho hasn't been active in a while	00:34
LjL	(here)	00:34
LjL	anyway i'm being told i'm an idiot for connecting to freenode with my real IP, apparently it's not their fault they're making sociopaths and DDOS'ers ops, it's my fault for not buying a VPS	00:35
LjL	so just to make them happy i'll yank my router from the socket	00:35
LjL	and reconnect it when it will reasonably give me a new IP	00:35
nixonix	yeah i think i saw palasso on some tech chans there a few months back	00:35
LjL	de-facto, as to that, i suppose i can change it trivially to make it mention "COVID", but like, it doesn't really clarify how it's related to COVID :P	00:36
LjL	nixonix, i half wanted to tell him something but i'm really a bit scared of talking to the "wrong" person who actually roots for freenode and that person snitching that i'm telling them to come to Libera	00:36
LjL	because that's the climate there	00:36
nixonix	palasso wont do stuff like that	00:37
de-facto	LjL, well the first tool is about Coronaviruses (including SARS-CoV-2 causing COVID)	00:38
de-facto	the second link is only about SARS-CoV-2 spike mutations in GISAID	00:38
de-facto	CoVsurfer is developed by A*STAR Bioinformatics Institute (BII), Singapore.	00:39
LjL	nixonix, but i've missed the moment because he's gone now :(	00:41
nixonix	here twitter accounts of some healthcare officials, persons there that is, can be informative for stuff like about recent variant findings	00:41
de-facto	<a href="https://mendel3.bii.a-star.edu.sg/METHODS/corona/gamma/">CoVsurver - CoronaVirus Surveillance Server</a> provides 3D structural visualization and lists variations for comparing a given protein or nucleotide sequences in FASTA format with appropriate reference sequences of Coronaviruses (including SARS-CoV-2 causing COVID). <a href="https://www.gisaid.org/hcov19-mutation-dashboard/">hCoV-19 Spike Glycoprotein Mutation Surveillance	00:41
de-facto	Dashboard</a> summarizes the newest mutations of SARS-CoV-2 spike protein submitted to the GISAID database.	00:41
nixonix	he was on truth a few months back too, what was the network where it is now..	00:42
nixonix	rizon or the one starting with e	00:42
nixonix	efnet. i think it was on rizon tho, truth chan	00:43
de-facto	LjL, forget it i am blind	00:46
de-facto	"CoVsurver can automatically find the closest strain to compare a protein or nucleotide to among the ones currently known, and show a 3D view of it with the differences highlighted"	00:46
de-facto	you already have it in there	00:46
de-facto	arrr	00:46
LjL	oh	00:47
LjL	i didn't realize that was the same, i assumed it wasn't there when you did %links mendel3 ;(	00:47
de-facto	yeah me neither, it got another more clear url in your links	00:47
de-facto	%links CoVsurver	00:48
Brainstorm	de-facto, https://corona.bii.a-star.edu.sg/ (CoVsurver) can automatically find the closest strain to compare a protein or nucleotide to among the ones currently known, and show a 3D view of it with the differences highlighted	00:48
-RSSBot[LjLmatrix- Recent Commits to links:master: Add GISAID Mutation Dashboard ( https://github.com/ljl-covid/links/commit/6a7e4c1ab20fb7579702e929fd96b02560cfb86f )		00:53
Brainstorm	New from https://covid19.specops.network : ljl-covid: Add GISAID Mutation Dashboard → https://is.gd/bqfjdk	00:54
nixonix	i havent read much about curevac. how was its efficacy vs other mrna vaxes?	00:58
nixonix	i had read that bert's article before, but somehow i cant remember its efficacy. and against which variants	00:59
nixonix	.seen itchyjunk	00:59
Brainstorm	Updates for Canada: +13 deaths (now 25909) since 23 hours ago	01:07
de-facto	thats because they dont have finished their trials yet	01:09
nixonix	ah, ok	01:09
de-facto	they have problems accumulating enough cases because of low incidence in their target areas	01:09
de-facto	so might need to continue until August or such	01:10
de-facto	id guess their efficacy would be similar to the other ones	01:10
nixonix	i remember in early july i think, az or prob somebody from oxfords team promised she can give efficacy information in august, something like if its good enough or not. that early info never came i think, until the published results then later	01:11
de-facto	but since the other two mRNA vaccines, BioNTech and modeRNA were tested against the B.1 variant they had the luxury of not having to deal with evasive mutants, if ever any trial will come out with such fantastic numbers is with doubt	01:12
nixonix	novavax has had difficulties, something like availability of bioreactor bags, so they extended their trials	01:12
nixonix	vlp with saponin adjuvant	01:12
de-facto	yep	01:12
de-facto	LjL, router still on the wall? :D	01:13
nixonix	do they use original wuhan strain or some more modern variant for those newer vaccines then?	01:13
nixonix	or perhaps modified so it has improved efficacy for the most important ones	01:14
LjL-Matrix	de-facto: more or less. znc is hard to die so I had to recycle and get a new IP twice	01:14
LjL-Matrix	I'm still worried they have my email though	01:14
Brainstorm	New from r/WorldNews: worldnews: Thailand denies blocking exports of AstraZeneca vaccines after Taiwan says Thailand is prioritising AstraZeneca Covid-19 vaccines for itself and not sending them to Taiwan → https://is.gd/xrgxbo	01:16
de-facto	nixonix, the newer updates are against B.1.351 (SA VoC) afaik	01:17
nixonix	617.2 would be more important, it seems	01:18
de-facto	thats because it got the most evasive capabilities observed so far	01:18
nixonix	depends on study, lemme see if i find	01:18
de-facto	B.1.351 got around one order of magnitude neutralization evasion (against B.1.1.7 afaik) while B.1.617.2 may be around 5-fold or such	01:18
de-facto	yeah i think there are slightly different results	01:19
nixonix	NAbTs were 5·8-fold reduced against B.1.617.2 relative to Wild-type (95%	01:20
nixonix	CI 5·0–6·9), significantly more reduced than against B.1.1.7 (2·6-fold vs Wild-type, 95% CI 2·2–3·1), and on a similar order to the reduction observed against B.1.351 (4·9-fold vs Wild-type, 95% CI 4·2–5·7)	01:20
nixonix	damn web client sorry	01:20
nixonix	https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(21)01290-3/fulltext	01:20
de-facto	interesting	01:22
nixonix	and it doesnt help if its optimized for SA variant if its not around much longer	01:22
nixonix	when the indian one will prob be dominant soon	01:22
nixonix	unless another one will overtake it	01:23
de-facto	until...	01:23
de-facto	its only a question of time	01:23
nixonix	i though the ceiling for transmissibility of these type of viruses were lower. i guess theres no ceiling	01:23
nixonix	there was a this week in virology podcast (i didnt watch, but i heard), where some virologists thought, that because its not benegicial for viruses to become more leathal, it wont happen	01:25
de-facto	hmm what would be the determining limits for that?	01:25
nixonix	spring 2020	01:25
de-facto	i think it depends on when the transmission happens in the disease progression, if its presymptomatic it would not nessecarily be a disadvantage for viral replication to later cause severe symptoms unless it would lead to more containment for such a mutant	01:27
nixonix	D614G, we were chatting about that in may 2020 or so, i was looking some stuff what was thought about its increased infectivity, and it seemed to me if it infects cells more efficiently, it would be more lethal too	01:27
nixonix	unless at the same time something made it less lethal, so it would balance it out	01:28
de-facto	well yeah and now B.1.1.7 is 10-fold of B.1 (D614G) on cellular level	01:28
nixonix	and thats what is thought currently, really happened. the same change both made it more infective, and also made it more vulnerable to antobodies	01:28
nixonix	so the lethality didnt increase with that mutation	01:29
de-facto	the lethal property of COVID is more the late immune-run-away reaction	01:29
nixonix	you have source to that? 1.1.7 cell infectivity	01:29
de-facto	.title https://science.sciencemag.org/content/early/2021/05/24/science.abi5273 <-- Fig 3 shows roughly 1 log10 difference between B.1.1.7 and non-B.1.1.7 viral loads	01:31
Brainstorm	de-facto: From science.sciencemag.org: Estimating infectiousness throughout SARS-CoV-2 infection course \| Science	01:31
de-facto	in vivo that is	01:31
nixonix	ty, ill look at that tomorrow	01:32
nixonix	those virologists in that podcast (i was told) couldnt think one example of increased lethality with other viruses	01:36
nixonix	june 3, so might be outdated info already: "~2.5x higher risk of hospitalisations"	01:39
nixonix	https://twitter.com/dgurdasani1/status/1400523953853108226	01:39
de-facto	well hopefully transitioning from naive to non-naive immune systems in terms of having seen some variant of SARS-CoV-2 already will make it much less severe on the longterm	01:39
de-facto	yeah it will spread in schools a lot now	01:40
de-facto	just because children are not vaccinated and gather there	01:40
nixonix	you mean when it will mostly spread around immunized ppl, vaxed or natural?	01:40
nixonix	germans approved it for 12-15. finland will likely follow, despite there has been healthcare official statements lately that they might not	01:41
nixonix	but i dont believe they wont	01:41
de-facto	i think both will happen, much stricter selection of evasive and more fit variants in breakthrough cases of immunized but also less severe in the longterm because the immune system already knows the pathogen from a previous variant	01:41
de-facto	it might mean much more aggressive variants for non-vaccinated people with naive immune system though	01:42
de-facto	yeah approved BNT162b2 from 12 years, but recommended only for such with pre-existing conditions (risk groups) because we dont have enough data yet for a generic recommendation from STIKO	01:43
nixonix	seen that telomere study? preprint but looked plausible	01:43
nixonix	you were hit harder than old people, telomere shortening	01:44
nixonix	prob oxidative stress that damages chromosomes	01:44
LjL	i saw that, rather terrifying	01:44
de-facto	but is that not a thing that generally would happen with inflammation on that magnitude?	01:44
de-facto	(not sure i remember what they wrote in there)	01:45
nixonix	better have a jab than even think about that imo	01:45
de-facto	of course	01:45
nixonix	i dont think it can be common phenomenom with inflammations if sars2 infection will cut like 5 years was it. because most of us had i negative already	01:46
nixonix	*it	01:46
de-facto	btw IFR doubles with each increase of 5.75 years	01:47
de-facto	(not sure if thats related though)	01:47
nixonix	https://www.cdc.gov/coronavirus/2019-ncov/covid-data/investigations-discovery/hospitalization-death-by-age.html	01:48
nixonix	and what would be interesting, if those new variants have changed those ratios for severity. and perhaps the ratio of transmissibility, like do kids transmit more kent variant compared to adults, than with earlier variants	01:51
nixonix	which was something brits thought at some point, but they used to go back and forth with those early estimates	01:51
nixonix	as they prob will with this indian variant too	01:51
de-facto	i think its more or less the same in terms of viral loads	01:52
de-facto	i mean in regard to age	01:52
de-facto	kids will have a lot of B.1.617.2 just because its now the VoC on rise and they wont have vaccine protection when their schools are fully reopened	01:53
de-facto	so they will be without protection against whatever mutant is prevalent at that time, right now it probably is the delta voc	01:53
de-facto	for the very majority it wont be severe (hopefully) but for some of them it might cause nasty things like long covid and MIS-C	01:54
de-facto	id guess vaccination would be a good idea but we have to base such statements on data we dont have yet afaik	01:55
de-facto	it has to be a clear benefit to risk ratio win for each individual child, we cant argue with epidemic group immunity etc	01:56
nixonix	how common is mis-c and for what age of kids?	01:56
de-facto	i dont know exactly, but its a severe thing for those that get it	01:57
nixonix	mrna vaccines for adults, excluding anaphylaxis that should be avoided, risk of death is prob under 1/1M, for those not too old and fragile	01:58
de-facto	children really deserve our very best care, they have been carrying a big burden with closed schools etc so far	01:58
nixonix	then there are prob those heart inflammations, but mostly mild	01:58
nixonix	they have an "emergency" meeting for them in thursday i think. prob mostly due to image of vaccines than anything else	01:58
nixonix	in usa that is	01:59
de-facto	yeah they are going ahead with their vaccination so soon we will have much more data for them	02:00
nixonix	but yeah, going to younger age groups, its time to find out how big a problem it is	02:00
de-facto	afaik several experts from Harvard have been recommending that course of action in USA	02:00
nixonix	you mean recommending delaying vax for under 12 yo?	02:01
de-facto	there is not approval for under 12	02:01
de-facto	i mean recommending with approved vaccination from 12	02:01
nixonix	i know, they are testing it for much younger currently, and also vaccinating 12+	02:02
de-facto	yeah its time to test that, we dont have any protection for them so far	02:02
nixonix	so are they recommending delaying	02:02
de-facto	idk i always think we should have data for any recommendation, and that is what they are accumulating with testing	02:03
nixonix	what i heard, those tests were supposed to go step by step, like 1 or 2 years at time. i dont know how it is tho, but that was supposed to be the plan	02:03
nixonix	according to some finnish healthcare officials couple months ago	02:04
de-facto	my guess would be that it will turn out to work just fine, even better than for adults, but we need to see that in the data	02:04
nixonix	cant be sure, pre puberty immune system is different	02:04
LjL	well they are seeing myocarditis in younger people so at some point the risk/benefit ratio may get skewed against benefit for very young people	02:04
nixonix	then theres that heart thing	02:05
LjL	of course it's also possible that COVID does shorten telomeres in younger people and they'll die younger or some other devilry, but...	02:05
nixonix	recruiting kids of md's here, what i heard	02:05
de-facto	yeah we need to have enough data to also see very rare side effects, one in tens of thousands may be visible soon i guess	02:05
nixonix	that telomere thing should be investigated asap	02:06
de-facto	also auto-immune things, if existing probably will show in the very first months (when immune system changes take place),	02:06
nixonix	you guys seen antivax chatter around s-protein toxicity and a canadian immunologist byram bridle?	02:10
nixonix	yuri prob has	02:11
nixonix	then another name that they have mentioned is peter mccullough. i think he's been vocal about ivermectin in usa. some cardiologist	02:11
LjL	i saw an article on a study on s-protein toxicity	02:12
nixonix	those claims are false anyway. toxicity think, theres very little s-protein after mrna vax in plasma, around 1M times less than with infection	02:12
nixonix	*thing	02:13
nixonix	so if you feel like countering those claims in social media or something, ill find material for you. i just did that for awhile here	02:13
nixonix	japanese pfizer data they refer and spread snapshot about large amounts collecting to ovaries, has got some women thinking about fertility	02:15
nixonix	that pic is only partial, the amount is less than 1% that will show up from the other side that they omitted from the pic	02:16
nixonix	and its not even s-protein that they measured, but radioactive labelled lipids of nanoparticles	02:16
LjL	my social media are this channel	02:18
nixonix	and byram bridle just got over 200k for his own vaccine project, that could come out in 2-4 years (he is vocal in media against mrna vaccines that were developed "too fast")	02:18
nixonix	and his own vax will be whole virus vax, despite that betacoronaviruses nucleocapsids are dangerous, and therefore not used in those approved westerd vaccines	02:20
nixonix	they learned that when studied sars-1 vaccines	02:20
nixonix	autoimmune reactions, ade, autoantibodies, stuff like that appeared	02:21
de-facto	interesting but isnt that also in inactivated vaccines?	02:22
nixonix	yup. but flu vaccines are different, its not a prob with them	02:23
nixonix	in chines whole virus vaccines, who knows	02:23
de-facto	hmm maybe never exposed? are inactivated SARS-CoV-2 virions internalized by cells still?	02:23
de-facto	and also does not happen in reconvalescent	02:24
nixonix	they are broken by cytotoxic immune cells	02:24
de-facto	yeah then they should see nucleocapsid i guess	02:25
de-facto	btw you know about codon optimization right?	02:26
de-facto	there is also the opposite of that, codon-deoptimization, making translation less efficient	02:26
nixonix	for vaccines?	02:27
de-facto	exactly	02:27
Brainstorm	New from BBC Health: Covid: Lockdown easing in England to be delayed by four weeks: Senior ministers sign off a decision to pause the lifting of Covid restrictions in England beyond 21 June. → https://is.gd/GHKth4	02:27
de-facto	doing such codon-deoptimization one could severely slow down SARS-CoV-2 reproduction on cellular level, buying the immune system a lot of time advantage to launch an appropriate neutralizing response	02:27
de-facto	that would mean creating a stable codon-deoptimized version of SARS-CoV-2 (and its variants) for vaccination	02:28
nixonix	are we talking about self-spreading vaccines? that i thougt i invented, but it was a thing before really...	02:28
nixonix	so not an original idea :)	02:29
nixonix	just a bit dangerous. and people wouldnt be happy	02:29
nixonix	that happened with some inactivated vaccine, what was it against again	02:30
de-facto	https://codagenix.com/vaccine-programs/covid-19/	02:30
Brainstorm	Updates for United Kingdom: +5505 cases (now 4.6 million), +7 deaths (now 128032) since 21 hours ago — Sierra Leone: +39 cases (now 4388) since 22 hours ago — France: +56 deaths (now 110477) since 21 hours ago — Netherlands: +566 cases (now 1.7 million) since 21 hours ago	02:33
nixonix	intranasal prob less a problem. hopefully	02:35
de-facto	https://clinicaltrials.gov/ct2/show/NCT04619628	02:36
nixonix	there are several intranasal vaccine projects, at least couple of different viral vectors (ad5 in finland, then something else, vsv perhaps) and other technologies too	02:36
nixonix	supposedly would stop early infection with mucous membrane antibodies. but the protection wouldnt be that lasting	02:37
de-facto	intranasal may be a step forward, with any type of a vaccine delivered that way it would mean also inducing IgA on mucus hence where the wild type also enters opposed to current IM injections mainly producing IgM and finally rising long term IgG	02:37
de-facto	yes exactly	02:38
nixonix	tried to find if the crazy canadian immunologists canced drug derived sars2 vacc was killed or attenuated	02:38
nixonix	i dont think there will be much market for those in the west, when those that get vaccinated already had their mrna shots	02:39
nixonix	maybe in some other countries	02:39
de-facto	oh i think it might be very good for updating, just a spray in the nose and done	02:39
nixonix	if you get it faster for new variants. but will you	02:40
nixonix	on shot in the shoulder i dont think its a big prob. for those that already had 2-3, so there wont be mental blocks	02:41
de-facto	hmm why not? idk how exactly they do this, but basically i think they can "print out" the DNA sequence, translate that to RNA and build virions from that	02:41
nixonix	maybe some of the anti-mrna people will accept nasal vaccines	02:41
nixonix	production, do they have resources to produce updated vaccines faster than mrna vaccines?	02:42
de-facto	i think intranasal really would increase the probability for achieving neutralizing immunity by vaccination	02:42
de-facto	i dont know actually how fast or slow updates would be, afaik for mRNA its in the range of 6 weeks or such	02:43
de-facto	since idk how they would produce such attenuated virions en masse once they were created from in-silico to in-vitro i dont have a clue about comparing update delays	02:45
de-facto	i think they would have to be grown in some kind of cell cultures, hence purifying that after production may be a challenge	02:45
nixonix	maybe, lets see. in estonia they are currently marketing prophylactic nasal spray, antibodies from immunized cows	02:45
de-facto	yet same also is the case for those adenovirus vectors	02:45
nixonix	doesnt need medical approval, because they cant think if its a grocery or what	02:46
de-facto	interesting, any data on how well that works?	02:46
nixonix	yeah, it was on the level that none of our customers have got the rona. and the tests were for 20 or so if i recall	02:46
nixonix	bioblock	02:47
de-facto	hmm N=20 is not enough for any stats, but yeah maybe a start...	02:47
nixonix	no, it was 16, i checked	02:48
nixonix	but they are planning 300 ppl trials. its already sold there, tho	02:48
nixonix	https://www.iltalehti.fi/ulkomaat/a/ccb8b61e-4202-4795-af92-968feb1722ce	02:48
de-facto	thats cool they are already testing in humans then, yet with low prevalence locations it might be a challenge to estimate proper breakthrough rates	02:49
nixonix	it probably does nothing anyway	02:50
nixonix	heres on, then i have to go, you guys seen this? https://www.nature.com/articles/s41586-021-03647-4	02:51
nixonix	SARS-CoV-2 infection induces long-lived bone marrow plasma cells in humans	02:51
nixonix	but they didnt find out the share of protective antibodies, and would that be the same with vaccines	02:52
nixonix	there are couple of new studies for protection lasting, different age groups and strangely differing results. in italy and usa if i recall	02:52
nixonix	protection from primary infection, that is	02:53
nixonix	in italy, very good, in usa a bit less. around 8 months after infection both i think	02:53
nixonix	so when the circulating antibodies that are secreted continally will wane out, there will be those plasma cells that will last for life. will they help and if then how much, thats the question	02:55
de-facto	there was a comparison study	02:55
nixonix	like preventing severe symptoms	02:55
de-facto	.title https://www.nature.com/articles/s41591-021-01377-8	02:56
Brainstorm	de-facto: From www.nature.com: Neutralizing antibody levels are highly predictive of immune protection from symptomatic SARS-CoV-2 infection \| Nature Medicine	02:56
de-facto	Convalescent does not look too bad in that	02:56
de-facto	yet i wonder how comparable their datasets really are	02:57
de-facto	different studies, different variants, different cohorts, different endpoints etc	02:57
de-facto	anyhow i really have to get some sleep, i have to wake up early tomorrow	02:57
de-facto	looking forward to seeing you more often nixonix, was a pleasure :)	02:58
nixonix	was that the australian model?	02:58
nixonix	ok see you	02:58
Brainstorm	New from r/WorldNews: worldnews: Russia scrambles to contain a new surge, as most of its people appear to be avoiding the Sputnik vaccine. → https://is.gd/Ah9ENG	03:18
Brainstorm	Updates for Lesotho: +62 cases (now 10921) since a day ago	03:35
Brainstorm	Updates for United Kingdom: +5489 cases (now 4.6 million), +6 deaths (now 128034) since 21 hours ago — Canada: +532 cases (now 1.4 million) since 21 hours ago — Netherlands: +523 cases (now 1.7 million), +1 deaths (now 17848) since 21 hours ago — France: +50 deaths (now 110480) since 21 hours ago	05:02
Lindisfarne	flu is goin around the US, I caught it	05:12
Brainstorm	New from r/WorldNews: worldnews: G7 summit in Cornwall branded ‘colossal failure’ as promises on climate, aid and vaccines fall short → https://is.gd/nTesQF	05:23
Brainstorm	Updates for Belgium: +573 cases (now 1.1 million), +7 deaths (now 25088) since a day ago	05:40
Brainstorm	New from Politico: Biden in Europe: Transatlantic teamwork lifts coronavirus recovery, says ECB’s Christine Lagarde → https://is.gd/flxtcA	07:05
Brainstorm	Updates for Moscow, Russia: +7704 cases (now 1.2 million), +69 deaths (now 20907) since a day ago — Unknown, Colombia: +2553 cases (now 28519) since 11 days ago — Moscow Oblast, Russia: +953 cases (now 281621), +9 deaths (now 6267) since a day ago — India: +30318 cases (now 29.5 million), +2515 deaths (now 371806) since 22 hours ago	07:32
Brainstorm	New from r/WorldNews: worldnews: Calgary hospital has 22 cases linked to Delta COVID-19 variant, including 10 fully vaccinated → https://is.gd/cx1BlP	07:36
Brainstorm	Updates for Mongolia: +2263 cases (now 78347), +10 deaths (now 369) since 23 hours ago — Laos: +14 cases (now 2010) since 21 hours ago	08:34
Brainstorm	New from Reddit (test): CoronaVirus_2019_nCoV: What You Need To Know About The Delta COVID-19 Variant → https://is.gd/iqOZxn	09:10
Brainstorm	New from Reddit (test): CoronavirusUK: Covid vaccination: All adults in Wales offered first jab → https://is.gd/vaSXje	10:01
Brainstorm	New from The Indian Express (Health): Health: Covid-19 and blood donation: All your questions answered → https://is.gd/7nwor4	10:42
el2	/	10:44
Brainstorm	New from StatNews: Opinion: America’s broken PPE supply chain must be fixed now: Few realize that the structural problems in the supply chain that plagued the government's Covid-19 response haven't been fixed. It's crucial to address these vulnerabilities now. → https://is.gd/sRacvC	11:03
Brainstorm	New from r/WorldNews: worldnews: Lockdown easing in England to be delayed by four weeks → https://is.gd/rormQI	11:33
Brainstorm	Updates for Germany: +50 cases (now 3.7 million) since 5 hours ago	11:40
Brainstorm	New from BMJ: A new deal for surgery: but what does it really mean?: The covid-19 pandemic has caused the largest ever waiting list for NHS treatment, with 4.95 million people waiting—430 000 of those for over a year.1 The Royal College of Surgeons of England are... → https://is.gd/vmJy1n	11:54
Brainstorm	New from BBC Health: Covid vaccination: All adults in Wales offered first jab: All over-18s have been offered a first vaccination six weeks ahead of schedule, Wales' health minister says. → https://is.gd/Sho83z	12:05
Brainstorm	New from StatNews: Novavax Covid-19 vaccine highly effective in late-stage trial, long-awaited results show: Novavax’s Covid-19 vaccine was highly effective in preventing symptomatic infections, hospitalizations, and severe illnesses, long-awaited results from the company’s Phase 3 trial revealed. → https://is.gd/DkUems	12:15
Brainstorm	Updates for Gambia: +8 cases (now 6016) since 2 days ago	12:36
Brainstorm	New from The Indian Express (Health): Destination of the week: Monuments, museums to reopen from June 16 → https://is.gd/cYIAyr	12:47
Brainstorm	New from The Indian Express: World: Novavax: Large study finds Covid-19 shot about 90% effective → https://is.gd/rcYqVS	12:57
Brainstorm	New from StatNews: STAT+: GSK pays up big for rights to TIGIT-targeted cancer immunotherapy from Iteos: Iteos Therapeutics said it has sold ownership rights to an experimental anti-TIGIT cancer antibody to GlaxoSmithKline — the most recent deal for a drug in the unproven, but highly sought-after… → https://is.gd/uL4nke	13:08
Brainstorm	New from Reddit (test): Covid2019: Doctors in India are reporting COVID-19 patients with gangrene, hearing loss, and diarrhea → https://is.gd/Z4Yn3Z	13:18
Brainstorm	New from BMJ: Covid-19: US regulator raises “significant concerns” over safety of rapid lateral flow tests: The US Food and Drug Agency (FDA) has raised concerns about the safety and the marketing of rapid lateral flow covid-19 tests, which are the cornerstone of the UK’s mass testing programme.On 10... → https://is.gd/EyrnqG	13:59
frtnx	after not getting the memo and visiting the freenode ghost town im happy to see the usual attendance	14:00
frtnx	was starting to think people stopped caring	14:00
Brainstorm	New from The Indian Express (Health): Health: New Covid guidelines for children: A doctor highlights key points → https://is.gd/SnBzEH	14:10
Brainstorm	New from r/WorldNews: worldnews: Covid: Lockdown easing in England to be delayed by four weeks → https://is.gd/WZY9Rq	14:21
Brainstorm	New from WHO Euro: WHO Regional Director sets focus on equity, drug security and health systems during Saint Petersburg International Economic Forum: The need to ensure drug security and equitable access to vaccines while strengthening national health systems has been highlighted during the COVID-19 pandemic. During a week-long visit to the Russian [... want %more?] → https://is.gd/09h01Q	14:31
Brainstorm	New from r/WorldNews: worldnews: Powerful new COVID-19 vaccine shows 90% efficacy in a clinical trial, might boost world's supply. Thе vaccine usеs a protein of SARS-CoV-2, a different technology than the COVID-19 vaccines authorized so far, and delivered 100% protection against moderate and severе disease → https://is.gd/yUuRUI	14:41
Brainstorm	New from r/WorldNews: worldnews: US Embassy Mocked for Donation 80 Vaccine Vials to Trinidad and Tobago → https://is.gd/GfuxR8	15:23
Brainstorm	Updates for Nepal: +2049 cases (now 610521), +53 deaths (now 8465) since 23 hours ago	15:30
Brainstorm	New from StatNews: Pharma: STAT+: Pharmalittle: Novavax says Covid-19 shot is highly effective; doctors scramble to advise patients on Alzheimer’s drug → https://is.gd/hndyd8	15:33
Brainstorm	New from r/WorldNews: worldnews: G7 Meeting: Biden demands international investigation into Chinese lab leak theory - Biden and other world leaders have called for access to Wuhan labs to determine whether Covid-19 was result of ‘experiment gone awry’ → https://is.gd/dzeTsb	15:54
Brainstorm	New from The Lancet (Online): [Correspondence] SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness: On May 19, 2021, the Delta Variant of Concern (VOC), formerly known as the Indian VOC or B 1.617.2, became the dominant strain of SARS-CoV-2 in Scotland. The Alpha VOC (formerly known as the Kent VOC, [... want %more?] → https://is.gd/2l0I26	16:05
Brainstorm	Updates for Bangladesh: +3050 cases (now 829972), +54 deaths (now 13172) since 19 hours ago	16:32
Brainstorm	New from BBC Health: Covid: Lockdown easing in England to be delayed by four weeks: Most current Covid rules will remain for four more weeks after 21 June, government sources say. → https://is.gd/GHKth4	17:18
Brainstorm	Updates for Iraq: +5040 cases (now 1.3 million), +31 deaths (now 16736) since 23 hours ago — Switzerland: +684 cases (now 700735) since 2 days ago	17:34
Brainstorm	New from BBC Health: Covid-19: Vaccine booster study begins in Cambridge: The Cov-Boost study is testing seven vaccines to see which works best as a third dose. → https://is.gd/0iWGUH	17:40
Brainstorm	New from Shane Crotty: @profshanecrotty: R to @profshanecrotty: Really nice safety profile of the vaccine. Very little reactogenicity. → https://is.gd/n6B7fa	17:51
Brainstorm	New from Shane Crotty: @profshanecrotty: This beautiful paper on 1 year neutralizing antibodies and memory B cells is out now in Nature. @NussenzweigL https://www.nature.com/articles/s41586-021-03696-9 → https://is.gd/cMGbgt	18:01
Brainstorm	New from r/WorldNews: worldnews: Millions of Pakistanis threatened with cell phone cut-off if they don't get a COVID vaccine → https://is.gd/olCVmi	18:11
Brainstorm	New from CIDRAP: Novavax COVID vaccine 90% effective in phase 3 trial: Mary Van Beusekom \| News Writer \| CIDRAP News Jun 14, 2021 The vaccine showed 100% protection against severe illness and 93% against variants of concern. → https://is.gd/PM0Ou5	19:32
Brainstorm	Updates for United Kingdom: +6119 cases (now 4.6 million) since 17 hours ago — Canada: +7 deaths (now 25910) since 22 hours ago	19:39
Brainstorm	New from Politico: British politics: Boris Johnson announces four-week delay to full exit from lockdown → https://is.gd/NxULPH	19:43
Brainstorm	Updates for Switzerland: +2 deaths (now 10861) since 2 hours ago	19:59
Brainstorm	New from The Indian Express: World: China’s ‘Bat Woman,’ at the center of a pandemic storm, speaks out → https://is.gd/VBXJPa	20:11
Brainstorm	Updates for Spain: +2689 cases (now 3.7 million) since 2 days ago — Italy: +907 cases (now 4.2 million), +36 deaths (now 127038) since a day ago	20:36
Brainstorm	New from Gazzetta Ufficiale italiana: MINISTERO DELL'INTERNO - DECRETO 28 maggio 2021: Riparto, per l'anno 2021, del Fondo in favore dei piccoli comuni conmeno di 500 abitanti, per lo svolgimento delle funzioni fondamentali,anche in relazione alla perdita di entrate connessa all'emergenzaepidemiologica da COVID-19. (21A03595) → https://is.gd/Q1BMNp	21:23
Brainstorm	New from CIDRAP: COVID-19 Scan for Jun 14, 2021: COVID-19 physician deaths N95 advice during COVID-19 SARS-CoV-2 levels in kids, adults → https://is.gd/PUhdCU	21:44
Brainstorm	Updates for Malawi: +79 cases (now 34564) since a day ago — France: +15 deaths (now 110492) since 19 hours ago	21:45
Brainstorm	New from r/WorldNews: worldnews: The US Embassy in Trinidad and Tobago was mocked after announcing it had donated 80 vials of COVID-19 vaccine to the nation of 1.4 million people → https://is.gd/ivYVIp	22:14
aradesh	UK is delaying lockdown end. rip	22:24
Brainstorm	Updates for Bahamas: +107 cases (now 12199), +1 deaths (now 237) since 3 days ago	22:34
LjL	aradesh, was imaginable given the new spike	23:10
LjL	aradesh, it's not utterly scary yet, but look, https://offloop.net/covid19/?default=United%20Kingdom;Italy&cumulative=no&smooth=yes	23:11
aradesh	italy looks to be doing ok	23:14
Brainstorm	New from COVID19 Vaccine Tracker: Andy Becker: Altimmune Inc: AdCOVID → https://is.gd/bnKPpU	23:16
LjL	aradesh, yeah fortunately the UK is not "critical" either, i mean it's a spike, but not a runaway spike, and the deaths so far are unchanged	23:20
LjL	but it's right there at the limit	23:20
aradesh	annoying that it won't go away :3	23:25
aradesh	'night.	23:25
Brainstorm	New from CIDRAP: Spread of Delta COVID-19 variant slows UK reopening: Lisa Schnirring \| News Editor \| CIDRAP News Jun 14, 2021 In other global developments, the WHO welcomes vaccine donations from the G7 meeting. → https://is.gd/0hR4oh	23:26
Brainstorm	Updates for Canada: +10 deaths (now 25919) since 22 hours ago	23:37
Brainstorm	New from StatNews: Extra Covid vaccine may help protect transplant patients: A small study offers the first hint that an extra dose of Covid-19 vaccines just might give some organ transplant recipients a needed boost in protection. → https://is.gd/vWTBJK	23:47
de-facto	UK looks like R~1.3 hence they got Tdouble ~ 11 days	23:50
dTal	I'm happy for other people to get it - more herd immunity for me :p	23:53
de-facto	each 13 contacts happening now must be reduced to 7 contacts to regain control with R~0.7	23:59

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