libera/##covid-19/ Wednesday, 2021-01-20

DocScrutinizer05	sounds good	00:04
DocScrutinizer05	and yes, that's what they told	00:04
LjL	in the end our government baaarely got a majority in the Senate	00:10
LjL	iow they got a relative, not absolute majority	00:10
LjL	because Renzi's party abstained	00:10
LjL	it's going to either be shaky for a long time, or just collapse	00:11
de-facto	yet stability and agility is of quite some importance especially in crisis times	00:14
Brainstorm	Updates for Rwanda: +289 cases (now 11548), +2 deaths (now 148) since a day ago	00:14
DocScrutinizer05	LjL: oh, they formed a new one, or established a coexistence or whatever?	00:21
Brainstorm	New from NPR: Pharmacist Accused Of Tampering With COVID-19 Vaccine Doses Charged With Misdemeanor: Steven Brandenburg, the Wisconsin pharmacist who admitted to removing some 570 doses of the Moderna vaccine from cold storage last month, has been charged with attempted criminal damage to property. → https://is.gd/Yaklt6	00:21
p1gasssu	what is the efficacy of single dose of Pfizer?	00:21
DocScrutinizer05	a very good question	00:21
LjL	DocScrutinizer05, it's all pretty unclear in typical italian fashion. Renzi wanted to get out of the majority, but some in his party didn't (or that's the story i hear anyway), so they abstained, so from now on they'll vote either for or against things on their own merits. then a couple of senators from Forza Italia (Berlusconi's party, until now and still currently in the opposition) actually voted for the government, and i think some other random	00:22
LjL	people from other parties too, as well as 3 senators for life (who are like 90 and came to the Senate for this one thing but certainly won't be around to vote for each individual law)	00:22
DocScrutinizer05	it seems it's higher than most expect. I heard the second dose is primarily for durability of the immunization, not so much for a huge part of the initial immunity	00:23
DocScrutinizer05	LjL: italy live	00:24
DocScrutinizer05	you prolly got more goverments since WW-II than all your neighbors together ;-D	00:25
LjL	that's not always a bad thing i think	00:27
LjL	but sometimes it's a bad thing	00:27
LjL	p1gasssu, if you read their phase 3 paper there is a graph that shows very clearly how the cases diverge between vaccine arm and placebo arm. i get the impression, aside from exact numbers, that it's like DocScrutinizer05 says	00:28
de-facto	.title https://www.nejm.org/doi/full/10.1056/NEJMoa2034577 <-- p1gasssu look at Figure 3	00:28
LjL	%link pfizer phase 3	00:28
Brainstorm	LjL, https://www.pfizer.com/news/press-release/press-release-detail/pfizer-and-biontech-announce-vaccine-candidate-against (Pfizer and BioNTech Announce Vaccine Candidate Against COVID-19 Achieved Success in First Interim Analysis from Phase 3 Study) in a press release where they state that their BNT162b2 vaccine has more than 90% efficacy, based on 94 participant who got COVID-19 [... want %more?]	00:28
Brainstorm	de-facto: From www.nejm.org: Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine \| NEJM	00:28
LjL	you win i lose	00:28
de-facto	"Between the first dose and the second dose, 39 cases in the BNT162b2 group and 82 cases in the placebo group were observed, resulting in a vaccine efficacy of 52% (95% CI, 29.5 to 68.4) during this interval and indicating early protection by the vaccine, starting as soon as 12 days after the first dose."	00:28
p1gasssu	someone was quoting from this : https://www.eldiario.es/internacional/inyeccion-unica-dosis-vacuna-efectiva-esperado_1_6944139.html	00:28
LjL	oh that's much lower than i thought	00:28
LjL	how many of those cases were during the first 10-12 days?	00:29
de-facto	keep the following in mind though: those infections seen in the vaccination group directly after first dose probably originate from transmissions prior to or before the protection started at ~12 days after first dose	00:30
de-facto	so actually those very many very early cases woudl have to be subtracted because there could not possibly have been a protection from the first shot already in place	00:31
CoronaBot	04/r/covid19: Rogue antibodies could be driving severe COVID-19 (83 votes) \| https://www.nature.com/articles/d41586-021-00149-1 \| https://redd.it/l0u6q4	00:31
LjL	%cases japan	00:32
Brainstorm	LjL: In Japan, there have been 334328 confirmed cases (0.3% of the population) and 4548 deaths (1.4% of cases) as of 7 hours ago. 6.0 million tests were performed (5.5% positive). See https://offloop.net/covid19/?default=Japan for time series data.	00:32
de-facto	https://en.wikipedia.org/wiki/Vaccine_efficacy	00:33
LjL	%title https://www.theguardian.com/world/2021/jan/19/hospitals-japan-close-collapse-serious-covid-cases-soar	00:33
de-facto	.title	00:33
Brainstorm	de-facto: From en.wikipedia.org: Vaccine efficacy - Wikipedia	00:33
Brainstorm	LjL: From www.theguardian.com: Hospitals in Japan close to collapse as serious Covid cases soar \| World news \| The Guardian	00:33
LjL	"The increase, coupled with the discovery of the first recorded community transmissions of a fast-spreading strain of Covid-19 initially identified in Britain, is adding to pressure on the prime minister, Yoshihide Suga, to move quickly to protect stretched medical services."	00:33
p1gasssu	de-facto, so that graph figure 3, shows 1 dose reduces incidence for the full 112 days	00:34
p1gasssu	?	00:34
de-facto	p1gasssu, that graph shows the number of symptomatic COVID-19 cases over time to compare the vaccinated with the unvaccinated group	00:34
LjL	we can't know that	00:35
LjL	we don't know what a single dose does past the time a single does has been used	00:35
DocScrutinizer05	>>vaccine efficacy of 52% (95% CI, 29.5 to 68.4) during this interval and indicating early protection by the vaccine, starting as soon as 12 days after the first dose<< and increasing even beyond nominal date of second dose, also without second dose	00:35
LjL	DocScrutinizer05, how is that known? was there a single-dose arm?	00:35
de-facto	VaccineVfficacy = (AttackRateUnvaccinated - AttackRateVaccinated) / AttackRateUnvaccinated with AttackRateX = Cases / Susceptible	00:35
p1gasssu	i've actually had 1 dose myself	00:36
de-facto	go for the second dose in time similar to the one in the tirals	00:36
de-facto	*phase III trials	00:36
DocScrutinizer05	LjL: it's heneric knowledge about immunity buildup after vaccination. From Drosten podcast	00:36
p1gasssu	yeah I'm scheduled	00:36
LjL	DocScrutinizer05, are we sure we can extrapolate generic knowledge to a type of vaccine we're just now trying, on a disease we didn't know about until a year ago?	00:37
DocScrutinizer05	immunity from first shot takes 8 weeks and more to completely build up to what it gets from only one shot	00:37
DocScrutinizer05	yes, since this is generic immune system stuff common to all faintly similar cases	00:38
p1gasssu	i'm thinking a week after 2nd dose to being more active	00:39
de-facto	hence for BNT162b2 between 1st and 2nd dose we would have ARU = 82 / 18325, ARV = 39 / 18198 giving VE = (ARU - ARV) / ARU = ((82 / 18325) - (39 / 18198))/ (82 / 18325) = 0.521071 indeed their ~52%	00:40
de-facto	so how many cases should we subtract for the starting period then?	00:40
DocScrutinizer05	the way immune system reacts to the pathogen doesn't differ no matter if the pathogen is synthesized in a own cell from a mRNA or it's some dead or modulated virus or fragments of that virus	00:40
DocScrutinizer05	at least that's what I understood from that podcast	00:43
DocScrutinizer05	the statement been sth like >>second shot doesn't contribute much to the efficiency but mainly to the duration, so the immunity stays for years<<	00:44
p1gasssu	so maybe 8 weeks from 1st does is ideal	00:46
p1gasssu	dose	00:46
DocScrutinizer05	the recommended window for second dose BNT162 is up to 6 weeks iirc	00:51
DocScrutinizer05	though 8 weeks won't be a huge problem most likely	00:52
DocScrutinizer05	just they didn't test it	00:52
p1gasssu	I mean I'll get 2nd does @ 3 weeks, but then when is ideal to return to the world	00:52
DocScrutinizer05	aaah, you're "safe" after week4 iirc	00:53
DocScrutinizer05	de-facto: does the phase3 paper say in which week the antibody level reached a plateau?	01:00
Brainstorm	New preprint: Prediction of Ciclesonide Binding Site on Middle-East Respiratory Syndrome Coronavirus Nsp15 Multimer by Molecular Dynamics Simulations by Shun Sakuraba et al, made available as preprint on 2021-01-19 at https://api.figshare.com/v2/articles/13602731	01:04
de-facto	DocScrutinizer05, no idea you would have to look yourself	01:14
de-facto	afaik Moderna published antibody decline for longer periods, i guess only with graphs	01:14
de-facto	dangit i want the raw data of the BNT162b2 trial	01:18
de-facto	from the numbers the vaccinated group always stayed below the unvaccinated group, even prior to a possible onset of protection from first dose it seems	01:20
de-facto	in the first 12 days id estimate ~47 cases in both the placebo and vaccinated group if vaccination could not have had any effect but the vaccinated group only got 39 cases between the doses thats already 21 days (in which the placebo group got 82 cases)	01:21
Brainstorm	Updates for France: +14709 cases (now 3.0 million), +744 deaths (now 71342) since 23 hours ago — Netherlands: +5738 cases (now 925883), +89 deaths (now 13162) since 23 hours ago — Switzerland: +67 deaths (now 8859) since 21 hours ago	01:22
p1gasssu	de-facto, I don't think they get into it, thats a short paper	01:23
de-facto	in placebo we would have 82-47 = 35 and in vaccinated ~4 group between 12 days after 1st dose and date of 2nd dose (21 days after 1st dose) hence VE = ((35/21686) - (4/21669)) / (35/21686) = 0.885625 or ~86%	01:26
de-facto	does my estimation make any sense?	01:26
de-facto	its from 12->21 days after 1st dose in the zoomed graph in https://www.nejm.org/na101/home/literatum/publisher/mms/journals/content/nejm/2020/nejm_2020.383.issue-27/nejmoa2034577/20210108/images/img_xlarge/nejmoa2034577_f3.jpeg	01:27
de-facto	estimation of those 47 cases in placebo group in first 12 days would be 82*12/21 = 46.8571 ~ 47	01:29
de-facto	but the quality of immune protection probably increases even after 21 days from 1st dose even without second dose, but thats just a quess without any data	01:31
de-facto	and also those 4 cases, they were taken from that graphic with narrowing eyes in suspicion	01:33
de-facto	hence i want the raw data	01:33
DocScrutinizer05	de-facto: too low numbers	01:33
de-facto	?	01:33
DocScrutinizer05	not statistically relevant	01:34
Brainstorm	New from The Atlantic: The Pandemic Is Now in Biden’s Hands: Tomorrow, America inaugurates a new president. With the transfer of power comes the transfer of responsibility for the COVID-19 pandemic. On the eve of Joe Biden’s inauguration, the toll of the pandemic stands at 23.9 million cases and 392,428 deaths, according to the COVID Tracking [... want %more?] → https://is.gd/DAxJNe	01:34
DocScrutinizer05	it's like "in 60 dice throws we expect 10 times a 6, but there were 15"	01:35
DocScrutinizer05	your math is probably right but meaningless	01:36
DocScrutinizer05	my take on it	01:36
de-facto	what i dont really understand is: if both cohorts, placebo and verum are of similar size, how come placebo would have ~47 cases (from linear interpolation) in first 12 days but not the vaccinated group (assuming there could have no protection occured)?	01:38
de-facto	DocScrutinizer05, and the graphic kinda indicates that the slope does not have a visible kink from the impact of 2nd dose, hence it cant have had such a dramatic effect on additional cases as the 1st dose clearly separating verum from placebo by its kink	01:46
LjL	We all have our kinks	01:47
de-facto	id even say the slope stays more or less at those ~90%-ish value after the first 12 days	01:47
de-facto	lil isnt rapid change of slope called a kink in the curve?	01:48
LjL	It was just a joke	01:49
de-facto	lol i know	01:49
LjL	I agree with DocScrutinizer05 though, I can't prove in with math but just intuitively it seems to me the difference you see between the 12 days in verum vs placebo could just be a little expectable statistical fluke. If not, then perhaps some early-bird antibodies begin to have some action even before 10 days?	01:51
de-facto	so no kinky curve at 2nd dose in verum cohort would mean very good protection already from 1st dose on :P	01:52
LjL	Well what protection comes up with your formula if you subtract the cases in the first 12 days from both arms?	01:52
de-facto	thats exactly what i tried above	01:53
de-facto	ignore first 12 days and look at data from day 12 up to day 21 (2nd dose) but not after day 21 because it could have had an additional influence	01:54
LjL	de-facto: then maybe I'm misunderstanding something. I thought you could get the exact number of cases by looking at the points in the graph but I might remember wrong as I've not actually looked at the graph again	01:55
de-facto	yeah but some points may represent several cases	01:55
LjL	No chance of raw data being provided as attachments, or perhaps in the FDA report?	01:56
de-facto	its not always the same amount the go up	01:56
de-facto	i tried looking for supplemental material but it does not include raw data	01:56
LjL	I see	01:56
de-facto	one can ask Pfizer and has to provide a reason then they give it	01:57
LjL	Well, I think that qualitatively we can say the protection is good after those 12 days. Quantitatively maybe we can't say exactly.	01:57
LjL	The German equivalent of a FOIA?	01:57
de-facto	well since the curve for the verum cohort is not kinky at 2nd dose the majority of protection was already there (hence must have originated from 1st dose)	01:58
LjL	I tend to agree, although there could be further slight divergence after the second dose that is not very visible but adds some percents	01:58
de-facto	otherwise 2nd dose would have more impact and produce a visible kink at the curve	01:58
de-facto	yeah sure there is a slight difference, so maybe from 86%->94% or such?	01:59
LjL	Possible	01:59
de-facto	i just dont understand why both curves dont overlap prior to those 12 days where protection is assumed to kick in	02:00
de-facto	maybe the vaccinated stayed more at home because of fatigue? :D	02:00
de-facto	and of course protection already smoothly begins before 12 days	02:02
de-facto	yet verum is consistently below placebo even in the first 7 days	02:03
de-facto	ok well that for sure is not statistically significant, so yeah probably should not think too much about it	02:04
LjL	you're getting a little too fixated over it perhaps, but your hypothesis that maybe the vaccinated people stayed at home more due to side effects seems plausible to me	02:05
de-facto	what really is very much significant is the separation of both curves at that ~12 days point after 1st dose and once the slopes separated they stay more or less constant at their very much different rates of new cases, hence the protection is really extremely good staying consistently at those 90%-is values	02:07
de-facto	i wonder if Israel provides separated data for infections in non-vaccinated vs vaccinated, maybe even with vaccination dates attached? :D	02:12
de-facto	would be largest trial we have ongoing ...	02:13
de-facto	two additional columns in their database for new detected infections: 1st vaccine dose and 2nd vaccine dose date	02:14
de-facto	hopefully they thought about that opportunity it should be in their health system data anyhow	02:15
de-facto	LjL https://www.fda.gov/media/144246/download page 58	02:31
de-facto	they provide a column at the bottom of the graphic	02:31
de-facto	err row even with (weekly?) columns?	02:32
LjL	de-facto, yeah i don't understand the timescale of that	02:34
LjL	i was thinking about Israel earlier, we should focus on their data	02:34
LjL	don't know how much they tend to use Hebrew versus English	02:34
LjL	de-facto, but let me understand, is this actually an arm where they only took one dose?	02:34
LjL	oh yeah it must be weekly	02:35
de-facto	.title https://imgur.com/a/GJeNle9 https://i.imgur.com/KdCfORb.png <-- extracted the graphic	02:35
Brainstorm	de-facto: From imgur.com: BNT162b2:Â Cumulative Incidence Curves for the First COVID-19 Occurrence After Dose 1 â Dose 1 All-Available Efficacy Population - Album on Imgur	02:35
LjL	119/7 = 17 which is the number of datapoint shown	02:35
LjL	what does "No. at risk" mean though?	02:36
LjL	it goes down	02:36
LjL	to zero	02:36
de-facto	so for cases between 14 days and 21 days after 1st dose we would have ARU = (73 - 55) / 20366; ARV = (39 - 37) / 20281; VE = (ARU - ARV) / ARU = 0.888423 ~ 89% fitting in the ~90%-ish slope of the vaccinated saturating towards 94% 7 days after 2nd dose onwards	02:43
de-facto	number at risk I understand as current participants in that arm able to be susceptible for an infection	02:44
de-facto	equation from https://en.wikipedia.org/wiki/Vaccine_efficacy VaccineVfficacy = (AttackRateUnvaccinated - AttackRateVaccinated) / AttackRateUnvaccinated with AttackRateX = Cases / Susceptible	02:46
Brainstorm	New from BBC Health: Covid smear-test delays prompt calls for home HPV tests: Delays to smear tests in lockdown prompt cervical cancer charities to call for home-testing kits. → https://is.gd/IaUrgz	02:48
de-facto	"<DocScrutinizer05> de-facto: does the phase3 paper say in which week the antibody level reached a plateau?" not this paper but another paper does go into every detail of the immunogenicity of BNT162b2	03:01
de-facto	.title https://www.medrxiv.org/content/10.1101/2020.12.09.20245175v1	03:02
Brainstorm	de-facto: From www.medrxiv.org: BNT162b2 induces SARS-CoV-2-neutralising antibodies and T cells in humans \| medRxiv	03:02
de-facto	page 32: Figure 1 \| BNT162b2-induced IgG concentrations and virus neutralisation titers.	03:02
de-facto	similar to page 81 of the FDA paper "Figure A3.1. Geometric Mean Concentrations and 95% CI: SARS-CoV-2 S1-binding IgG Level Assay – Phase 1, 2 Doses,	03:03
de-facto	21 Days Apart – 18-55 Years of Age – BNT162b2 – Evaluable Immunogenicity Population"	03:03
de-facto	so 2nd dose does increase binding IgG binding GMC 7-fold in the young 18-55y and 26-fold in the older 65-85y between 21d and 28d (hence impact from 2nd dose)	03:07
de-facto	thats quite a lot esp for the elderly	03:08
de-facto	set seems protection is already there even from the first dose	03:08
de-facto	those were the FDA paper numbers	03:09
de-facto	the medrxiv paper shows also a virus neutralization titer graph with similar results	03:11
de-facto	~16-fold increase in virus neutralization by 2nd dose	03:12
de-facto	so it seems protection already is very good after 1st dose, 2nd dose pushes antibody levels even further up (for the young 7-fold, especially for the elderly 26-fold, hence almost 4 times more than for younger), so 2nd dose probably making the immunity more long lasting especially in the elderly	03:16
de-facto	Does that answer your question DocScrutinizer05 ?	03:16
de-facto	there is no plateau but a maximum at day 28 after first dose (one week after 2nd dose)	03:18
de-facto	daily decay of IgG level ca 1.2%	03:27
de-facto	on a linear fit model for day 28 till day 85	03:27
Shaded	Got my first dose today, least painful shot I've had in a long time. No side effects so far	03:28
de-facto	nice to hear :)	03:28
de-facto	would be interesting if you keep us updated about your experience for a few days	03:29
de-facto	Shaded, you got the BioNTech/Pfizer vaccine right?	03:32
Shaded	de-facto: I'll definitely let you know if anything changes. Yes, I got the pfizer	03:35
de-facto	nice one :)	03:35
de-facto	id wish i could get it too already	03:35
de-facto	yet its not available here in Germany for "normal" people like me	03:36
Shaded	I got very lucky, jumped on a batch reserved for young people who are immunocompromised	03:37
de-facto	When i fit a nonlinear model like Exp[ Log[2] t / t_half] on the IgG antibody titers i get a t_half = 34.7d hence they decay by half every ~35 days or month	03:41
de-facto	if they decay with that exponential rate it would mean the 2nd dose pushes the IgG titers above the level of the first dose for a duration of ~139.37 days or roughly 4.65 months	03:45
Brainstorm	New from Bloom Lab: @VinciZijun: RT by @jbloom_lab: Our newest data showed antibody and memory B cell responses in a cohort of 20 volunteers who received either the Moderna (mRNA-1273) or Pfizer/BioNTech (BNT162b2) vaccines. 1/ https://www.biorxiv.org/content/10.1101/2021.01.15.426911v1 → https://is.gd/lRcsfd	03:50
de-facto	oooh very interesting paper ^^	03:51
LjL	"However, activity against SARS-CoV-2 variants encoding E484K or N501Y or the K417N:E484K:N501Y combination was reduced by a small but significant margin."	03:53
de-facto	yeah :/	03:54
LjL	"However, neutralization by 14 of the 17 most potent mAbs tested was reduced or abolished by either K417N, or E484K, or N501Y mutations."	03:54
de-facto	btw correction: 2nd dose pushes IgG titers for 110 days above the one on day 21 (from first dose)	03:54
de-facto	.title https://twitter.com/VinciZijun	03:58
Brainstorm	de-facto: From twitter.com: error parsing title ('NoneType' object has no attribute 'string')	03:58
de-facto	Vinci Zijun Wang @VinciZijun Immunologist from Nussenzweig's lab at Rockefeller University	03:59
Brainstorm	New from The Indian Express: World: Live Updates: On eve of inauguration, Joe Biden pays tribute to victims of Covid-19 → https://is.gd/ALioRg	04:02
de-facto	"Our experiments indicate that these variants, and potentially others that carry K417N/T, E484K and N501Y mutations, can reduce the neutralization potency of vaccinee plasma. The comparatively modest effects of the mutations on viral sensitivity to plasma reflects the polyclonal nature of the neutralizing antibodies in vaccinee plasma."	04:18
de-facto	"Nevertheless, emergence of these particular variants is consistent with the dominance of the class 1 and 2 antibody response in infected or vaccinated individuals and raises the possibility that they emerged in response to immune selection in individuals with non-sterilizing immunity"	04:19
de-facto	"What the long-term effect of accumulation of mutations on the SARS-CoV-2 pandemic will be is not known, but the common cold coronavirus HCoV-229E evolves antigenic variants that are comparatively resistant to the older sera but remain sensitive to contemporaneous sera"	04:22
de-facto	.title https://www.biorxiv.org/content/10.1101/2020.12.17.423313v1	04:22
Brainstorm	de-facto: From www.biorxiv.org: A human coronavirus evolves antigenically to escape antibody immunity \| bioRxiv	04:22
de-facto	"Thus, it is possible that these mutations and others that emerge in individuals with suboptimal or waning immunity will erode the effectiveness of natural and vaccine elicited immunity. The data suggests that SARS-CoV-2 vaccines may need to be updated and immunity monitored in order to compensate for viral evolution."	04:22
de-facto	from that second paper about HCoV-229E	04:24
de-facto	"In some cases, sera that neutralize contemporaneous 229E viral strains with titers >1:100 do not detectably neutralize strains isolated 8–17 years later. The decreased neutralization of “future” viruses is due to antigenic evolution of the viral spike, especially in the receptor-binding domain. If these results extrapolate to other coronaviruses, then it may be advisable to periodically update SARS-CoV-2 vaccines."	04:24
Brainstorm	Updates for France: +18727 cases (now 3.0 million) since 20 hours ago — St. Vin. and Gren.: +108 cases (now 602) since 23 hours ago — Netherlands: +4419 cases (now 926951), +92 deaths (now 13186) since 20 hours ago — New Zealand: +5 cases (now 2267) since 2 days ago	04:41
Brainstorm	New from The Indian Express: World: Deep in remote Amazon, indigenous villagers receive coronavirus vaccine → https://is.gd/ff1JYA	04:51
Brainstorm	New from r/WorldNews: worldnews: It took 4 years of intense combat to kill 407k Americans in WW2. It took COVID-19 and mismanagement by the Trump administration only one to reach 400k+ deaths → https://is.gd/LICKbW	05:16
Brainstorm	New from The Indian Express: World: Germany warns of border closures amid fear of COVID-19 mutations → https://is.gd/7SbQBL	05:41
rmonten[m]	So Israel's vaccinations are going super fast (30% had a 1st shot already, about 1%/day extra) so when should we expect their case numbers go down drastically?	05:46
de-facto	very good question, so we just tried to guess the protection 14 days after 1st shot from symptomatic infections to be around 89% or such, but how much does it protect from transmission with asymptomatic infection?	06:13
de-facto	daily new infections N(t) = N(t0) * R ^ ((t-t0)/t_serial) at time t are an extrapolation from a known value N(t0) at time t0 with assumed constant Reproduction Number R multiplied by itself as many times as there fit generations of serial time t_serial between t and t0	06:17
de-facto	but what if reproduction number R itself it time dependent R(t)? then it would have to be calculated in an iterative way say k~(t-t0)/t_serial hence. N(t) = N(t0) * R(t0) * R(t0 + t_serial) * .... * R(t0 + k * t_serial)	06:21
de-facto	if a vaccine protects with an efficiency of e(t) from transmission (not only symptomatic infection) a given reproduction number R(t) in an non-vaccinated population would be reduced to Rv(t) = R(t) * ( 1 - e(t) * v(t) ) for a given partition v(t) in the whole population	06:24
de-facto	hence plugging that into above iterative approach for time dependent reproduction we would get N(t) = N(t0) * R(t0) * R(t0 + t_serial) * .... * R(t0 + k * t_serial) * ( 1 - e(t0) * v(t0) ) * ( 1 - e(t0 + t_serial) * v(t0 + tserial) ) * ... * ( 1 - e(t0 + k * t_serial) * v(t0 + k * t_serial) )	06:28
de-facto	Israel is changing both R(t) (with lockdown measures to contain their outbreak) and v(t) (with doing their vaccinations) at the same time	06:33
de-facto	and the efficiency e(t) to prevent virus transmission by vaccination (even for asymptomatic infections) is unknown afaik	06:34
de-facto	since they focused on vaccinations for the vulnerable (and probably have given most of them the first shot already) their protections should be visible on reduction in fatalities as soon as those cases that got infected prior to that protection becoming effective (maybe 2 weeks after they received their first shot) had their outcome determined (delay may be long though, 2-4 weeks after infection or such)	06:39
de-facto	so if we dont see a significant drop in their fatalities 4-6 weeks after a significant portion of the vulnerable have received their first shot in Israel something must have went wrong	06:41
rmonten[m]	de-facto: thanks for that elaborate answer! I'll definitely be keeping a close eye on their numbers in the coming weeks.	06:46
rmonten[m]	I don't have a difference equation to justify it, but if they keep vaccinating at this rate, they might complete everyone's second dose around the end of March or so (assuming ++1%/day and ~80% of the population eligible & willing, although that may be optimistic)	06:51
rmonten[m]	So at least by then, they'll be able to relax measures	06:51
Brainstorm	New preprint: SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma by Constantinos Kurt Wibmer et al, made available as preprint on 2021-01-19 at https://biorxiv.org/cgi/content/short/2021.01.18.427166 [... want %more?]	06:57
de-facto	btw just thought about a continuous way of above discrete product	07:15
de-facto	a discrete product R1 * R2 * ... * Rk = Exp[ Log [ R1 * R2 * ... * Rk ] ] = Exp[ Log[R1] + Log[R2] + ... Log[Rk] ] ~ Exp [ Int[ Log[ R(m) ], dm with m=1...k ] ] hence could be approximated by an integral over the natural log in an exponential	07:16
de-facto	that would give the continuous approach for a time varying reproduction R(t) by the number of infections N(t) = N(t0) * Exp[ Int[ Log[ R(tau) ] dtau ] ] with the time integral (dtau) in the limits from t0 to t	07:19
Brainstorm	Updates for New Hampshire, United States: +1845 cases (now 58709), +5 deaths (now 938) since 2 days ago — France: +24701 cases (now 3.0 million), +726 deaths (now 71412) since 23 hours ago — Sevastopol, Ukraine: +100 cases (now 8516), +5 deaths (now 329) since 23 hours ago — United Kingdom: +33407 cases (now 3.5 million), +1612 deaths (now 91557) since 23 hours ago	07:35
de-facto	well actually the time integral would have to be normalized by generation time t_serial	07:49
Brainstorm	New from Trevor Bedford: @trvrb: R to @trvrb: And all this said, I'll be getting the vaccine as soon as I'm able. We have an amazing vaccine now that works against currently circulating viruses. And if it becomes necessary, this emerging situation can be dealt with through a forthcoming vaccine update. 10/10 → https://is.gd/R9Cf2S	08:09
Brainstorm	Updates for Belgium: +1479 cases (now 681250), +82 deaths (now 20554) since a day ago	08:18
Brainstorm	New from r/Coronavirus: Daily Discussion Thread \| January 20, 2021: The WHO pages contain up-to-date and global information. Please refer to our Wiki for additional information. → https://is.gd/6TC3lP	09:10
gigasu_shida	brilliant stuff de-facto ! bye	09:40
Brainstorm	New from BBC Health: Covid smear-test delays prompt calls for home HPV tests: Delays to smear tests in lockdown prompt cervical cancer charities to call for home-testing kits. → https://is.gd/IaUrgz	09:48
Brainstorm	New from Medical Xpress: WHO says UK strain in over 60 countries as Biden mourns COVID victims: The UK coronavirus strain has spread to at least 60 countries, the World Health Organization reported Wednesday, after US President-elect Joe Biden led a moving tribute to American victims. → https://is.gd/fnYX4c	10:12
Brainstorm	New from Medical Xpress: Partial lockdown in Beijing over COVID-19 outbreak: A partial lockdown was imposed on the Chinese capital Wednesday, with 1.6 million residents banned from leaving Beijing, after a handful of cases were detected. → https://is.gd/7yLjzo	10:24
Brainstorm	New from StatNews: The 9 biggest challenges Biden will face on Covid-19, from today on: It’s hard to overstate how many mammoth challenges Biden will face, starting today, as he wrangles with the Covid-19 pandemic. Here are 9 of the biggest. → https://is.gd/JxtkOk	10:37
Arsanerit	Does anyone know when the German FFP2/surgical mask order takes effect? It was announced last night.	10:39
Arsanerit	I ordered FFP2 masks but they have a 2 week delivery time :/	10:41
Brainstorm	New from StatNews: Opinion: Welcome back to the global health stage, America. You have a lot of work to do: By forging a new era of American partnership on global health with WHO and others, a new chapter will not only end the hardships of this global pandemic but lay… → https://is.gd/gzX4ES	10:49
Brainstorm	New from r/WorldNews: worldnews: India, ‘pharmacy of the world’, starts exporting COVID vaccines → https://is.gd/KdHEuy	11:26
Brainstorm	New from Virological.org: Latest posts: Spatio-temporal heterogeneity and the spread of lineage B.1.1.7 in the United Kingdom: Materials and Methods Mobile device data insights: We use anonymised and aggregated mobile data insights collected from the network operator, O2. The data is extrapolated to give a picture of movement trends of the UK [... want %more?] → https://is.gd/nS2tr0	11:51
Brainstorm	New from Il Sole 24 Ore: Covid-19, le big del pharma puntano sulla collaborazione: Addio alla guerra commerciale: Sanofi potrebbe fornire una soluzione alla crisi delle forniture Pfizer, mentre la svizzera Lonza produce componenti per Moderna → https://is.gd/ykPv3A	12:04
Brainstorm	New from Reddit (test): CoronaVirus_ITALIA: Evoluzione dei Paesi con il maggior numero di Vaccini Covid-19 Somministrati ogni 100 persone → https://is.gd/HuADDY	12:16
Brainstorm	New from r/WorldNews: worldnews: Preliminary results on new Covid-19 mutation found in South Africa. Has ability to bypass current immune response, reinfecting already immune Humans. → https://is.gd/itPwxc	12:41
Brainstorm	Updates for UAE: +3506 cases (now 263729), +6 deaths (now 762) since 22 hours ago	12:51
Brainstorm	New from BBC Health: (news): Birmingham and Nottinghamshire trusts offer 24-hour Covid vaccines → https://is.gd/BbAWs5	13:30
Brainstorm	New from StatNews: Pfizer-BioNTech Covid-19 vaccine works just as well against variant first detected in U.K., study indicates: The Covid-19 vaccine from Pfizer-BioNTech appears to work just as well against a fast-spreading variant of the coronavirus first identified in the United Kingdom as it does against earlier forms… → https://is.gd/FPtkpN	13:42
Brainstorm	Updates for Falkland Is.: +3 cases (now 35) since 7 days ago	13:53
Brainstorm	New from WHO Euro: (news): Health system strengthening and COVID-19 response in focus during WHO/Europe Regional Director’s visit to Ukraine → https://is.gd/0vYztC	13:55
DocScrutinizer05	>><LjL> DocScrutinizer05, are we sure we can extrapolate generic knowledge to a type of vaccine we're just now trying...<< https://www.reddit.com/r/Coronavirus/wiki/faq/#wiki_why_are_existing_vaccine_testing_paradigms_useful_for_testing_safety_of_mrna_vaccines.3F	13:56
DocScrutinizer05	>><de-facto> maybe the vaccinated stayed more at home because of fatigue? << quite plausible explanation	14:01
DocScrutinizer05	>><de-facto> Does that answer your question DocScrutinizer05 ?<< yes, many thanks :-)	14:03
Brainstorm	New from Medical Xpress: Turkey vaccinates one million people in first week: Turkey has vaccinated more than one million people against the novel coronavirus in the first week of a national inoculation drive, according to health ministry figures issued Wednesday. → https://is.gd/veXcpW	14:07
DocScrutinizer05	>>"However, neutralization by 14 of the 17 most potent mAbs tested was reduced or abolished by either K417N, or E484K, or N501Y mutations."<< mRNA should become multi-variant mix immediately	14:07
genera	maybe you have to keep vaccinatees at home between dose 1 and 2	14:10
DocScrutinizer05	sound consideration but probably neither realistic nor highly effective	14:15
DocScrutinizer05	anyway escape is a massive concern and we should already adapt the mRNA vaccines to include any foreseeable variants now, even if they are not found in the wild at large scale or at all	14:17
Brainstorm	New from New Scientist: Global spread of UK coronavirus variant could overwhelm health systems: The highly infectious B.1.1.7 coronavirus variant from the UK has now been reported in more than 50 countries, placing new urgency on the race to vaccinate the vulnerable → https://is.gd/l8EuyS	14:19
genera	maybe if we had tested the vaxes for the normal time period we would have found	14:19
genera	gosh ist mein Englisch schlecht.	14:19
DocScrutinizer05	even if the recent vaccine is supposed to be effective still against those variants (is it really?), adapting the vaccine to exactly cover the new variants will allow for even further mutations from those new variants that would then _not_ be covered anymore by the original "old" mRNA code	14:20
Arsanerit	I suspect that the scientists working at the vaccine companies know what they are doing and need to do.	14:29
ubLIX[m]	bookmark to finish reading later: https://blog.jonasneubert.com/2021/01/10/exploring-the-supply-chain-of-the-pfizer-biontech-and-moderna-covid-19-vaccines/	14:30
DocScrutinizer05	Arsanerit: hmm, yes we'd all hope so	14:37
Brainstorm	New from EMA: What's new: Medicine: Human medicines European public assessment report (EPAR): COVID-19 Vaccine Moderna, COVID-19 mRNA Vaccine (nucleoside modified), COVID-19 virus infection, Date of authorisation: 06/01/2021, Status: Authorised → https://is.gd/ApJcx9	14:57
CoronaBot	04/r/covid19: COVID19 Vaccine DOES NOT cause infertility! Please read our article (fertility physicians) (92 votes) \| http://www.fertstertdialog.com/posts/covid-19-vaccine-and-infertility-baseless-claims-and-unfounded-social-media-panic \| https://redd.it/l17mtn	15:01
CoronaBot	04/r/covid19: mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants (81 votes) \| https://www.biorxiv.org/content/10.1101/2021.01.15.426911v1 \| https://redd.it/l0yqe6	15:01
Brainstorm	New from Medical Xpress: Getting the COVID vaccine? A good night's sleep will help: Want to get the most out of your COVID-19 vaccine? Make sure you get some good rest before you get your shot, sleep experts say. → https://is.gd/9Ttc0C	15:09
CoronaBot	04/r/coronavirus: 400 Lights, For 400,000 Dead, Illuminate Lincoln Memorial Reflecting Pool (10088 votes) \| https://www.npr.org/sections/coronavirus-live-updates/2021/01/19/958449203/400-lights-for-400-000-dead-to-illuminate-lincoln-memorial-reflecting-pool \| https://redd.it/l0vwg1	15:13
Brainstorm	Updates for Benin: +144 cases (now 3557) since 6 days ago — Germany: +14129 cases (now 2.1 million) since 23 hours ago	15:14
Brainstorm	New from EMA: What's new: General: Treatments and vaccines for COVID-19: authorised medicines → https://is.gd/jcC1iP	15:22
Brainstorm	New from StatNews: Pharma: STAT+: Pharmalittle: Pfizer and BioNTech say vaccine is effective against Covid-19 variant; U.S. to join COVAX initiative → https://is.gd/ZhX1fM	15:35
Brainstorm	New from Medical Xpress: School closures still 'last resort' despite variants: WHO: Schools should only close as a last resort while research is under way into whether the new coronavirus variants affect children differently, the World Health Organization said Wednesday. → https://is.gd/1sKQUx	15:48
DocScrutinizer05	last resort??? how's that any resort? that's the possibly last leak in the kettle	15:52
DocScrutinizer05	and you're not done until you closed enough leaks so you keep some of the water inside when you need it	15:53
DocScrutinizer05	actually usually you want to close ALL leaks	15:54
DocScrutinizer05	an approach like >>duh, this leak is in an inconvenient to fix location, let's rather see if we can reduce diffusion of liquid through metal some more, maybe paint it<< is idiocy	15:57
DocScrutinizer05	honestly, I'm not all that happy with WHO performance	15:59
genera	microbial life matters too!	15:59
DocScrutinizer05	more often than not I just think >>STFU<<	16:00
Brainstorm	New from Ars Technica: Science: The persistence of memory in B cells: Hints of stability in COVID immunity → https://is.gd/qDeIRT	16:00
Brainstorm	New from Scientific American: Health: The White House--Scene of COVID Outbreaks under Trump--Will Get a Deep Clean for President-Elect Biden → https://is.gd/z6aUAS	16:12
Brainstorm	Updates for Switzerland: +2727 cases (now 504918), +32 deaths (now 8891) since 15 hours ago	17:06
Brainstorm	New from ClinicalTrials.gov: (news): Feasibility of Ayurveda in Patients With Mild-to-Moderate COVID-19: A Community-Based Participatory Research → https://is.gd/14f2uS	17:16
Brainstorm	Updates for Portugal: +14647 cases (now 581605), +219 deaths (now 9465) since a day ago — United Kingdom: +16294 cases (now 3.5 million), +664 deaths (now 92134) since 23 hours ago — Netherlands: +5114 cases (now 929574), +93 deaths (now 13253) since 20 hours ago	17:31
CoronaBot	04/r/coronavirus: Pfizer-BioNTech vaccine found to be effective against Covid variant discovered in the UK (10466 votes) \| https://www.cnbc.com/2021/01/20/covid-pfizer-biontech-vaccine-likely-to-be-effective-against-uk-variant.html \| https://redd.it/l17fm1	17:50
LjL	Germany has more than 1700 deaths today?	18:25
Brainstorm	New from EMA: What's new: News: Extra dose from vials of Comirnaty COVID-19 vaccine → https://is.gd/CY0OSH	18:30
Brainstorm	Updates for St. Barthelemy: +49 cases (now 300) since 5 days ago — Canada: +5100 cases (now 723538), +147 deaths (now 18338) since 22 hours ago	18:58
Brainstorm	New from Medical Xpress: EU moves to bloc-wide recognition of antigen tests: EU envoys on Thursday struck preliminary agreement on having antigen tests for COVID-19 carried out in any member country recognised by all 27 countries in the bloc, diplomats told AFP. → https://is.gd/Y9tePQ	19:07
de-facto	RKI COVID-19 Germany 2021-01-20: Weekly Incidence 123.5/100k, Infections +15974 (2068002 total), Fatalities +1148 (48770 total), COVID@ICU 4808 (incl 2764 on ventilator)	19:13
de-facto	LjL, what makes you think 1.7k fatalities in Germany?	19:16
LjL	de-facto, my parents told me	19:17
de-facto	also the source of worldometers does state 1139 fatalities https://interaktiv.tagesspiegel.de/lab/karte-sars-cov-2-in-deutschland-landkreise/	19:17
LjL	maybe they misheard about England which has 1820 :\	19:18
de-facto	covidly says +1.154	19:18
de-facto	for Germany	19:19
genera	and johns hopkins?	19:20
de-facto	yeah UK does not look good at all unfortunately https://coronavirus.data.gov.uk/	19:20
de-facto	JHU says 1734 fatalities for Germany yesterday	19:21
de-facto	hmm	19:22
de-facto	thats a weird spike	19:22
genera	rki says 989 for yesterday. hm.	19:22
LjL	i don't think it's great that Pfizer has halted production, even if it's to make improvements... gee, we're in an extremely time-sensitive situation at this point :(	19:22
de-facto	yeah but scaling production cap is even more important imho	19:23
de-facto	its not good that we have to wait for production to resume ofc, but if it resumes with bigger rates its better at some point in the future then	19:24
de-facto	like when the scaled up production rate catched up with the vaccination rate loss we have to pay for it right now	19:24
LjL	unless by that point we've all already caught some more aggressive variant	19:24
de-facto	yeah but vaccination is not really capable to prevent transmission in terms of herd immunity until late summer or such anyhow	19:25
de-facto	and yeah its not good that its so slow, i always kept repeating that	19:25
LjL	what'd have been great is if they could have started a new production plant and then temporarily stopped the old one for upgrades	19:27
LjL	tons of money, but, hey, fine, let's give them tons of money	19:27
ubLIX[m]	de-facto: eyeballing the rise over the last 4 months, 1734 doesn't really look like a spike, just the trend	19:27
de-facto	i wont post data here, but a view on https://ourworldindata.org/covid-vaccinations tells that we will see effects first in Israel, hence its worth a really close observation in terms of dynamics both in incidence and fatality	19:27
de-facto	Germany 7d rolling average daily fatalities would be ~860-ish with spikes reaching ~1200-ish or such	19:28
de-facto	it even looks like its plateauing there at ~860-ish on average	19:29
ubLIX[m]	hmm. true. i was looking at the non-smoothed data	19:29
de-facto	active cases went from ~400k on Christmas back to ~300k today	19:30
ubLIX[m]	catch up of reporting delays?	19:30
de-facto	yeah my suspicion aswell	19:30
DocScrutinizer05	>><LjL> i don't think it's great that Pfizer has halted production,<< I heard -20% for one week	19:31
de-facto	i think i heard somewhere that BioNtech got the Marburg facility approved for production	19:32
Brainstorm	New from r/WorldNews: worldnews: China Is Pushing a Groundless Theory That US Labs Leaked COVID → https://is.gd/9C18Lc	19:32
LjL	italy's vaccination curve is looking atrocious, if it's not the manufacturer's fault, then what are we even doing	19:32
de-facto	hence id guess we possibly might see some output from it in not too far in the future (no idea how long it will take them to get it running)	19:32
DocScrutinizer05	and after that ramped up production so mid of February they are within schedule again and from then on superior to schedule	19:33
DocScrutinizer05	marburg approval is a fact, yes	19:33
DocScrutinizer05	unrelated though	19:33
de-facto	yeah still relevant for supply chain of BNT162b2	19:36
DocScrutinizer05	>><ubLIX[m]> catch up of reporting delays?<< we had reporting failures 2 and 3 days ago	19:37
ubLIX[m]	that would do it	19:38
DocScrutinizer05	a very simplistic look at numbers for newcases: 7d ratio ca. -20%, so a R_eff of ~0.9	19:39
DocScrutinizer05	we need 0.7	19:40
de-facto	yeah and numbers become as trustworthy as prior to holidays between the years again	19:40
DocScrutinizer05	with (pre)B1.1.7 we need 0.4	19:40
de-facto	was B.1.1.7 like 150% or such	19:41
DocScrutinizer05	125%	19:41
DocScrutinizer05	err	19:41
DocScrutinizer05	135%	19:41
de-facto	only that i though i remember one and a half from UK report somewhere	19:41
DocScrutinizer05	Drosten mentioned some new study yesterday: [19 Jan 2021 21:14:25] <DocScrutinizer05> ooh, I wanted to drop a factoid: B1.1.7 new refined estimation for "improvement factor": down from "40-70%" to "pretty much 35%"	19:42
de-facto	.title https://www.medrxiv.org/content/10.1101/2020.12.30.20249034v2 linked from https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/covid-19/report-42-sars-cov-2-variant/	19:43
Brainstorm	de-facto: From www.medrxiv.org: Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data \| medRxiv	19:43
de-facto	"There is a consensus among all analyses that the VOC has a substantial transmission advantage, with the estimated difference in reproduction numbers between VOC and non-VOC ranging between 0.4 and 0.7, and the ratio of reproduction numbers varying between 1.4 and 1.8."	19:43
de-facto	hence ~160%	19:43
DocScrutinizer05	I said "new study"	19:44
de-facto	oh interesting, havent read it, where is it?	19:44
DocScrutinizer05	podcast	19:44
de-facto	ah yeah i havent listened to it yet	19:44
Brainstorm	New from NPR: Biden Adviser Sees Local Answers To Boosting Mask Use, Speeding Up Vaccinations: For two of the biggest obstacles to curbing the pandemic, it won't just be federal officials who will lead the way, says Dr. Celine Gounder, a member of Joe Biden's COVID-19 advisory board. → https://is.gd/2cbLSv	19:45
de-facto	DocScrutinizer05, is it among those here somewher? https://www.ndr.de/ratgeber/gesundheit/Podcast-mit-Drosten-und-Ciesek-Links-zu-Corona-Studien,corona2636.html	19:46
de-facto	maybe this? https://cmmid.github.io/topics/covid19/uk-novel-variant.html	19:48
de-facto	"We estimate that VOC 202012/01 is 56% more transmissible (95% credible interval across three regions 50-74%) than preexisting variants of SARS-CoV-2. We were unable to find clear evidence that VOC 202012/01 results in greater or lesser severity of disease than preexisting variants."	19:49
de-facto	yeah its difficult to get it exactly right, but all the numbers look like 160%-ish so one and a half probably is not too wrong then	19:50
de-facto	hence if we now had reached endemic R~1 we would need to do as much as reaching R~0.66=1/1.5 with the normal variant to reach endemic with the B.1.1.7 variant	19:52
DocScrutinizer05	I only can cite Drosten and that was [19 Jan 2021 21:39:47] <DocScrutinizer05> the new study is based on "random tests" not "test on symptoms" AIUI <DocScrutinizer05> Drosten said it's difficult to get real numbers, but it seems it's more like 35% than 40-70% but it depends a lot on where you look at	19:52
DocScrutinizer05	[19 Jan 2021 21:41:29] <LjL> well, 35% is already a change over "we don't really have evidence it infects more"	19:53
de-facto	hmm ok i have not listened to his podcast yet, i only looked at his link section	19:53
DocScrutinizer05	[19 Jan 2021 21:41:35] <DocScrutinizer05> the really important finding is: it IS more infectious	19:53
de-facto	yeah	19:53
de-facto	if we would target 0.75 with normal variant we would have to reach 0.5 with B.1.1.7 or such	19:54
de-facto	thats almost impossible :/	19:54
DocScrutinizer05	thus <DocScrutinizer05> a very simplistic look at numbers for newcases: 7d ratio ca. -20%, so a R_eff of ~0.9. we need 0.7, with (pre)B1.1.7 we need 0.4	19:56
de-facto	Germany barely scratched R~0.75 in first wave, so R~0.5 would be really hard	19:56
DocScrutinizer05	indeed	19:57
de-facto	not saying its impossible but we would have to get better than ever then	19:57
DocScrutinizer05	though we learned a few things (did we? really???) - e.g. WEAR MASKS!!	19:57
de-facto	possibly (i hope so, not sure)	19:58
DocScrutinizer05	close scjools, and all offices	19:58
DocScrutinizer05	Laschet again goes "my way" regarding schools. I really hate this guy	20:00
de-facto	if we can come in the rage of 4k-5k daily new infections i might begin to see some hope	20:00
DocScrutinizer05	oops sorry. This was the green one, Kretschdingens	20:00
de-facto	yeah dont get me started on that one	20:01
DocScrutinizer05	senile	20:01
de-facto	we have to make the best out if it and i think Merkel knows what is important, so the more they listen to her the better	20:02
de-facto	she always forced the ministers to listen to scientific experts until they began to abandon their false hopes and started to trust science again (at least that is my hope)	20:03
Brainstorm	New from ScienceMag: Hurley, J. M.: [Editors' Choice] Could COVID-19 eliminate the alarm clock? → https://is.gd/gXHJ8I	20:09
Brainstorm	Updates for Mozambique: +1126 cases (now 29396), +18 deaths (now 271) since 18 hours ago — Malawi: +971 cases (now 14851), +17 deaths (now 353) since 23 hours ago — Spain: +41576 cases (now 2.4 million), +464 deaths (now 54637) since 23 hours ago — Italy: +13568 cases (now 2.4 million), +524 deaths (now 83681) since a day ago	20:12
DocScrutinizer05	well, then when you hear idiots like that guy spok4esman of employers >>the very low infection rate of TWO to FOUR PERCENT[!!!] shows we don't drive the pandemic and don't need regulations that make home office mandatory<<	20:18
de-facto	who?	20:19
DocScrutinizer05	Tagesschau, Arbeitgeberverband sprecher	20:20
de-facto	yeah i dont even know why to listen to his position, its his job to go into opposition to anything proposed that might restrict the freedom of companies not to implement NPIs	20:21
Brainstorm	New from StatNews: Biden, in inaugural address, pledges the U.S. ‘can overcome’ Covid-19: Biden used key moments of his inaugural address to highlight the pandemic’s immense death toll and to issue a forceful pledge that the country can bring the pandemic to an… → https://is.gd/TW2Y2J	20:22
DocScrutinizer05	https://i.imgur.com/xtuErxc.jpg hte problem is this Stefan Wolf guy is the president of metalworks employers association and sets a mindset many employers will adopt	20:24
DocScrutinizer05	so yeah, it's his job and probably uttering such BS is the best he could do to actually make at least a few people think	20:25
DocScrutinizer05	I mean, 2 to 4% REALLY????	20:26
DocScrutinizer05	low????	20:26
de-facto	close them for a month to give them time to come up with some sane concepts :D	20:26
DocScrutinizer05	yes	20:26
de-facto	if infection rate is above average they clearly did something wrong there and pose a problem for the public	20:27
DocScrutinizer05	production CLOSED. You may implement home office, or simply keep out of business. Exceptions need to get requested by officials and approved, otherwise legal prosecution	20:28
DocScrutinizer05	>>mimimimimimi we already DID get acrylic sheets!!1!!<<	20:30
de-facto	well Arbeitsschutz needs to be up to date, probably was really their recommondation back then	20:31
de-facto	based on knowledge half or three quarters a year ago?	20:31
DocScrutinizer05	>>why are we punished now, we did follow the rules and now the rules become more tough<< You wonder why evolution engaged into the effort to develop synapses for such folks	20:32
de-facto	whatever imho they need to go ahead and do whatever is necessary in their (individual) case to prevent infections and the most efficient concept probably would be based on the current knowledge. Maybe for some companies its not possible to implement it, but then they cant stay open.	20:33
DocScrutinizer05	they're still playing hide and seek and think their opponent (whoever that is, prolly the government) doesn't play fair	20:33
de-facto	imho if a company has a working concept that does not allow for hygiene concepts to be implemented in an efficient way they should become insolvent and disappear, because they also would be a thread to biosecurity in the future with their approaches	20:34
DocScrutinizer05	yep	20:34
DocScrutinizer05	lemme cite a yesterday's statement of a similar clown, transscript by google voice input, incl initial moderator comment (sorry, german lang)	20:37
DocScrutinizer05	>> Personalleiter bei einem Fahrzeugbauer in Flensburg 270 seiner Beschäftigten arbeiten im Büro allen hier Mobile Arbeit zu ermöglichen da verpflichtend sei nicht möglich: die Hardware ist nicht vorhanden die hat ja anderen Server dididie Server Kapazität ist nicht vorhanden aehm, nicht jeder hat überhaupt noch auch die Möglichkeit von zu Hause aus zu arbeiten und diverse Auflagen und Verordnung können leider nicht	20:37
DocScrutinizer05	eingehalten werden - es geht nicht<<	20:37
DocScrutinizer05	do your homework, jackass! you had 9 months to accomplish it	20:38
bloody_noob259[m	Indeed 9 month should be enough to at least enable VPN access to the Servers for those office workers	20:40
de-facto	well let me put it like this: the highest SARS-CoV-2 contaminated environment probably is in the COVID stations in hospital and somehow they found concepts to protect their employees, hence for what reason should other working places be unable to do the same?	20:41
de-facto	then they must force their employees into full PPE with respirators if they really cant think of any better concept for their environment	20:41
DocScrutinizer05	because >>the servers err the the the server capacity ist there<<	20:42
de-facto	its irrelevant for PPE	20:42
de-facto	basically if they say its not possible they say they are not willing to protect their employees with proper PPE	20:42
DocScrutinizer05	but but but... that COSTS MONEYS	20:42
de-facto	then they should work together to make a more efficient supply chain	20:43
de-facto	win win	20:43
de-facto	and btw it would be good if it costs a lot of money because maybe it would give motivation to think about new innovative ways to bring down incidence	20:47
bloody_noob259[m	Just saw the state oft germany I live in wants to distribute free FFP2 masks to every adult. Guess they might become mandatory in public transfer and shops instead of surgeon masks OR ffp2 https://www.butenunbinnen.de/nachrichten/politik/bremen-ffp-masken-fuer-alle-100.html	20:57
bloody_noob259[m	* Just saw the state of germany I live in wants to distribute free FFP2 masks to every adult. Guess they might become mandatory in public transfer and shops instead of surgeon masks OR ffp2 https://www.butenunbinnen.de/nachrichten/politik/bremen-ffp-masken-fuer-alle-100.html	20:57
de-facto	would make sense if their motivation was to mitigate aerosol transmission, surgeons mask dont fit airtight enough for that	20:58
bloody_noob259[m	Yes it would indeed make sense	20:59
bloody_noob259[m	The Senate will come together tomorrow for Discussion of new rules	21:00
pigughs	https://journals.sagepub.com/doi/full/10.1177/0300891620974755	21:01
de-facto	LjL might find that one interesting ^^	21:02
de-facto	.title	21:02
Brainstorm	de-facto: From journals.sagepub.com: Unexpected detection of SARS-CoV-2 antibodies in the prepandemic period in Italy - Giovanni Apolone, Emanuele Montomoli, Alessandro Manenti, Mattia Boeri, Federica Sabia, Inesa Hyseni, Livia Mazzini, [...]	21:02
LjL	that might be doubly interesting because... it could well be the study that my dad took part in	21:03
LjL	%link lung cancer	21:04
Brainstorm	LjL, Sorry, nothing found. Try with broader keywords	21:04
LjL	so this puts it back to September... can all of them be false positives? it's 23 people out of 162 in September	21:04
LjL	Evaluation of anti-SARS-CoV-2 functional neutralizing antibodies (NAbs) was performed for all 111 SARS-CoV-2 RBD-positive samples using a cytopathic effect (CPE)–based live virus microneutralization assay in a high-containment biosafety level 2 laboratory. Six of the 111 SARS-CoV-2 RBD-positive patients were positive in the qualitative CPE-based microneutralization test. Of these, four samples were collected in October (two on the 7th, one each on th	21:06
LjL	e 8th and the 21st), one in November, and one in February. Three of the positive NAb samples were from Lombardy, one from Lazio, one from Tuscany, and one from Valle d’Aosta. The presence of functional anti-SARS-CoV-2 NAbs at the beginning of October 2019 further supports the early unnoticed circulation of the virus in Italy, particularly in Lombardy.	21:06
LjL	so at least they double-checked, and at least they have true positives in October	21:06
LjL	but they didn't sequence them :\	21:07
DocScrutinizer05	hmmmm >>The serologic assay used in this study is an in-house designed RBD-based ELISA, namely, VM-IgG-RBD and VM-IgM-RBD, and is a proprietary assay developed ...<< I'd like to see the evaluation data of the test itself	21:09
DocScrutinizer05	aah there we are https://journals.sagepub.com/doi/full/10.1177/0300891620974755#	21:09
DocScrutinizer05	umm sorry	21:10
DocScrutinizer05	https://www.biorxiv.org/content/10.1101/2020.08.10.243717v1	21:11
pigughs	https://twitter.com/Laurie_Garrett/status/1351668010419974144?s=20	21:12
LjL	DocScrutinizer05, again though as far as i understand, no matter how well their ELISA performed, they found some positives in that "live virus microneutralization assay" which i assume should be definitely reliable	21:13
Brainstorm	New from https://covid19.specops.network : ljl-covid: Add links to assays used in Italian lung cancer blood sample study → https://is.gd/IkuIvl	21:23
de-facto	.title https://www.biorxiv.org/content/10.1101/2021.01.18.427166v1 <-- sounds like bad news :/	21:27
Brainstorm	de-facto: From www.biorxiv.org: SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma \| bioRxiv	21:27
Brainstorm	de-facto: From www.biorxiv.org: SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma \| bioRxiv	21:27
de-facto	"Here we show that this lineage exhibits complete escape from three classes of therapeutically relevant monoclonal antibodies. Furthermore 501Y.V2 shows substantial or complete escape from neutralizing antibodies in COVID-19 convalescent plasma."	21:28
de-facto	o> "These data highlight the prospect of reinfection with antigenically distinct variants and may foreshadow reduced efficacy of current spike-based vaccines."	21:28
DocScrutinizer05	LjL: yes, if it can be reasonably ruled out that they _all_ were false positives then tehre's no doubt. Just it needs that evaluation to trust the study based on this test	21:34
DocScrutinizer05	and I'm happy it's there so all fine	21:34
Brainstorm	New from StatNews: Here’s the letter Amazon sent President Biden offering to help with Covid-19 vaccinations: In a letter to Biden, Amazon said it is "prepared to leverage our operations, information technology, and communications capabilities" to help with Covid-19 vaccine distribution. → https://is.gd/uJ8JN0	21:35
DocScrutinizer05	de-facto: thus [20 Jan 2021 14:07:58] <DocScrutinizer05> >>"However, neutralization by 14 of the 17 most potent mAbs tested was reduced or abolished by either K417N, or E484K, or N501Y mutations."<< mRNA should become multi-variant mix immediately	21:37
de-facto	this paper above kinda reads a bit alarming	21:41
DocScrutinizer05	[20 Jan 2021 12:41:29] <Brainstorm> New from r/WorldNews: worldnews: Preliminary results on new Covid-19 mutation found in South Africa. Has ability to bypass current immune response, reinfecting already immune Humans. → https://is.gd/itPwxc	21:44
Arsanerit	Should we all panic?	21:44
DocScrutinizer05	won't help, so nope	21:45
DocScrutinizer05	save your panic potential for when it may make a difference	21:45
DocScrutinizer05	like, when the idiots out in the streets still don't get it that "stay at home, don't meet anybody" is the new hot shit	21:47
de-facto	no panic no, but those variants are indeed of concern	21:48
DocScrutinizer05	massive concern	21:48
Brainstorm	Updates for Eswatini: +346 cases (now 13789), +24 deaths (now 427) since a day ago — Netherlands: +5129 cases (now 929590) since 23 hours ago	21:58
CoronaBot	04/r/covid19: SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma (80 votes) \| https://www.biorxiv.org/content/10.1101/2021.01.18.427166v1 \| https://redd.it/l11m2u	22:22
de-facto	there exactly what i linked above ^^	22:36
Brainstorm	Updates for France: +20021 cases (now 3.0 million) since 21 hours ago	23:12
dTal	wait, doesn't that mean vaccines won't work either	23:12
Brainstorm	New from Medical Xpress: UK virus variant sweeps world as Biden warns worse is to come: A coronavirus variant that emerged in England has swept through more than 60 nations including China, officials confirmed on Wednesday, as Joe Biden warned during his inauguration as US president the deadliest phase of the contagion was yet to come. → https://is.gd/gjEhgD	23:13
dTal	if the immune response from the actual virus doesn't work on the new variant, then we can't expect the vaccine targeting the original virus to either	23:13
dTal	well, shit	23:14
raccoon_dog	Yeah, because if you're already immune, it means you've either had the virus previously (jury's out on this I think) or you're vaccinated.	23:14
raccoon_dog	So, yeah. The grim answer is, well, the answer.	23:14
de-facto	i means that neutralization capability from vaccinated is indeed affected, it does not mean that its not effective at all or such things and also this is preprint non-peer reviewed, yet the findings are concerning imho	23:14
Arsanerit	the "south african variant" is not covered by the vaccine?	23:14
raccoon_dog	Arsanerit: That's what the preliminary results seem to suggest, but see what de-facto said. More research is required for sure.	23:16
de-facto	we have to wait for more data but imho it shows that those "immuno-escape" claims have to be taken seriously	23:16
CoronaBot	04/r/covid19: The impact of vitamin D supplementation on mortality rate and clinical outcomes of COVID-19 patients: A systematic review and meta-analysis (87 votes) \| https://www.medrxiv.org/content/10.1101/2021.01.04.21249219v1 \| https://redd.it/l1eilw	23:17
de-facto	yet as always in science results have to be reproducible so we will see what will develop out of this, i would not go and panic or such, but also we cant simply "brush away" all claims of immuno-escape variants (they do that to some degree, hence its crucial to find out how much evasive potential they have and in which cases)	23:18
Arsanerit	I'll just stay home for the next 5 years then.	23:18
de-facto	we dont have indications that its more dangerous, so if you get it it most likely will be just as if you would get an other variant, yet the concern is with (partial) evasion of immunity	23:19
LjL	"just as if you would get an other variant" = 44% chance of still having symtoms after 6 months, taking the number from the latest paper that bugged me about it	23:20
LjL	so still pretty bad news	23:20
de-facto	i meant if you are naive (in terms of immunity) it does not really matter (at least we have no reason to assume more severity), for those with antibodies it has to be investigated what this means in terms of clinical progressions etc	23:22
de-facto	i mean that was to be expected its the natural evolution of all those CoVs (well and other viruses too)	23:30
Brainstorm	New from r/WorldNews: worldnews: Researchers succeed in taking first photo of coronavirus → https://is.gd/2r7YRM	23:38
LjL	it might have been to be expected, but it kinda wasn't happening before we finally had a vaccine in sight	23:44
LjL	so it's a bit demoralizing anyway, uh	23:44
de-facto	well again we should wait for the discussion about this from the immunologists	23:50

Generated by irclog2html.py 2.17.0 by Marius Gedminas - find it at https://mg.pov.lt/irclog2html/!