libera/##covid-19/ Monday, 2021-02-08

de-facto	(paraphrased by me)	00:00
DocScrutinizer05	yeah	00:00
de-facto	i think those trials in SA with other vaccines have much more weight, its in the wild with real virus and real humans	00:01
de-facto	every vaccine developer not experimenting with updates in their lab would have to expect that at some point opposition will outperform with updates	00:02
de-facto	hence i suspect any sane vaccine developer does that already	00:02
* DocScrutinizer05 thinks of next Wednesday's german covid MPK and plays "killing joke - Pandemonium" https://youtu.be/7CpaCbmRYpE&list=PLMAVATSiJAflWVaqazZM3LXBnx2digfCu		00:04
de-facto	i wont repeat my mantra otherwise LjL might kill me, but you know the one with caps...	00:05
DocScrutinizer05	https://youtu.be/A4wdbibV3IM	00:06
de-facto	DocScrutinizer05, from your quote earlier today "Pfizer expects to nearly cut in half the amount of time it takes to produce a batch of COVID-19 vaccine, from 110 days to an average of 60, as it makes the process more efficient and production is built out, the company told USA TODAY." <-- what takes them so long for producing a batch?	00:07
de-facto	is it like 6 weeks for updates and then 9 weeks for producing it?	00:08
LjL	I'm not killing anyone today, it's my day off	00:08
de-facto	phew	00:08
LjL	Do we have any usable information at all on whether Pfizer will work on SA?	00:08
LjL	or just that in vitro study from a while ago (which was Moderna anyway, right?)	00:09
de-facto	%papers BNT162b2 E484K	00:11
de-facto	%papers BNT162b2 E484K	00:11
Brainstorm	de-facto, 4 papers: The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera. by Sonia Jangra et al, made available as preprint on 2021-01-29 at https://medrxiv.org/cgi/content/short/2021.01.26.21250543 [... want %more?]	00:11
de-facto	%more	00:11
Brainstorm	de-facto, [...] Neutralization of spike 69/70 deletion, E484K, and N501Y SARS-CoV-2 by BNT162b2 vaccine-elicited sera by Xuping Xie et al, made available as preprint on 2021-01-27 at https://biorxiv.org/cgi/content/short/2021.01.27.427998 [...] → https://paste.ee/p/NuJZA	00:11
Brainstorm	de-facto, [...] research published in The Lancet Public Health journal. → https://paste.ee/p/n9wnK	00:11
px	qa/qc is pretty strict. 60 days for the whole process is pretty impressive	00:12
px	testing for lot-to-lot variations, making sure no one sneezed in a batch	00:13
LjL	de-facto, hmm, were you looking for one of those that show up in https://paste.ee/p/NuJZA ? i'm not sure i know which one you're referring to	00:14
DocScrutinizer05	>><de-facto> is it like 6 weeks for updates and then 9 weeks for producing it?<< yes, that was my calculation that resulted in >>so in 4 months we will see<<	00:15
de-facto	.title https://www.biorxiv.org/content/10.1101/2021.01.15.426911v2 LjL, i guess you meant that one with in vitro	00:16
Brainstorm	de-facto: From www.biorxiv.org: mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants \| bioRxiv	00:16
de-facto	so yeah not in vivo	00:16
de-facto	hmm	00:16
LjL	oh, of course, mRNA-elicited... sorry, i'm a bit confused (as usual)	00:16
LjL	yeah this is probably the one i remembered, although i thought it was only about Moderna, but instead it's both	00:17
pigughs	Several manufacturers have said they were addressing the problem by developing new versions of their vaccines, which could act as booster shots. The Food and Drug Administration has said it is working on a plan to allow those new vaccine versions to be authorized.	00:18
LjL	yes, but the problem IMO is time, time	00:19
de-facto	hmm always worth a check https://twitter.com/jbloom_lab and https://twitter.com/profshanecrotty	00:19
de-facto	could not find anything new there yet	00:19
LjL	unless we do ultra-strict lockdowns (and we aren't doing them, no matter how much de-facto wants them), in Europe at least, these variants will become overwhelming before we have a booster	00:19
LjL	(probably before we even have given the first shot of the vaccine to a significant percentage of people)	00:20
de-facto	hence my mantra of ...	00:20
LjL	de-facto, yeees but even if we stop travel now, it's late, too many yellow dots all over Europe already	00:20
DocScrutinizer05	wait, sorry. de-facto you assume those 110 now 60 days were with 6 weeks for a new mRNA version? I read that as simply producing one batch of regular BNT152b2	00:20
px	some of the mab treatments can be used to keep the variants at bay while a booster is developed	00:21
LjL	i thought 6 week was the time they quoted for designing a new version of the vaccine	00:21
DocScrutinizer05	6 weeks for new mRNA version on top of that	00:21
de-facto	DocScrutinizer05, afaik the head of BNT said 6weeks for updating the template and at least another 6 weeks for production	00:21
Brainstorm	Updates for Montserrat: +2 cases (now 17) since 22 hours ago	00:21
de-facto	yeah	00:21
LjL	px, mAbs are very expensive, they are really only used (in my country at least) in triage for people who are at very high chance of being hospitalized or even need ICU	00:21
pigughs	so in summary, the variants may be able to outpace any vaccine going forward	00:22
px	I mean, those ARE the people we should be focusing on anyway right	00:22
DocScrutinizer05	so it was 60 days plus 267days then	00:22
LjL	de-facto, FYI, i wasn't sure but i just checked again, i have the two twitter accounts you mentioned in Brainstorm. not sure i remember it posting anything from them though...	00:22
DocScrutinizer05	they better start	00:22
DocScrutinizer05	ed yesterday	00:23
LjL	px, the people we should be focusing on should be at minimum everyone who ends up hospitalized, and ideally everyone, since even with a mild course, you can have long-term effects	00:23
LjL	if a variant is much more infectious, the hospitals will be overwhelmed even if the ICUs themselves aren't	00:23
LjL	look at how many deaths per day the UK has had recently	00:23
de-facto	DocScrutinizer05, hmm not sure id say at least 60+67 but maybe even 60+26*7 (though id assume the first)	00:23
LjL	(though deaths are not the only metric)	00:24
de-facto	LjL, yeah the ones from y	00:24
Brainstorm	New from r/WorldNews: worldnews: South Africa puts AstraZeneca vaccinations on hold over variant data → https://is.gd/BT0fWG	00:25
LjL	hmm, Brainstorm posted only one time from Shane Crotty, and a few times from JBloom	00:25
DocScrutinizer05	pigughs: >>variants may be able to outpace...<< I guess they already did	00:26
pigughs	DocScrutinizer05: unless booster are a faster process	00:26
LjL	Brainstorm is not doing what it should. it filters posts (including Twitter ones) for COVID-related keywords, but there's a ton of posts by Shane Crotty in the past few days that have those keywords, so...	00:27
LjL	unless it's nitter's fault, i dunno. at any rate it's not doing what i want it to	00:27
de-facto	hmm if new variants appear randomly and the frequency of their occurrence is proportional to the number of viral replications taking place on a cellular level with fading incidence their frequency should also fade i guess?	00:28
pigughs	Developers of the AstraZeneca and University of Oxford vaccine said on Sunday that they expected to have a modified version of their vaccine available by the fall.	00:29
LjL	oh. ugh. de-facto, when i went to https://nitter.net/profshanecrotty/rss it told me "Instance has been rate limited. Use another instance or try again later." - can you verify if it does the same for you?	00:29
de-facto	so if we manage to 1) bring down incidence with NPIs 2) vaccineate everyone at highest rate with most up-to-date polyclonal template of latest s-protein variants we might have the best chance to outrun evasion mutant frequency	00:29
de-facto	LjL, same from here	00:29
LjL	maybe i should use a less-well-known instance in Brainstorm	00:29
ryouma	where do you get an estimage of proportion currently contagious for a given county or state?	00:31
DocScrutinizer05	de-facto: >>vaccineate everyone at highest rate with most up-to-date polyclonal...<< except those don't exist yet?	00:31
DocScrutinizer05	ryouma: basically you take last cases per day and multiply those by e.g. 14 days	00:32
de-facto	well or add up the last 14 days of incidence	00:33
DocScrutinizer05	yeah, if you want it on the percent exact	00:33
de-facto	and take them times $dart_scaling_factor	00:33
ryouma	and those numbers are usable for this estimate? i.e. testing rates and sampling b8iases do not vary too much?	00:33
de-facto	$dark_scaling_factor	00:34
DocScrutinizer05	dart sounded good - BULLSEYE!!!	00:34
de-facto	e.g. if they happen to find 5x as many seropositive (in random sampling ELISA antibody tests) as they found accumulated positive PCR tests for the same cohort that $dark_scaling_factor=5	00:35
ryouma	so for like the whole of usa it is something like 100k cases per day so scaling * 14 * in this case 100k	00:35
ryouma	then divide into population	00:35
DocScrutinizer05	yep	00:36
de-facto	USA > 10M active cases https://www.worldometers.info/coronavirus/country/us/	00:36
ryouma	so it could be like some unknown person would hve a 1/6 chance of being contagious or so?	00:37
darsie	Active known or active actual cases?	00:37
LjL	i think it also depends on, do you considered people who are either in hospital or supposedly self-quarantining as contagious?	00:37
ryouma	i am considering a repairman where i live	00:37
de-facto	well active is SUM(known infected) - SUM(not died in time)	00:37
LjL	some more advanced SIR models include a category for people who are "removed" from the community	00:37
de-facto	if they are contagious? idk	00:37
* darsie is confused.		00:38
ryouma	for my purposes i would remove those who are not contacting anybody	00:38
LjL	de-facto, well a rough think you can do is to consider the likely number in the last 5 days, which is the average before you get symptoms and (hopefully) self-quarantine. but 5 may not be a real-life number here.	00:38
LjL	ryouma, for your purposes i think any calculation we can do with known cases is mostly academic ;(	00:39
LjL	it's going to be very hard to estimate just what the risk for you is	00:39
de-facto	indeed	00:39
DocScrutinizer05	ryouma: 1/6? 10M/<population-USA>	00:39
LjL	ryouma, do you know about https://www.microcovid.org/ ? it isn't magic, it also uses known numbers and a model, but maybe it could ease some decisions	00:39
de-facto	that would be 3% or 1/30	00:40
de-facto	yeah thats a neat one :)	00:40
de-facto	btw if USA got so many cases, why did they not breed some fancy new variants? due to not sequencing enough to find them?	00:41
ryouma	that might be the site i was thinking of hta tuses a scaling factor	00:41
de-facto	actually thats kinda weird...	00:42
LjL	de-facto, there was something about a "Californian variant" but then i didn't hear anything further	00:43
de-facto	yeah	00:43
de-facto	https://covariants.org/variants/S.L452R	00:43
LjL	ryouma, at the end of it it says that you should consider 1% if you're a regular person but 0.1% if "high caution" (by which they mean you're in contact with people who have COVID, but likely you should also be considered in that)	00:43
ryouma	strange it does not have option for indoor masked	00:43
LjL	ryouma, hmm i think it probably assumes that you will be masked outdoors, because there may be other people than the one(s) you have decided to spend time with	00:45
LjL	further down, it does ask whether other people around you will be masked, and what type of masks	00:45
de-facto	https://cov-lineages.org/lineages/lineage_B.1.429.html	00:45
de-facto	maybe USA also is careful about which sequences or variants they publish?	00:47
ryouma	strange it does not have option for INDOOR masked	00:48
ryouma	it says airplane is 1/6 risk of indoors	00:49
LjL	well, airplanes generally change all the air inside them much more often than a typical home	00:49
LjL	ryouma, those activities are just examples anyway, "pre-built" one, but if you want a specific case you just fill in all the fields	00:50
ryouma	oh? my brain might ot be up to this but i will try	00:51
ryouma	i will keep some windows open	00:51
LjL	yeah see it says "Search for an activity or build your own below"?	00:52
ryouma	it seems to like my p100 and assumes i cover the valve, which, i think maybe i will put a rag over it and tape that well	00:52
LjL	(inside the text box where you can search for an activity)	00:52
ryouma	ah	00:52
LjL	it has examples like "One night-stand with a random person" :P i want to bet there are myriads more activities less dangerous than that	00:52
ryouma	is moldex medical grade n95? it is certified buyt it is intended for construction etc. poresumably.	00:54
LjL	i don't know what medical grade entails in the context of N95 masks	00:56
LjL	surgical masks have layers to protect from splashes, N95 doesn't	00:56
de-facto	bin_bash, found something you might like to read https://twitter.com/profshanecrotty/status/1357357180609912832 https://twitter.com/VikiLovesFACS/status/1353295630102372353 maybe it got some useful links?	00:56
de-facto	about pregnancy and vaccinations	00:57
ryouma	"We recommend the basic particle filters, not the VOC filters, which are harder to breathe through and do not provide additional protection." --- i wonder if that refers to effectiveness or just comfort	00:58
ryouma	reasonable prices online for 3m. i have a honeywell though and won't hav etime to get a 3m and guessing htey are about they same	00:59
LjL	"Following the publication of the interim data showing that the vaccine is safe in pregnant animals on	00:59
LjL	the 10 th December, and pressure from pregnant workers on the frontline, who did not want to be	00:59
LjL	denied protection against the virus, the government changed its advice" ← my question on this is... why do people need to be denied the vaccination, in any case? is it impossible to have guidance where your doctor cautions against vaccination if you're pregnant, but after giving you all the fact, still allows you to make the choice? people feel better when they feel they have control over personal choices.	00:59
bin_bash	de-facto: thanks! i'll chedck it out	00:59
bin_bash	tonight is the american superb owl (super bowl) so im watching that	01:00
LjL	ewewew	01:00
LjL	ryouma, i paid around €7.50 for a 3M but apparently it looks very different from "American" 3M's (at least the one bin_bash has)	01:00
LjL	it seems kinda better as a mask, but the elastic bands seem worse	01:01
de-facto	oh enjoy, i hope i did not bother you by highlighting, i just have seen that recommended link (and Shane Crotty should be quite competent about immunology)	01:02
ryouma	the sidte recommended 3m half faceplate. that was 42usd	01:03
ryouma	for their half faceplate rec -- idr if it reced n95 brands	01:04
-Synapsestorm- 🏠 Linog! Earthquake! Lindol! Sismo! 5.4 Mb tremor, registered by alomax, with 47 reports, occurred 11 minutes ago (00:00:44 UTC), during daytime, Philippine Islands Region (5.62, 127.09) ± 3 km, ↓41 km likely felt 330 km away (in Davao City…) by 2.6 million people (alomax.free.fr)		01:12
LjL	ryouma, a half faceplate with reusable filters may be expensive but then you can... well, reuse the filters, a number of times. but it'll probably have a valve...?	01:16
Brainstorm	Updates for France: +10075 cases (now 3.4 million) since 22 hours ago — Netherlands: +2015 cases (now 1.0 million) since 22 hours ago	01:23
ryouma	i find htat my half faceplate seals well although it feels too large and have tested it using obvious bssic inhale exhale tests covering stuff with hand. it has triple flange medical grade siliicone., i am going to hafe to tape a rag over the exhale valve. i wish i had a surgical mask to tape over valve. we have been self-isolating for months with shopper and decontaminate items though.	01:46
ryouma	the half faceplates though use a dumb valve (for intake after hte filters and for exhaust). that really gets sticky. the n95 valves ar emuch better.	01:47
ryouma	i think 3m uses dumb valves also	01:47
ryouma	for their half faceplates. just a disk.	01:48
ryouma	idk why y7ou said and asked that	01:48
ryouma	i was saying the rec if you get those is for 3m and for p100 not hte voc. not sure if hte not voc rec was for efficacy or just comfort.	01:49
Brainstorm	New from r/WorldNews: worldnews: Iranian cleric offers helpful advice to those seeking COVID19 vaccination → https://is.gd/hpgDJo	02:10
DocScrutinizer05	a random sidenote about non-representative observation: I see _a_lot_ more FFP2 masks lately, like compared to 3 weeks ago. Not only in shops but even walkers on pavement, bicycle drivers etc. It might look like Rt going down slightly since 7 days	02:17
de-facto	here they are sold at the supermarket near the cashier (yet one needs one to enter the supermarket in advance)	02:29
de-facto	i guess if antigen tests would be made available to the people (in the supermarkets) they also would find broad usage and help a lot (not sure of that ever will happen though)	02:31
DocScrutinizer05	7 days are only 3 significant days, plus 4 "immature" last ones still about to stabilize	02:31
DocScrutinizer05	I'm two minds about quicktests - they might help, or they will cause people to take more risks since they think they are "safe"	02:33
Brainstorm	New from r/WorldNews: worldnews: Greek PM criticized over lunch with 40 people that breached Covid-19 restrictions → https://is.gd/YZu4yY	02:35
DocScrutinizer05	when I look at poll results though, it seems 60+% are smarter and better informed than our politicians	02:35
DocScrutinizer05	so odds are the quicktests indeed might help more that they would do damage	02:36
de-facto	if we have quicktests available but dont use them broadly we never will know. if they are problematic they still can be adjusted etc	02:36
DocScrutinizer05	than*	02:36
de-facto	i am pretty sure they are helpful though	02:36
de-facto	tbh i am quite angry we still dont have them available to everybody	02:37
DocScrutinizer05	how would you adjust behavior of people who think "hey I'm negative, so I may visit my parents finally" or similar lines of reasoning?	02:38
de-facto	if we have any technology that might be of help, we need to give it to the people in large quantities as soon as possible	02:38
de-facto	those people would visit their parents anyhow	02:38
DocScrutinizer05	for sure the (official) rationale for not selling quicktests to everybody is a braindamaged one	02:39
de-facto	and people also can learn, for example if media informs them properly etc	02:39
de-facto	yeah and that assumption in itself is braindamaged imho	02:39
de-facto	the pandemic situation only can be fought successfully in a decentralized way by the people themselves	02:39
de-facto	hence the only chance we have is to employ their brains and give them any technology we have to help	02:40
DocScrutinizer05	full ack	02:40
de-facto	holding back is wasting time	02:40
DocScrutinizer05	also empower them to drive the situition by themselves, in a sense like the NO-Covid paper suggests	02:41
DocScrutinizer05	everybody motivated and willing to bring down incidences locally since it will immediately pay back to them	02:42
de-facto	i think its very important to give the people a realistic sense about that its all in their own hands and government cant take that responsibility from them	02:43
DocScrutinizer05	exactly that	02:43
DocScrutinizer05	also there were concerns about incidences not going down in several german federal states. I think that only applies to Bremen and Saarland, if any	02:54
DocScrutinizer05	for Saarland that's a problem	02:54
DocScrutinizer05	both are really "tiny" but I wonder what's going haywire there	02:57
DocScrutinizer05	Saarland may be border to France	02:57
Brainstorm	Updates for Germany: +4511 cases (now 2.3 million), +130 deaths (now 62128) since 15 hours ago — United Kingdom: +11892 cases (now 3.9 million), +280 deaths (now 112479) since 19 hours ago	03:15
bloody_noob259[m	<DocScrutinizer05 "also there were concerns about i"> Bremen.City is.going slowly down used to be around 79 is now ~65 you have to keep in mind the federal state of bremen mainly consists of.two larger.cities: Bremen and Bremerhaven. The numbers in Bremerhaven are worrysome tough: https://www.butenunbinnen.de/nachrichten/gesellschaft/corona-virus-zahlen-infektion-bremen-100.html	03:28
bloody_noob259[m	* Bremen.City is.going slowly down used to be around 79 is now ~65 you have to keep in mind the federal state of bremen mainly consists of.two larger.cities: Bremen and Bremerhaven. The numbers in Bremerhaven are worrysome tough ~148: https://www.butenunbinnen.de/nachrichten/gesellschaft/corona-virus-zahlen-infektion-bremen-100.html	03:29
Brainstorm	New from The Indian Express: World: South Africa puts AstraZeneca vaccinations on hold over variant data → https://is.gd/JqmvqT	03:35
Brainstorm	New from BBC Health: (news): Covid: Public can be confident in UK's vaccines, Nadhim Zahawi says → https://is.gd/PNG1Eg	05:52
LjL	uhm, no they can't	06:01
LjL	it's funny i'd see such a headline just when it's proven that AZ doesn't work against important variants	06:01
LjL	ubLIX, ↑	06:01
ubLIX	"... appeared to work well against the variants currently dominant in the UK."	06:03
ubLIX	oh dear	06:03
LjL	"Data on two new coronavirus vaccines that could be approved soon - one from Novavax and another from Janssen - appear to offer some protection.	06:03
LjL	And early results from Moderna suggest its vaccine is still effective against the South Africa variant."	06:03
LjL	so let's not dance around it	06:03
LjL	it's AstraZeneca that is just not a good vaccine	06:03
LjL	it was poor from the start, and it's getting useless with upcoming variants	06:03
LjL	but the UK is very invested in it, more than the EU (with its ridiculous numbers of vaccinations done)	06:04
ryouma	what is the summary of variants	06:04
ryouma	there are uk and sa variants and they are bad in some respect and where are they now everywhere?	06:04
LjL	ryouma, also the Brazilian variant, which i understand is similar to the SA one in some ways	06:06
LjL	the UK variant is pretty much everywhere in already well-established clusters	06:06
LjL	SA and Brazilian have been found in many places, but not yet very present	06:06
LjL	the UK variant is apparently still susceptible to most vaccines, but the SA variant isn't (and i don't really know about the Brazil variant)	06:06
LjL	and now in the UK, i'm not sure whether it's a SA variant or the UK variant gaining a new E484K mutation, but it's quite possibly starting to behave like the SA one i.e. escape vaccines	06:07
ryouma	are they only bad wrt vaccines?	06:07
LjL	AstraZeneca is probably particularly susceptible because it just didn't create a very great immune response to begin with	06:07
LjL	but there are no studies on humans with the mRNA vaccines and the variants yet, so who knows about those either	06:08
LjL	ryouma, no, they can also be bad in terms of reinfections	06:08
LjL	there is something unclear going on in Manaus, Brazil	06:08
LjL	according to a seroprevalence survey, most of the population had already had COVID	06:08
LjL	but now they're catching it again	06:08
LjL	however the survey could have been flawed	06:08
LjL	it's not completely clear	06:08
LjL	but today's big news is that South Africa is no longer going to use AstraZeneca	06:09
LjL	in South Africa, the South Africa variant accounts for more than 90% of cases now	06:09
LjL	and if they thought AZ was still useful, at least for preventing severe disease, i bet they'd still use it	06:09
LjL	instead they announced they'll stop	06:09
ryouma	maybe vaccines will alter the landscape and new variants will appear becaiuse of them	06:10
ryouma	somebody said variants would have appeared if they existed but now we get them why	06:10
LjL	ryouma, that is possible, and look this is very close to being... some people would call it a conspiracy theory, i wouldn't call it such because i see no conspiracy, i just see a striking coincidence	06:10
ryouma	is it because of vaccines?	06:11
LjL	AstraZeneca had vaccine trials in the UK, in South Africa, in Brazil, and in the US	06:11
ryouma	i thought they were not really wisdewspread yet	06:11
LjL	and where is it that important variants arose? in the UK, in South Africa, in Brazil, and maybe this Californian variant in the US	06:11
LjL	ryouma, for all i know, the vaccine-escaping mutants could have arisen in people in the trials who had had an AZ jab, and it turned out that it was enough to stop severe disease, but also allowed the virus to stay around long enough to mutate and escape the vaccine	06:12
LjL	disclaimer: this is very much my own theory and i'd probably get yelled at by any virologist or epidemiologist or whatever	06:12
LjL	but i just find it an unlikely coincidence	06:12
ryouma	it has been speculated that one enterovirus waws missed in the 23 or so enterovirus sepcies in one polio vaccine. leaving an environtment htat allowed that one to proliferated. idk if it was proved or disproved.	06:12
LjL	god it's 6:15 am	06:13
LjL	i will sleep	06:13
LjL	take care	06:13
Brainstorm	New from EurekAlert!: 79% decrease in primary care visits, 56-fold increase in virtual care: COVID-19 pandemic: In the early months of the COVID-19 pandemic, there was an almost 80% decrease in primary care office visits in Ontario and a 56-fold increase in virtual visits, found new research in CMAJ ( Canadian Medical Association Journal ). → https://is.gd/FkjwAY	06:29
pwr22	Hopefully the AZ vaccine isn't totally ineffective against the current pool of strains	06:39
Brainstorm	New from The Indian Express: World: Ebola resurfaces in previous epidemic zone of Congo, WHO says → https://is.gd/5NO8BG	06:41
Brainstorm	New from r/WorldNews: worldnews: Serum Institute India's vaccination doses departs for Barbados, Dominica from Mumbai → https://is.gd/fy1Lm4	06:54
Brainstorm	New preprint: Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States by Nicole L. Washington et al, made available as preprint on 2021-02-07 at https://medrxiv.org/cgi/content/short/2021.02.06.21251159 [... want %more?]	06:58
Brainstorm	New from r/WorldNews: worldnews: Hedge funds bet on oil's 'big comeback' after pandemic hobbles producers → https://is.gd/kxBO82	07:19
Brainstorm	Updates for Minas Gerais, Brazil: +11699 cases (now 774111), +263 deaths (now 15930) since 2 days ago — Paraiba, Brazil: +2642 cases (now 198124), +23 deaths (now 4146) since 2 days ago — France: +14786 cases (now 3.4 million), +128 deaths (now 78995) since 23 hours ago — United Kingdom: +15868 cases (now 4.0 million), +374 deaths (now 112573) since 23 hours ago	07:29
Brainstorm	New from r/WorldNews: worldnews: Oil prices climb back to pre-pandemic levels → https://is.gd/pmdKjz	07:56
Brainstorm	New from Science-Based Medicine: The latest antivax false claim: mRNA vaccines against COVID-19 are not vaccines, but “medical devices” or “gene therapy”: There's a new antivaccine talking point in town, and it's just as much disinformation as other antivaccine talking points. It's the claim that mRNA COVID-19 vaccines are not really vaccines [... want %more?] → https://is.gd/4jtIfe	09:09
zutt	%cases sweden	09:09
Brainstorm	zutt: In Sweden, there have been 588062 confirmed cases (5.7% of the population) and 12115 deaths (2.1% of cases) as of 2 days ago. 5.5 million tests were performed (10.7% positive). See https://offloop.net/covid19/?default=Sweden for time series data.	09:09
zutt	%cases israel	09:09
Brainstorm	zutt: In Israel, there have been 692101 confirmed cases (7.5% of the population) and 5121 deaths (0.7% of cases) as of an hour ago. 11.0 million tests were performed (6.3% positive). Fatality can be broadly expected to lie between 0.9% (assuming prevalence as in tests) and less than 0.8% (considering only deaths and recoveries). See https://offloop.net/covid19/?default=Israel for time series data.	09:09
Brainstorm	New from Medical Xpress: Canada's first case of Brazilian virus strain detected: Health authorities in Toronto announced Sunday that a resident had been diagnosed with the Brazilian variant of COVID-19, marking Canada's first known case of the mutated virus. → https://is.gd/A7gwd4	09:21
Brainstorm	New from Medical Xpress: Russia's Sputnik V vaccine gets all-clear in Hungary: Hungarian health authorities have approved Russia's coronavirus vaccine Sputnik V, the government said Sunday, with 40,000 doses of the jab already to be given. → https://is.gd/OD5kTO	09:34
CoronaBot	/r/covid19: COVID-19-related psychological distress and engagement in preventative behaviors among individuals with severe mental illnesses (80 votes) \| https://www.nature.com/articles/s41537-021-00136-5 \| https://redd.it/lf2tsp	09:40
Brainstorm	New from StatNews: Opinion: Telehealth’s critics have it right: The industry must evolve: For #telehealth to succeed after the pandemic, it must push the boundaries of what it means to provide quality care. → https://is.gd/CbguAs	10:48
Brainstorm	New from r/WorldNews: worldnews: Oxford Covid vaccine 10% effective against South African variant, study suggests \| World news → https://is.gd/gNyJym	11:13
Brainstorm	New from BBC Health: South Africa halts AstraZeneca vaccine over new variant: A study of the vaccine's effectiveness against the South Africa variant shows "disappointing" results. → https://is.gd/r2BeIL	11:37
Brainstorm	New from BMJ: Researchers must contribute to responsible reporting of suicide: In their editorial on trends in suicide in the covid-19 pandemic, John and colleagues discuss the role of the media in preventing suicide.1 We would like to add that academics themselves need to... → https://is.gd/NgGqMq	12:02
Brainstorm	New from BMJ: Japan should aim to eliminate covid -19: Compared with other G7 countries, Japan has been relatively successful in mitigating the spread of covid-19.1 However, Japan has the second worst record in the Western Pacific region, with over 40... → https://is.gd/aAyvod	12:14
Brainstorm	New from PubMed: Randolph H L Wong: Launching the E-vita Open Neo amid COVID-Challenges and strategies → https://is.gd/rtTozB	12:26
Brainstorm	New from ECDC: Infographic: Mutation of SARS-CoV2 - current variants of concern: This infographic provides information on the three current variants of concern detected in the UK, South Africa, Brazil and Japan. → https://is.gd/c6udxj	12:39
zutt	%cases finland	13:09
Brainstorm	zutt: In Finland, there have been 47969 confirmed cases (0.9% of the population) and 688 deaths (1.4% of cases) as of 29 minutes ago. 2.9 million tests were performed (1.6% positive). Fatality can be broadly expected to lie between 0.8% (assuming prevalence as in tests) and less than 2.2% (considering only deaths and recoveries). See https://offloop.net/covid19/?default=Finland for time series data.	13:09
zutt	%cases denmark	13:10
Brainstorm	zutt: In Denmark, there have been 201752 confirmed cases (3.5% of the population) and 2213 deaths (1.1% of cases) as of 5 hours ago. 14.4 million tests were performed (1.4% positive). Fatality can be broadly expected to lie between 2.7% (assuming prevalence as in tests) and less than 1.1% (considering only deaths and recoveries). See https://offloop.net/covid19/?default=Denmark for time series data.	13:10
Brainstorm	New from BBC Health: (news): Covid: 'No deportation risk' for illegal migrants getting vaccination → https://is.gd/S20ztl	13:16
de-facto	.title https://virological.org/t/b-1-258-a-sars-cov-2-variant-with-h69-v70-in-the-spike-protein-circulating-in-the-czech-republic-and-slovakia/613	13:35
Brainstorm	de-facto: From virological.org: B.1.258∆, a SARS-CoV-2 variant with ∆H69/∆V70 in the Spike protein circulating in the Czech Republic and Slovakia - nCoV-2019 Genomic Epidemiology - Virological	13:35
Brainstorm	New from BBC Health: (news): Covid: How worrying are the UK, South Africa, and Brazil coronavirus variants? → https://is.gd/4gbOmY	13:53
Brainstorm	Updates for Germany: +5008 cases (now 2.3 million) since 21 hours ago	14:19
Brainstorm	Updates for Kuwait: +996 cases (now 171994), +3 deaths (now 969) since 23 hours ago	14:50
Brainstorm	New from Derek Lowe: @OpenMindTV: RT by @Dereklowe: NEW POD: Drug discovery chemist and @ScienceMagazine blogger @Dereklowe discusses what has stalled vaccine production and how manufacturers are readying updated formulas to combat the virus mutations. LISTEN: https://open.spotify.com/episode/7s8l85nqhUlkd2zzW8QUqT → https://is.gd/1IXdom	14:55
CoronaBot	/r/covid19: Association of Psychiatric Disorders With Mortality Among Patients With COVID-19 (80 votes) \| https://jamanetwork.com/journals/jamapsychiatry/fullarticle/2775179 \| https://redd.it/lf2v2h	15:24
CoronaBot	/r/coronavirus: Biden: 'Absolutely' will use NFL sites for vaccine (10111 votes) \| https://www.espn.com/nfl/story/_/id/30855417/president-joe-biden-plans-take-nfl-offer-use-stadiums-vaccines \| https://redd.it/lf2b9e	15:30
Brainstorm	New from StatNews: STAT+: Pharmalittle: South Africa halts rollout of AstraZeneca Covid-19 vaccine; Pfizer to cut vaccine production time in half: South Africa is halting its rollout of the Covid-19 vaccine from AstraZeneca and the University of Oxford, following a new analysis that suggests the shot “provides minimal protection” against mild… → https://is.gd/R1ig3c	15:32
Brainstorm	Updates for Switzerland: +3280 cases (now 535153) since 23 hours ago	15:40
CoronaBot	/r/covid19: Neutralization of viruses with European, South African, and United States SARS-CoV-2 variant spike proteins by convalescent sera and BNT162b2 mRNA vaccine-elicited antibodies (87 votes) \| https://www.biorxiv.org/content/10.1101/2021.02.05.430003v1 \| https://redd.it/lf7uph	15:48
Brainstorm	New from r/Coronavirus: Coronavirus: [CROSSPOST] AskScience AMA Series: We are Bechara Choucair, Carole Johnson, and Tim Manning, the vaccine, testing, and supply coordinators for the White House COVID-19 Response Team. AUA! → https://is.gd/uE7fvs	16:10
lazysundaydreams	%cases Czechia	16:14
Brainstorm	lazysundaydreams: In Czechia, there have been 1.0 million confirmed cases (9.7% of the population) and 17333 deaths (1.7% of cases) as of 6 hours ago. 6.6 million tests were performed (15.8% positive). Fatality can be broadly expected to lie between 1.0% (assuming prevalence as in tests) and less than 1.8% (considering only deaths and recoveries). See https://offloop.net/covid19/?default=Czechia for time series data.	16:14
kevin-oculus	%cases Sweden	16:23
kevin-oculus	%cases Sweden	16:23
Brainstorm	kevin-oculus: In Sweden, there have been 588062 confirmed cases (5.7% of the population) and 12115 deaths (2.1% of cases) as of 3 days ago. 5.5 million tests were performed (10.7% positive). See https://offloop.net/covid19/?default=Sweden for time series data.	16:23
Brainstorm	New from Virological.org: Latest posts: Preliminary in silico assessment of the specificity of published molecular assays and design of new assays using the available whole genome sequences of 2019-nCoV: Updated to 466,524 COVID-19 WGS from GISAID. Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from [... want %more?] → https://is.gd/gGK3QE	16:36
Brainstorm	New from r/WorldNews: worldnews: British teen emerges from nearly year-long coma to pandemic-hit world → https://is.gd/HWYs3F	16:48
Brainstorm	Updates for Netherlands: +29 deaths (now 14454) since 23 hours ago	16:54
Brainstorm	Updates for United Kingdom: +15571 cases (now 4.0 million), +385 deaths (now 112798) since 23 hours ago — Canada: +39 deaths (now 20776) since 23 hours ago	18:03
aloe[m]1	%cases Turkey	18:04
Brainstorm	aloe[m]1: In Turkey, there have been 2.5 million confirmed cases (3.0% of the population) and 26797 deaths (1.1% of cases) as of 21 hours ago. 30.8 million tests were performed (8.2% positive). Fatality can be broadly expected to lie between 0.4% (assuming prevalence as in tests) and less than 1.1% (considering only deaths and recoveries). See https://offloop.net/covid19/?default=Turkey for time series data.	18:04
CoronaBot	/r/covid19: Measuring the impact of COVID-19 vaccine misinformation on vaccination intent in the UK and USA (83 votes) \| https://www.nature.com/articles/s41562-021-01056-1 \| https://redd.it/lfbfkr	18:25
Brainstorm	New from BBC Health: (news): Covid: Over-70s told to contact NHS for their vaccine → https://is.gd/PpdF3e	18:34
Jigsy	%cases UK	18:48
Brainstorm	Jigsy: In United Kingdom, there have been 4.0 million confirmed cases (6.0% of the population) and 112798 deaths (2.8% of cases) as of 44 minutes ago. 78.2 million tests were performed (5.1% positive). See https://offloop.net/covid19/?default=United%20Kingdom for time series data.	18:48
Brainstorm	New from Shane Crotty: @profshanecrotty: R to @profshanecrotty: which is not a surprise to those of us who have worked in the HIV vaccine field! → https://is.gd/saAoZ9	18:59
Brainstorm	New from BBC Health: Covid: Boris Johnson 'very confident' in vaccines being used in UK: A small study suggests the AstraZeneca vaccine may be less effective against the South African variant. → https://is.gd/Lxfs4T	19:11
blkshp	It's a lottery what you get here, my mum was most chuffed when she got pfeizer and all her friends got oxford lol	19:27
-RSSBot[LjLmatrix- Feed: Convocazione del Consiglio dei Ministri n. 96 ( http://www.governo.it/it/articolo/convocazione-del-consiglio-dei-ministri-n-96/16169 )		19:34
-RSSBot[LjLmatrix- Feed: Consiglio dei Ministri n. 96 ( http://www.governo.it/it/articolo/consiglio-dei-ministri-n-96/16170 )		19:34
Brainstorm	New from University of Washington: New COVID-19 Literature Situation Report: Summary of SARS-CoV-2 Novel Variants: covid-variants-banner-01.png At just over one year into the COVID-19 pandemic, evolution of SARS-CoV-2 has generated viral variants that differ in their genetic sequence from the strain first detected in December 2019. Evidence is emerging [... want %more?] → https://is.gd/2Uk8Rj	19:35
Brainstorm	Updates for Italy: +7969 cases (now 2.6 million), +307 deaths (now 91580) since 23 hours ago	19:42
Brainstorm	New from Medical Xpress: British COVID-19 variant gaining strong foothold in the United States: (HealthDay)—The highly contagious coronavirus variant that drove Britain into lockdown in December is now spreading quickly across the United States, a new study shows. → https://is.gd/InZrRo	19:48
LjL	blkshp, lucky	19:49
LjL	now every authoritative figure in the UK (if Johnson counts as that, lol) apparently needs to state that they have full confidence in AZ	19:49
LjL	do people really not see that they're saying that because AZ doesn't actually work (anymore)?	19:50
LjL	the UK can't afford to lose AZ as it's the vaccine they focused on the most, but at the same time, unless they rush to make a booster for the variant(s), right now it's unlikely to be much good	19:50
blkshp	I'm gettin a vaccine on Wednesday, it's not covid but I wont get MMR!	19:54
LjL	i couldn't even get the flu vaccine	19:58
LjL	this country is a disaster	19:58
Brainstorm	New from Medical Xpress: Bans on evictions, utility shutoffs are curbing COVID-19 infections: Study: (HealthDay)—Bans on evictions and utility shutoffs during the pandemic may not only be keeping people safe and warm in their homes: They might also limit the spread of COVID-19, new research suggests. → https://is.gd/MSMrPc	20:00
blkshp	I went to the docs for a Tetanus booster last year and the nurse tld me 13 years of data was missing, they hunted for it and eventually found it and all but one was on record. Pretty sure it's been had but no record they recommended i get one just to make sure it's done.	20:00
pwr22	<LjL "do people really not see that th"> Is there actually good data on that? I totally believe it may be less effective than the other jabs for the south africa varient but it's still probably better than nothing	20:12
pwr22	I would have thought there should be at least development work ongoing for new strains with all the vaccines I hope	20:13
pwr22	If not... well that's short sighted	20:13
pwr22	<LjL "i couldn't even get the flu vacc"> They phone me to get mine, had to go to the surgery at a precise time, they were only letting 4 people in at once, and you were directed to stand on a marker on the floor (1-4)	20:14
pwr22	When you went in, they put the jab straight in then send you out	20:14
pwr22	It was very efficient ha	20:14
pwr22	We were of course all masked up and stuff too	20:14
pwr22	and not allowed to touch anything	20:14
pwr22	and had to use hand sanitizer	20:15
LjL	pwr22, here it was all left up to GPs who usually rent small apartments for their practice, and in my region we simply didn't get enough vaccines (they didn't even have enough for the categories who usually get it free)	20:15
LjL	pwr22, there is work, Moderna is working on a booster for the variants, and they said it should take them about 6 weeks to have a variant vaccine developed. but... then you need to produce and distribute it, when potentially you still have large stocks (not really, right now, but potentially) of the older type :\	20:16
LjL	i see it as a very difficult race	20:16
LjL	as to AstraZeneca they didn't do a great job with their confusing trials to begin with in my opinion, and their vaccine didn't really seem all that effective on the initial variant in the first place	20:16
semitones	How are the Russian and Chinese vaccines doing?	20:22
semitones	I didn't realize vaccines would be so nationalized but I guess it makes sense that governments would vaccinate their populations first	20:23
blkshp	It's quite obvious really that the Huge miltinational pharmacutical would make the best. They get the most money!	20:24
blkshp	And have the experience. It's probably one good reason for the US drugs not being subscedised	20:25
de-facto	well to be fair we dont have any data that suggests that AZ shots cant protect from severe or fatal progressions, that recent trial was said to have taken place with young participants, too few of them to get data on severe cases that are rare in that age cohort	20:31
de-facto	hence i guess the assumption is likely to hold that protection for severe or fatal progressions still is there, even if not so much for symptomatic cases with the new variant	20:32
Brainstorm	Updates for France: +266 deaths (now 79166) since 23 hours ago	20:44
Brainstorm	New from r/WorldNews: worldnews: Quick-spreading coronavirus variant is doubling each 10 days within the US → https://is.gd/TQqrDq	20:45
-RSSBot[LjLmatrix- Feed: Bando per il finanziamento di progetti di cooperazione internazionale – pubblicazione della graduatoria e dell’elenco degli esclusi ( http://www.governo.it/it/articolo/bando-il-finanziamento-di-progetti-di-cooperazione-internazionale-pubblicazione-della )		20:59
de-facto	.title https://www.sciencemag.org/news/2021/02/south-africa-suspends-use-astrazenecas-covid-19-vaccine-after-it-fails-clearly-stop	20:59
Brainstorm	de-facto: From www.sciencemag.org: South Africa suspends use of AstraZeneca’s COVID-19 vaccine after it fails to clearly stop virus variant \| Science \| AAAS	20:59
pwr22	<LjL "as to AstraZeneca they didn't do"> Yeah I initially thought it was worse too though as more data came out it seemed that it wasn't too bad	21:00
pwr22	I do think the RNA based ones had a better overall result though	21:01
de-facto	.title https://www.youtube.com/watch?v=382YlYwEl5k not sure maybe there were some remarks in that?	21:02
Brainstorm	de-facto: From www.youtube.com: Media briefing on COVID-19 - YouTube	21:02
LjL	pwr22, i still have doubts that the "better" data may have been a little too cherry-picked	21:05
LjL	you can always find 100% efficacy if you take only the people who didn't get COVID :P	21:05
pwr22	We'll just have to see I guess	21:05
pwr22	I'm sure it will come to light in time if we vaccinate everyone and it just makes no difference 😀	21:06
Brainstorm	New from Medical Xpress: Is there a connection between vitamin D deficiency and COVID-19?: Several recent studies have looked at the impact of vitamin D on COVID-19. One study of 489 people found that those who had a vitamin D deficiency were more likely to test positive for the virus that causes COVID-19 than people who had normal levels of vitamin D. → https://is.gd/H3wyd7	21:09
Brainstorm	New from Medical Xpress: Diseases, Conditions, Syndromes: Illinois county reverses decision; will allow pregnant and lactating women to get COVID-19 vaccines → https://is.gd/df7vk5	21:21
Brainstorm	Updates for Spain: +46642 cases (now 3.0 million), +909 deaths (now 62295) since 2 days ago	21:21
Brainstorm	New from Ars Technica: Gaming & Culture: A couple clings to shared past amid a memory-wiping pandemic in Little Fish → https://is.gd/1Mpx1C	21:33
Brainstorm	New from r/WorldNews: worldnews: Researchers engineer a tiny antibody capable of neutralizing the coronavirus → https://is.gd/M1PKen	21:46
semitones	Lil ^ that is a cool article	22:00
semitones	Ljl ^^	22:00
Brainstorm	New from Medical Xpress: WHO warns against dismissing AstraZeneca vaccine after setbacks: The World Health Organization and its Covax partners cautioned Monday against dismissing AstraZeneca's COVID vaccine after several setbacks, insisting it remained an important, life-saving tool. → https://is.gd/4je53c	22:10
de-facto	btw that press conference from WHO i linked above (youtube) is quite interesting	22:37
Brainstorm	Updates for France: +362 deaths (now 79319) since 21 hours ago	22:54
CoronaBot	/r/covid19: Common asthma treatment reduces need for hospitalisation in COVID-19 patients, study suggests (83 votes) \| https://oxfordbrc.nihr.ac.uk/common-asthma-treatment-reduces-need-for-hospitalisation-in-covid-19-patients-study-suggests/ \| https://redd.it/lfkm6x	23:03
Brainstorm	New from In The Pipeline: How You Make an Adenovirus Vaccine: The other day I had a look at the process used to make the mRNA vaccines, so I thought it would be a good idea to do the same for the adenovirus vector ones, such as J&J, Oxford/AstraZeneca, CanSino, Gamaleya et al. It’s a different system, with its own advantages and disadvantages, and [... want %more?] → https://is.gd/SJUMRD	23:12
Brainstorm	Updates for Switzerland: +38 deaths (now 9651) since 7 hours ago	23:19
CoronaBot	/r/coronavirus: New U.S. COVID-19 deaths down, cases under 100K for 1st time since November (10163 votes) \| https://www.upi.com/Top_News/US/2021/02/08/New-US-COVID-19-deaths-down-cases-under-100K-for-1st-time-since-November/8431612785426/ \| https://redd.it/lfau20	23:33
Brainstorm	New from Shane Crotty: @profshanecrotty: R to @profshanecrotty: But, they also find that the immunized people now also make excellent neutralizing antibody responses to the South Africa variant! (B1351)A massive jump in neutralizing antibodies. → https://is.gd/wPHbT0	23:36
Jigsy	So Mom's cousin died of COVID-19 today.	23:45
CoronaBot	/r/covid19: Decreased SARS-CoV-2 viral load following vaccination (82 votes) \| https://www.medrxiv.org/content/10.1101/2021.02.06.21251283v1 \| https://redd.it/lfiqma	23:45
pwr22	Oh no ☹️	23:46
pwr22	I'm sorry to hear that	23:46
pwr22	How's she doing? Were they close?	23:47
Jigsy	She's a bit shocked.	23:47
Jigsy	I never met the guy, so I'm just indifferent about the entire thing.	23:48
Jigsy	I know that seems cold, but still.	23:48
Brainstorm	New from Shane Crotty: @profshanecrotty: R to @profshanecrotty: First evidence that an immunization can elicit high neutralizing antibodies against the SA variant (B1351). I.e., the variant is not invisible to good human antibodies. → https://is.gd/FGvSzg	23:49
Jigsy	Fucking thumb's driving me nuts.	23:51

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