libera/##covid-19/ Monday, 2020-12-21

LjL%title https://khub.net/documents/135939561/338928724/SARS-CoV-2+variant+under+investigation%2C+meeting+minutes.pdf/962e866b-161f-2fd5-1030-32b6ab467896?t=160847051145200:08
BrainstormLjL, the URL could not be loaded 00:08
LjLNERVTAG meeting on SARS-CoV-2 variant under investigation VUI-202012/0100:08
DocScrutinizer05you asked for a "source":  https://i.imgur.com/R4lsYj9.png00:26
de-factoyes i believe you, i was curious about further details like how they tested and for which mutations and combinations of mutations00:28
DocScrutinizer05%tr <de wir haben den Impfstoff gegen 19 bekannte Mutationen getestet und er hat bei allen angeschlagen00:28
BrainstormDocScrutinizer05, German to English: we tested the vaccine against 19 known mutations and it worked on all of them (MyMemory) — we tested the vaccine against 19 known mutations and it worked for all of them (Google) — We have the serum against 19 confessed mutations tested and he has near #all *angeschlagen (Apertium)00:28
DocScrutinizer05de-facto: well, they have their source in footnote?00:30
de-factoyeah i already looked for their press releases00:30
DocScrutinizer05I'd also be interested in details00:30
de-facto%title https://www.medrxiv.org/content/10.1101/2020.12.09.20245175v100:32
Brainstormde-facto: From www.medrxiv.org: BNT162b2 induces SARS-CoV-2-neutralising antibodies and T cells in humans | medRxiv00:32
de-factolinked from00:33
de-facto%title https://investors.biontech.de/news-releases/news-release-details/pfizer-and-biontech-provide-data-german-phase-12-study-further00:33
Brainstormde-facto: From investors.biontech.de: Pfizer and BioNTech Provide Data from German Phase 1/2 Study Further Characterizing Immune Response Following Immunization with Lead COVID-19 Vaccine Candidate BNT162b2 | BioNTech00:33
de-facto"Antibodies generated in trial subjects were able to neutralize pseudo-viruses representing 19 diverse SARS-CoV-2 variants, indicating potential for broad protection against viruses with reported mutations"00:33
de-facto"BNT162b2 immune sera efficiently neutralised 19 pseudotyped viruses (18 of which enter cells using an S protein with a different RBD variant, and one of which uses the dominant S variant D614G), indicating the potential for broad BNT162b2-elicited protection against reported mutations [1],[9],[10]"00:40
de-factocited from the medrxiv.org above00:41
de-facto%title https://www.nejm.org/doi/10.1056/NEJMoa2027906 ref [1]00:41
Brainstormde-facto: From www.nejm.org: Safety and Immunogenicity of Two RNA-Based Covid-19 Vaccine Candidates | NEJM00:41
de-facto%title https://www.nature.com/articles/s41586-020-2639-4 ref [9]00:41
Brainstormde-facto: From www.nature.com: Phase I/II study of COVID-19 RNA vaccine BNT162b1 in adults | Nature00:41
de-facto%title https://www.nature.com/articles/s41586-020-2814-7 ref [10]00:41
Brainstormde-facto: From www.nature.com: COVID-19 vaccine BNT162b1 elicits human antibody and T H 1 T cell responses | Nature00:41
BrainstormUpdates for Grenada: +9 cases (now 103) since 2 days ago01:20
LjL%title https://translate.google.com/translate?sl=auto&tl=en&u=https://www.repubblica.it/cronaca/2020/12/20/news/coronavirus_variante_positivo_in_italia-279229115/?ref%3DRHTP-BH-I278887413-P1-S4-T101:28
BrainstormLjL: From translate.google.com: Google Translate01:28
LjLCoronavirus, an Italian woman positive for the English variant: she is in isolation and has a strong viral load01:28
euod[m]LjL: fuck :(01:30
LjLi think this variant is probably everywhere already, euod[m]01:31
DocScrutinizer05:-/01:31
LjLthis press release has caused a lot of fretting in Europe but... the variant has been there for months01:31
LjLi don't get it01:31
euod[m]really? countries rejecting air traffic from the UK as of now seemed to suggest it's definitely new. 01:32
DocScrutinizer05LjL: still not even the "70%" are confirmed, right? quite possible the variant exists since months in the wild and the recently observed effects are only indirectly or not at all related to the mutation01:33
DocScrutinizer05euod[m]: sars-cov2 was allegedly "new" when it "spread from china" but then LjL enlightened me it was all over europe a 3 or 4 moths earlier?01:35
euod[m]huh?01:35
euod[m]that's CCP propaganda. 01:35
LjLeuod[m], it's not new, but the *analysis* of it from UK government committees, and resulting press conference, is new.01:35
LjLit's not CCP propaganda, fuck this, the studies were made here, by italians, not by the CCP01:36
LjLi'm tired of hearing science put down like that just because you don't like what it says01:36
LjLit doesn't seem to matter how much evidence accumulates, it will never be enough01:36
LjLit doesn't even mean it *didn't* spread from China. it just means it was in Europe months before what we know.01:37
LjLs/know/knew/, really, it's pretty well-established by now but maybe we need to exhume some thousands of bodies and PCR them for everyone to be convinced01:37
LjLsorry, my tone is needlessly aggressive. i've just been frustrated on this topic for a bit too long.01:39
DocScrutinizer05is there a section in "wiki" to link to01:43
DocScrutinizer05?01:43
DocScrutinizer05like %paper origin01:43
LjLDocScrutinizer05, %paper is to bring up preprints from the preVIEW service. %link(s) is the one that looks at my list of links01:47
LjLbut no, there is no section on origin01:47
LjLthere are individual links to the studies on wastewater01:47
LjL%links wastewater01:47
BrainstormLjL, Sorry, nothing found. Try with broader keywords 01:47
LjLor not01:47
LjL%links sewage01:47
BrainstormLjL, Sorry, nothing found. Try with broader keywords 01:47
LjL:\01:47
LjL%links milan01:47
BrainstormLjL, https://www.medrxiv.org/content/10.1101/2020.05.11.20098442v1.full (SARS-CoV-2 seroprevalence trends in healthy blood donors during the COVID-19 Milan outbreak), finding that among blood donors in Milan, Lombardy, around 4.6% were positive to IgG at the "start of the outbreak" on February 24, and around 7.1% by April 8, using a test with 98.3% specificity, yielding similar [... want %more?]01:47
LjL%more01:47
BrainstormLjL, [...] prevalence as a https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247\(20\ (Seroprevalence of SARS-CoV-2 in Hong Kong and in residents evacuated from Hubei province, China: a multicohort study)30053-7/fulltext) despite different specificity and sensitivity of tests → https://paste.ee/p/sgU5A01:47
LjLi thought i had those01:47
LjL%links sewer01:47
BrainstormLjL, Sorry, nothing found. Try with broader keywords 01:47
LjL%papers milan turin wastewater01:48
BrainstormLjL, SARS-CoV-2 has been circulating in northern Italy since December 2019: evidence from environmental monitoring by Giuseppina La Rosa et al, published on 2020-06-26 at http://medrxiv.org/cgi/content/short/2020.06.25.2014006101:48
LjLthis is a preprint but it was published later, don't remember on what journal01:48
LjLthe sequences for some of the proteins found in that sewage were published too01:48
BrainstormUpdates for France: +7557 cases (now 2.5 million) since 21 hours ago — Netherlands: +22 deaths (now 10511) since 21 hours ago01:52
DocScrutinizer05hehe %paper ;-D01:54
LjL%papers spain wastewater01:55
BrainstormLjL, 10 papers: First Data-Set on SARS-CoV-2 Detection for Istanbul Wastewaters in Turkey by Bilge Alpaslan Kocamemi et al, published on 2020-05-06 at http://medrxiv.org/cgi/content/short/2020.05.03.20089417 [... want %more?]01:55
LjL%papers wastewater barcelona01:55
BrainstormLjL, Sentinel surveillance of SARS-CoV-2 in wastewater anticipates the occurrence of COVID-19 cases by Gemma Chavarria-Miró et al, published on 2020-06-13 at http://medrxiv.org/cgi/content/short/2020.06.13.2012962701:55
LjLhm i shouldn't make the bot say "published on", since these *aren't* published01:55
LjL<Brainstorm> New from r/WorldNews: worldnews: Turkey bans flights from UK, Denmark, Netherlands and S.Africa amid new virus strain → https://is.gd/mFJjFF01:59
LjLthorough01:59
LjLDocScrutinizer05, now that i've added this to the links list, %links should work with any of the keyword in the relevant line02:01
LjL%links wastewater02:01
LjLwell, except i'm restarting the bot, i forgot02:01
LjL%links wastewater02:02
BrainstormLjL, https://www.sciencedirect.com/science/article/pii/S0048969720352402?via%3Dihub (SARS-CoV-2 has been circulating in northern Italy since December 2019: Evidence from environmental monitoring) was published on Nature and finds presence of viral RNA from wastewater in parts of northern Italy (Milan, Turin), with published partial sequences of the isolated RNA [... want %more?]02:02
LjLi'm confused02:46
LjLi thought Bell's palsy was mentioned in the Pfizer final study paper *and* in the FDA report02:46
LjLbut now i find no mention of it here https://www.nejm.org/doi/pdf/10.1056/NEJMoa2034577 or here https://www.fda.gov/media/144246/download02:47
LjLam i blind? is my ctrl+f broken?02:47
LjLthere is just "Facial paralysis" as part of a long list on page 80 at the FDA link02:47
LjLah... it is mentioned here https://www.fda.gov/media/144245/download02:50
BrainstormUpdates for New Zealand: +5 cases (now 2121) since a day ago02:51
the-wes%cases oregon03:20
Brainstormthe-wes: In Oregon, US, there have been 102930 confirmed cases (2.6% of the population) and 1341 deaths (1.3% of cases) as of 4 hours ago. 471935 tests were performed (21.8% positive). See https://offloop.net/covid19/?default=US for time series data.03:20
the-wes%cases kentucky03:22
Brainstormthe-wes: In Kentucky, US, there have been 242321 confirmed cases (5.5% of the population) and 2397 deaths (1.0% of cases) as of 3 hours ago. 743500 tests were performed (32.6% positive). See https://offloop.net/covid19/?default=US for time series data.03:22
pepeewhat are the news on the UK strain? is it true that many countries already confirmed having gotten it?03:26
LjLpepee, Italy did, i don't know about others, but some others have, i forget which03:43
LjLthe UK strain has been around for quite some time03:43
LjLthe only difference is that now we're worried about it, really03:43
LjLi think it's in all of Europe already, at least03:44
pepeeah03:44
CoronaBot04/r/coronavirus: U.S. Has Administered 556,208 Vaccine Shots in First Week (10070 votes) | https://www.bloomberg.com/news/articles/2020-12-20/u-s-has-administered-556-208-vaccine-shots-in-first-week?cmpid=socialflow-facebook-business&utm_medium=social&utm_source=facebook&utm_campaign=socialflow-organic&utm_content=business&fbclid=IwAR13Gw2pn8WECBtjDFcwg2lJa9Mq2MZe5oiIoLOrirUW2IpdW8XzJJx7Te0 | https://redd.it/kh3tuv04:35
CoronaBot04/r/covid19: Glycyrrhizin effectively neutralizes SARS-CoV-2 in vitro by inhibiting the viral main protease (81 votes) | https://www.biorxiv.org/content/10.1101/2020.12.18.423104v1 | https://redd.it/kgw7vj05:05
BrainstormUpdates for Belgium: +2170 cases (now 625930), +81 deaths (now 18626) since 23 hours ago05:36
BrainstormUpdates for Thailand: +382 cases (now 5289) since a day ago06:08
strike%cases USA06:17
Brainstormstrike: In US, there have been 18.3 million confirmed cases (5.5% of the population) and 324869 deaths (1.8% of cases) as of 3 hours ago. 234.2 million tests were performed (7.8% positive). Fatality can be broadly expected to lie between 1.3% (assuming prevalence as in tests) and less than 3.0% (considering only deaths and recoveries). See https://offloop.net/covid19/?default=US for time series data.06:17
CoronaBot04/r/covid19: Essential workers, older seniors next COVID vaccine priority groups (84 votes) | https://www.cidrap.umn.edu/news-perspective/2020/12/essential-workers-older-seniors-next-covid-vaccine-priority-groups | https://redd.it/kh755806:29
BrainstormUpdates for Germany: +6444 cases (now 1.5 million) since 15 hours ago — Nunavut, Canada: +1 deaths (now 1) since 3 days ago07:08
BrainstormUpdates for Gelderland, Netherlands: +1908 cases (now 73361), +6 deaths (now 1174) since 23 hours ago — Moscow Oblast, Russia: +1539 cases (now 138183), +13 deaths (now 2691) since 23 hours ago — Flevoland, Netherlands: +394 cases (now 16187) since 23 hours ago — Crimea Republic, Ukraine: +357 cases (now 21406), +7 deaths (now 420) since 23 hours ago07:36
de-facto[m]Seems like passengers arriving in airports from London yesterday all had to be tested via RT-PCR and then quarantined until results available, then have to go into isolation at home 10 days but can be tested sgain after 5 days to end it prematurely.07:43
de-facto[m]Hopefully they will really stick striclty to the rules of isolsting even on Christmas...07:44
de-facto[m]Above procedure applies for all negative testing results, if positive there will be some special isolation quarantine07:45
de-facto[m]Now any passenger travel from UK to Germany is illegal with exceotions for medical personal, crews and cargo.07:49
de-facto[m]I think similar rules apply for traveling from SA.07:50
de-facto[m]actually i think the prematureky ending of home isolation by negative test is a mistake 07:51
de-facto[m]Like after 5.2 days median incubation time only half became sick, hence the other half may potentially contain some infected individuals below testing threshold, making such compromises with containment for potential mutant strains is stupid imho they should be forced to isolate strictly at airport for 14 days and tested after that period.07:55
de-facto[m]Haha and yesterday i was joking about letting them sign a paper and then thinking the problem is solved. Little did i know ...07:59
de-factoLjL, i am not sure if that strain really would be expected to already have been around long time, i mean at least they seem to believe for some reason (higher viral loads, some stats about spreading dynamics?) that this variant it like 50%-70% more transmissible, hence assuming they are somewhat right about that and together with the known reproduction by the "normal" wildtype for normalization of reproduction in a region one should be 08:06
de-factoable to estimate the duration it is in community spread i think08:06
de-factohow long some single isolated cases of the mutant were around is indeed unknown though, but at least the duration of community spread should be estimate-able 08:07
de-factoRKI COVID-19 Germany 2020-12-21: Weekly incidence 197.1/100k, Infections +16643 (1510652 total), Fatalities +226 (26275 total), COVID@ICU 5070 (incl 2679 on ventilator)08:11
BrainstormUpdates for Russia: +29350 cases (now 2.9 million), +493 deaths (now 51351) since 23 hours ago09:21
de-facto%title https://jvi.asm.org/content/94/7/e00127-2011:53
Brainstormde-facto: From jvi.asm.org: Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus | Journal of Virology11:53
de-facto"Published online March 17, 2020."11:54
de-facto"Alarmingly, our data predict that a single N501T mutation (corresponding to the S487T mutation in SARS-CoV) may significantly enhance the binding affinity between 2019-nCoV RBD and human ACE2. Thus, 2019-nCoV evolution in patients should be closely monitored for the emergence of novel mutations at the 501 position (to a lesser extent, also the 494 position)."11:55
de-factoWell sound familiar?11:55
de-facto%title https://www.nature.com/articles/s41591-020-0820-9#ref-CR711:56
Brainstormde-facto: From www.nature.com: The proximal origin of SARS-CoV-2 | Nature Medicine11:56
de-facto"Published: 17 March 2020"11:57
de-facto"Six RBD amino acids have been shown to be critical for binding to ACE2 receptors and for determining the host range of SARS-CoV-like viruses7. With coordinates based on SARS-CoV, they are Y442, L472, N479, D480, T487 and Y4911, which correspond to L455, F486, Q493, S494, N501 and Y505 in SARS-CoV-2"11:57
de-factohttps://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41591-020-0820-9/MediaObjects/41591_2020_820_Fig1_HTML.png11:58
de-factohttps://en.wikipedia.org/wiki/VUI_%E2%80%93_202012/0112:25
de-facto%title12:25
Brainstormde-facto: From en.wikipedia.org: VUI – 202012/01 - Wikipedia12:25
de-factohttps://en.wikipedia.org/wiki/501.V2_Variant12:26
de-facto%title12:26
Brainstormde-facto: From en.wikipedia.org: 501.V2 Variant - Wikipedia12:26
BrainstormUpdates for Switzerland: +10002 cases (now 413991), +79 deaths (now 6697) since 23 hours ago12:35
de-facto%title https://www.sciencedirect.com/science/article/pii/S193131282030624712:46
Brainstormde-facto: From www.sciencedirect.com: Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition - ScienceDirect12:46
DocScrutinizer05another R_eff[-7d] = 1 day in Germany13:04
CoronaBot04/r/covid19: Mutant coronavirus in the United Kingdom sets off alarms but its importance remains unclear (81 votes) | https://www.sciencemag.org/news/2020/12/mutant-coronavirus-united-kingdom-sets-alarms-its-importance-remains-unclear | https://redd.it/khc07413:14
generawith r=1 it shoulnt be raising, rite?13:36
DocScrutinizer05genera: that's what I based it on, today's numbers = numbers [-7d], or call it incidences13:40
DocScrutinizer05well +200some13:40
generawell we in this county went into "status black" this monday so no r=1 here13:40
DocScrutinizer05so 1% rise in 7 days13:40
generathey ran out of colours ))13:41
DocScrutinizer05Switzerland?13:43
generaHessen13:45
DocScrutinizer05oh13:45
DocScrutinizer05genera: I can't see much extraordinary situation for Hessen13:53
generait is for each county on its own. we e g have >200 7day for 3 days in a row13:54
genera(and they have no other ideas what to do)13:55
DocScrutinizer05worst I see on RKI dashboard is LK Odenwaldkreis with 356.8 /100k7d13:56
generaya they have been high for some wweks13:57
de-factowhat I dont really like about the incidence trends in Germany is that many federal states seem to have a raise again for the peaks on Thursdays 2020-12-{3,10,17} 14:01
DocScrutinizer05yep14:04
DocScrutinizer05what I like is the seemingly solidifying trend in my stats http://reisenweber.net/et_al/covid/covid19_statistics.htm14:05
de-facto%title https://imgur.com/a/xWZ4mM6 https://i.imgur.com/KBdLF8U.png14:06
Brainstormde-facto: From imgur.com: COVID-19 Germany: Daily incidence of newly detected infections - Album on Imgur14:06
DocScrutinizer05https://i.imgur.com/CwwHC5H.png14:07
de-facto%title https://imgur.com/a/Fi2J1B1 https://i.imgur.com/8CTYD6C.png14:09
Brainstormde-facto: From imgur.com: COVID-19 Germany: Smoothed Reproduction numbers for daily infection incidence by federal states - Album on Imgur14:09
de-factoSeems like since begin of December most federal states got a Reproduction Number 1 < R < 1.25 so thats consistently R>1 hence its out of control even during the so called "Lockdown"14:10
DocScrutinizer05ej, we got two of those, one is not one week old yet14:12
DocScrutinizer05eh*14:12
DocScrutinizer05except in Bavaria where it's 2 weeks old now14:12
de-factoYeah we got many of whatever they call "lockdown" 14:12
DocScrutinizer05and I seem to see effects in statistics14:13
de-factowhat really matters though is daily incidence and today its roughly one incubation time after 2020-12-16, hence first chance to maybe the begin of an effect, yet more likely to show after 10-14 days hence 2020-12-26 or 2020-12-3014:14
DocScrutinizer05since 4 days I see R_eff drop, now several indicators say it's =114:14
de-factoit always drops at the end due to reporting delays14:15
de-factofor the last week or such you would need nowcasting for proper Reff14:15
DocScrutinizer05err nope, I don't look at those effects14:15
de-factothose effects are contained in the RKI numbers if you dont compensate for them with nowcasting14:16
DocScrutinizer05no, my data is stable afor older than 3 days14:16
de-factolooking at "COVID-19-Fälle/Tag nach Meldedatum*" from corona.rki.de it seems that last 3 weeks it is always rising14:18
DocScrutinizer05it's pretty simple to compare the diagram of a week ago with a new one and see how much the points contained in both are changing between them, you see those older 3 days in old diagram don't change much if at all, compared to any newer diagram14:18
de-factoyeah but if you compare todays incidence with the one from one week ago you have to do nowcasting for at least the next 3-5 days into the future14:19
de-factobecause from the reporting of those 3-5 days in the future there will be cases that will be accounted for today 14:20
DocScrutinizer05when you compare "reported today" which is the number prominently cited everywjere then there is no nowcasting involved whatsoever14:20
de-factowhich number?14:21
DocScrutinizer05since it's *always* just the "reported today" cases14:21
DocScrutinizer05the +16,64314:22
de-factook but compare it with what then?14:22
de-factoyou would have to write it down every day because its different from the one on "Meldedatum" graph14:23
DocScrutinizer05and, as I explained above, in my diagrams I don't do nowcasting and instead look only at data points older >>last meaningful datapoint:2020/12/17<<14:23
de-factobut to which number would you compare 16643 to then?14:24
DocScrutinizer05"they" write it down for me, in ZDF and they today reported "+200some compared to last monday"14:24
Jigsy%cases UK14:24
BrainstormJigsy: In United Kingdom, there have been 2.0 million confirmed cases (3.1% of the population) and 67452 deaths (3.3% of cases) as of 6 hours ago. 49.6 million tests were performed (4.1% positive). See https://offloop.net/covid19/?default=United%20Kingdom for time series data.14:25
DocScrutinizer05in my statistics I don't use those "raw daily reported"14:25
de-factoah ok well yeah if you write that number down everyday and not compare it to meldedatum in your graph or such that might be a proper comparsion for same conditions each day of the week14:25
DocScrutinizer05in my statistics http://reisenweber.net/et_al/covid/covid19_statistics.htm I do the "compare to last week" in foldedphase (red solid line), basically. Though on the real "meldedatum" cases (light pink) per RKI data14:31
DocScrutinizer05*both* ("ZDF" and my own stats) tell me we reached a R_eff=1 today14:32
DocScrutinizer05my stats need manual "nowcasting" since, as written in the note, the last few datapoints are not mature yet14:33
DocScrutinizer05even with such "manual nowcasting" they seem to indicate R_eff=114:33
DocScrutinizer05maybe 1.05 to 1.1 max14:34
de-factohttps://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Projekte_RKI/Nowcasting_Zahlen_csv.csv?__blob=publicationFile14:34
de-factoyeah maybe something like that but still R>114:35
BrainstormUpdates for Germany: +7506 cases (now 1.5 million) since 23 hours ago14:35
DocScrutinizer05I'm more interested in the R_eff trend which is pointing downward14:40
Elpolacode-facto: Hi, is tehere any legend for the .csv shared? English version maybe?14:41
DocScrutinizer05R_eff(fp) = 0,98 once 2020/12/1514:42
DocScrutinizer05oops 020/12/1614:43
de-facto%title https://imgur.com/a/btkJ3Fi https://i.imgur.com/LngZjgg.png source https://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Projekte_RKI/Nowcasting_Zahlen_csv.csv?__blob=publicationFile14:46
Brainstormde-facto: From imgur.com: COVID-19 Germany: Daily Incidence and Reproduction - Album on Imgur14:46
de-factoI am not so convinced still that the exponential growth trend is broken yet14:49
de-factolooking at those numbers from RKI14:50
Jigsy3>UK Prime Minister Boris Johnson is to hold a press conference.14:57
JigsyAnother one?14:57
JigsyI should probably head to the store now just incase...14:59
DocScrutinizer05boring "news": EMA approved BNT162b215:05
DocScrutinizer05realtime Emer Cooke /director EMA) on TV15:06
de-facto%title https://www.youtube.com/watch?v=9waGXIEg4cg15:18
Brainstormde-facto: From www.youtube.com: EMA press briefing – 21 December 2020 - YouTube15:18
de-facto%title https://www.ema.europa.eu/en/events/press-briefing15:19
Brainstormde-facto: From www.ema.europa.eu: Press briefing | European Medicines Agency15:19
de-facto"EMA is holding a virtual press briefing on the outcome of the meeting of EMA’s human medicines committee (CHMP), which will discuss the COVID-19 vaccine from BioNTech / Pfizer on 21 December.15:19
de-facto"15:19
de-facto"Speakers include Emer Cooke (EMA's Executive Director), Harald Enzmann (Chair of CHMP), Sabine Strauss (Chair of PRAC) and Marco Cavaleri (Head of Biological Health Threats and Vaccines Strategy). The press briefing will be moderated by Marie-Agnes Heine, EMA's Head of Communication."15:19
de-factohttps://twitter.com/EMA_News15:19
de-facto%title15:19
Brainstormde-facto: From twitter.com: error parsing title ('NoneType' object has no attribute 'string')15:19
de-factomeh15:19
de-facto"Latest news from the European Medicines Agency, the European Union agency responsible for the evaluation and supervision of medicines. RTs ≠ endorsement."15:20
de-factohttps://www.ema.europa.eu/en/events/press-briefing15:26
de-factoTHey will continue to collect data during ongoing vaccinations because no study could ever find the very rare sideeffects15:43
de-factoThey dont know yet if it will be effective against the new UK SARS-CoV-2 variant but they are confident that it might be effective because it was also effective against other mutations15:44
de-factoso the immune response is broad enough spread in variety to be able to catch at least the other mutations15:45
BrainstormUpdates for US: +186264 cases (now 18.3 million) since a day ago15:52
de-facto%title https://www.ema.europa.eu/en/news/ema-recommends-first-covid-19-vaccine-authorisation-eu15:56
Brainstormde-facto: From www.ema.europa.eu: EMA recommends first COVID-19 vaccine for authorisation in the EU | European Medicines Agency15:56
Arsanerit:)16:02
de-factohttps://www.ema.europa.eu/en/news/ema-recommends-first-covid-19-vaccine-authorisation-eu16:03
de-factohttps://www.ema.europa.eu/en/documents/product-information/comirnaty-product-information-approved-chmp-21-december-2020-pending-endorsement-european-commission_en.pdf16:04
de-factohttps://www.ema.europa.eu/en/documents/other/pharmacovigilance-plan-eu-regulatory-network-covid-19-vaccines_en.pdf16:04
de-factohttps://www.ema.europa.eu/en/medicines/human/summaries-opinion/comirnaty16:06
BrainstormUpdates for Namibia: +585 cases (now 19299), +3 deaths (now 180) since a day ago — Gibraltar: +38 cases (now 1282) since a day ago16:06
de-factohttps://www.ema.europa.eu/en/news/ema-publishes-safety-monitoring-plan-guidance-risk-management-planning-covid-19-vaccines16:07
BrainstormUpdates for Netherlands: +11168 cases (now 700873) since 23 hours ago — Barbados: +14 cases (now 321) since 2 days ago — Canada: +6008 cases (now 509918), +66 deaths (now 14245) since 23 hours ago16:38
JigsyYou know what's good about the COVID-19 vaccine?16:40
JigsyThat Martin Shkreli has absolutely no hand in it.16:40
JigsyCould you imagine if he did?16:40
JigsyProbably be something like $800/shot.16:40
jacklswwho is that martin shkreli?16:57
JigsySome asshole who increased the price of cancer medication simply because he could.16:58
JigsyHe's in prison at the moment.16:58
ElpolacoWhat about China actually. Will they vaccinate their citizens? It started in Wuhan, and now they're making the massive parties there.17:03
ElpolacoThe US and EU are still fightng with thath virus, since almost a year now17:04
BrainstormUpdates for Italy: +10869 cases (now 2.0 million), +415 deaths (now 69214) since 23 hours ago17:06
jacklswchina already completed isolation and contained the virus spread17:13
jacklswwhile the rest of the world struggle to balance between economy and pandemic17:13
louipcis it back to normal now17:13
louipci thought it was contained in taiwan too17:14
de-facto "Inside this California hospital, a ‘constant battle’ against covid-19" https://www.youtube.com/watch?v=qVwuRvM3h7U <-- warning may contain graphic content17:17
de-factocrazy many just wear surgical masks 17:20
BrainstormUpdates for United Kingdom: +30357 cases (now 2.1 million), +164 deaths (now 67616) since 9 hours ago — Arizona, US: +7748 cases (now 461345), +1 deaths (now 7972) since 23 hours ago17:20
de-factoah maybe ontop of N95?17:21
de-factoyeah looks like that17:21
darsieIs there also acoustic content in this video?17:21
louipcdouble mask plus face shield plus oxygen 17:21
louipcdarsie: yea theres sound17:21
de-factothey really seem to be at max capacity or beyond17:23
de-factodamn17:23
darsieWhy are they not wearing goggles? Are face shields better?17:30
de-factoidk maybe googles have condensation problems for long term usage? 17:34
de-factogoggles even 17:34
de-factolol17:34
louipcface shields got more coverage17:35
BrainstormUpdates for Greenland: +6 cases (now 25) since 12 days ago17:38
de-factoyeah that makes sense17:39
de-factohttps://www.reuters.com/article/us-health-coronavirus-usa-airlines/traffic-rises-at-u-s-airports-as-3-2-million-screened-over-weekend-idUSKBN28V1RI17:49
de-facto"TSA said it screened a total of 3.2 million people over the prior three days as holiday air travel began in earnest, including 1.06 million on Sunday. The total was down 58% over the 7.6 million people that were screened over the same period in 2019, the agency said."17:50
ElpolacoIs talking about vaccines banned here? Yesterday I shared my doubts about it on ##chat and I've almost been kicked.17:57
ElpolacoDid you read the "REG 174 INFORMATION FOR UK HEALTHCARE PROFESSIONALS"?18:03
louipchow do they even screen for virus18:03
ElpolacoThis vaccine was not tested as it should be. It has been created in very short time. What if there will be some long term side effects?18:03
ElpolacoNobody will be responsible for that18:04
louipcwhy not18:04
LjLElpolaco: China has already vaccinated a number of people, so much that they had a study on 50000 vaccinated people going abroad and none getting COVID18:04
Elpolacohttps://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/943417/Information_for_healthcare_professionals.pdf18:05
ElpolacoJust take a look18:05
louipcyea ##chat is not the best place for that discussion. this is more appropriate channel18:05
LjLTalking about vaccines is obviously not banned here, but your question surely went further than that without stating it. If I'm not wrong the thing you mention refers to the UK's requesting of an AI system to assist with adverse reaction monitoring18:05
louipcElpolaco: the commmon people are the ones that have power to hold politicians, or others accountable18:05
louipcthis has always been the case, but i guess we are more or less complacent18:07
louipcnot worth most people's time/effort18:08
ElpolacoWell, maybe the UK will have some AI monitoring system, but is it OK to test that vaccine on the scared population?18:11
LjLYou know what else hasn't been tested as it should(n't) be, but is kind of on its way there? The virus's ability to mutate in nasty ways. So far we've "only" enjoyed mutations that seem to make it more infectious, we also could get one that make it deadlier, although in general that's not in the virus's best interest... But that depends a lot on the specifics18:11
louipcis sars part of regular seasonal flu now?18:15
LjLLonger term effects aren't really tested even in other vaccines. Study participants are followed over time after the main part of the study ends, but the vaccine may be given to the population in the meanwhile. Given the situation we are in, I'd say yes, even if a phase 3 trial has been sort of rushed, as long as it seems solid (but I would watch carefully over conflicts of interest, given the vaccines had already been produced at scale before being approved) 18:15
LjLit seems to make that it would be unethical NOT to use it. Long term side effects of vaccines are uncommon, by the way. By far most side effects appear in the early months18:15
LjLlouipc: no, SARS is mostly extinct, and even if it weren't, it's got nothing to do with the flu18:16
ElpolacoFertility: It is unknown whether COVID-19 mRNA Vaccine BNT162b2has an impact on fertility.18:16
LjLSARS was much less easily spread than COVID, although it was deadlier, so after a while of fighting it, it kinda went away18:17
ElpolacoWhat if people after it will not be able to have children?18:17
LjLElpolaco: there is no evidence that it DOES have an impact either. They are just required by law to write that.18:17
LjLWell you know what HAS been shown to have a detrimental effect on fertility? Yep, COVID-19!18:18
ElpolacoLjL: Yeah, but they don't know that. It can make more damage than the covid itself18:18
LjLExtremely unlikely18:18
LjLAnd yeah well no, they did not wait for all the study participants to have children18:19
LjLAre you somehow under the impression they do wait for that in other vaccines?18:19
ElpolacoWell, other vaccines are tested for much longer than just few months18:20
DocScrutinizer05no, not really, just the tests are done less efficiently and concurrently18:33
DocScrutinizer05actually EMA (european medical agency) said it's been one of the most comprehensive and huge studies they ever seen. Even now already, without the "phase 4" long term observation it has gorgeous amounts of data and is considered very safe so far18:36
DocScrutinizer05for obvious reasons we don't really want to wait a 6 years to complete all long term monitoring on a test group before we start using a vaccine that has very few indications for any severe long term or late adverse effects18:38
DocScrutinizer05Elpolaco: and to give you some additional relief, the mRNA vaccine been developed years ago already, just been modified/adapted to be effective against sars-cov218:48
DocScrutinizer05the EMA approval is in no way tainted by rushing it, it complies with all regulations for a standard conditional (preliminary, not unlimited) approval of whatever remedy18:50
ElpolacoDocScrutinizer05: can you share some source of this information? I've never heard about it has been developed years ago.18:51
ElpolacoActually, I heard a lot about it's brand new18:51
DocScrutinizer05it's based on BioNTech's development fighting cancer. Sorry I don't have a link to a source at hand but it should be easy to google for it18:52
DocScrutinizer05basically BNT developed it to make your immune system fight cancer cells, and they simply adjusted the "viewfinder haircross" mRNA sequence to make your immune system fight the corona virus instead18:54
IndoAnonDocScrutinizer05: phase 3 volunteers should have been encouraged to copulate 19:02
IndoAnonWell, solving edge cases is important...  hindsight 20/20 19:02
LjLIndoAnon, the planet could do with a reduction in human fertility, anyway19:40
IndoAnonespecially africa19:40
IndoAnonTheir fertility is above 419:41
IndoAnonEven my nation barely above 2.519:41
louipcwhy LjL 19:42
LjLbecause we're clearly too many and unless we manage to change the way and amount we utilize energy, we're destroying the planet19:44
LjLviruses like SARS-COV-2 are themselves an example of what happens when we do that. destroy forests, get ever closer to wild animals that should be left alone... encounter their pathogens.19:44
LjLwe're going to get more of this.19:44
louipcyes nature 'fights back'19:46
louipcbut sounded like you have specific ideas of how nature should operate? i dunno19:47
BrainstormUpdates for Germany: +9101 cases (now 1.5 million), +239 deaths (now 26776) since 23 hours ago19:52
LjLi don't know what it sounded like, i only know what i said19:56
louipcsure19:58
louipcbut maybe the world has room for more humans19:59
louipcin that case "clearly too many" would be incorrect19:59
louipc"destroying the planet" also seems to be somewhat subjective too20:00
louipcbut we are definitely changing it20:00
benakautzer[m]https://twitter.com/TheBinderLab/status/1340966485775314947?s=1920:11
benakautzer[m]German thread about the new Corona strain in GB. 20:12
benakautzer[m]Just some explanation, not to much details (as these are still unknown). 20:12
BrainstormUpdates for Spain: +12662 cases (now 1.8 million), +334 deaths (now 49260) since 3 days ago20:20
BrainstormUpdates for Canada: +5911 cases (now 512198), +63 deaths (now 14278) since a day ago20:38
de-factoabout fertility, some of the highest ACE2 receptor concentrations (where SARS-CoV-2 can bind) is in the males testis20:47
de-factohopefully vaccinations could prevent infection there20:47
de-facto%title https://www.nature.com/articles/s41423-020-00604-520:47
Brainstormde-facto: From www.nature.com: Pathological and molecular examinations of postmortem testis biopsies reveal SARS-CoV-2 infection in the testis and spermatogenesis damage in COVID-19 patients | Cellular & Molecular Immunology20:47
louipclol dang20:48
louipcwait.. how age were these specimens20:48
de-factoold because it was a postmortem analysis20:49
de-factobut it demonstrates what COVID can do there, hence i think this is worrying 20:50
louipcalso nice sample size20:50
louipc" five COVID-19 patients and three uninfected controls"20:50
louipc!next20:50
louipc51, 62, 70, 78, and 83 years20:50
de-factoits not representative or such, it just confirms the suspicion that covid does infect where ACE2 concentrations are high20:51
louipcis this a legit science journal or what?20:51
de-factoyes of course it is20:51
de-factoits not meant to be representative of course it demonstrates that the virus is present there and can do damage20:52
de-factoalso it has been found in the sperm of alive males, hence it seems not only to happen to those they analyzed post mortem there20:52
generawhat kind of lab do you need for this work?20:52
de-factohow often it actually happens in young is unknown still afaik but this is nothing we would wish for20:52
de-factohence because you were talking about fertility and how this could be affected by COVID i thought this would be relevant to the discussion20:53
de-factogenera, idk but since SARS-CoV-2 is around anyhow probably pathology with some good PPE or such?20:54
de-factonot sure about that though20:54
de-facto%title https://jamanetwork.com/journals/jamanetworkopen/fullarticle/276565420:56
Brainstormde-facto: From jamanetwork.com: Clinical Characteristics and Results of Semen Tests Among Men With Coronavirus Disease 2019 | Infectious Diseases | JAMA Network Open | JAMA Network20:56
de-factofrom the first paper the conclusion is 21:03
de-facto"Collectively, our findings provide direct evidence that SARS-CoV-2 can infect the testis and GCs, indicating the potential impact of the COVID-19 pandemic on spermatogenesis and male fertility. Nevertheless, further study is essential to reveal the underlying mechanism of SARS-CoV-2 infection of testicular cells and the correlation of testis infection with the clinical course of COVID-19."21:03
Arsaneritcovid survivor = no more babies?21:05
de-factosecond paper concludes their results like this21:06
de-facto"Of these 38 participants who provided a semen specimen, 23 participants (60.5%) had achieved clinical recovery and 15 participants (39.5%) were at the acute stage of infection. Results of semen testing found that 6 patients (15.8%) had results positive for SARS-CoV-2, including 4 of 15 patients (26.7%) who were at the acute stage of infection and 2 of 23 patients (8.7%) who were recovering, which is particularly noteworthy"21:06
de-facto" But there was no significant difference between negative and positive test results for patients by age, urogenital disease history, days since onset, days since hospitalization, or days since clinical recovery."21:06
de-factoages were like 20s till 50s21:07
de-factoso i guess it shows 1) SARS-CoV-2 can do considerable damage to the sperm production ability of the male testis 2) it is present in the semen also of younger patients but we dont know how much damage it has done there21:09
de-factoNot sure what that actually means for fertility of a whole population, but for me those two papers are already enough to worry about COVID potentially affecting fertility (longterm? shortterm?) and i would want to stay clean of this nasty virus21:11
de-factoso if vaccination could prevent all that from happening it would be a very good thing21:12
de-factoand again this is not a representative study for a whole population, it just demonstrates a possible mechanism that should be taken into consideration for further investigation21:16
louipci figured the standard of a study would be higher for publication21:19
louipcbut i guess they are publishing preliminary investigations21:19
de-factowhat is your point actually?21:20
louipclarger sample size for example21:20
LjLa study isn't judged on things like the sample size, but only on what it *purports to represent* given the sample size it has21:20
LjLstudies on autopsies are not so common with COVID and definitely don't tend to have large sample sizes21:21
de-factothe first paper was about autopsy, they needed dead bodies and the agreement of relatives to use their bodies21:21
de-factothey never were meant or they never claimed to be representative, they investigated the underlying mechanism and effects21:21
LjLanyway, there are multiple studies suggesting that COVID affects the quality/viability of sperm, which i think is what de-facto was trying to point at21:22
LjLthere are no studies showing that for vaccines. of course it is still possible that vaccines also impact it, albeit unlikely, but what do you choose between something bad that you know *will* happen and something that you simply haven't ruled out?21:22
de-factothe second paper could have used a larger sample size indeed, i would think the same because it would be important to know how common it is for a certain degree of disease severity to have SARS-CoV-2 positive semen21:23
de-factoyet again what they show is that it is not so uncommon to find the virus there even in young people21:24
de-factoin my opinion things like autopsies are *very* important because this is a new virus hence we really need to understand more about what it is able to do in the body of an infected 21:26
de-factoalso it seems the virus has not really found its biological "niche" yet, affecting multiple organs when it is not contained by initial immune response success21:27
de-factoso investigating and uncovering mechanisms by autopsies is the only way to find out what SARS-CoV-2 does in those organs especially for severe cases21:28
de-factothen if the mechanism and the potential effects from that is somewhat understood it can be investigated further: 1) how often does it happen 2) how does it correlate to disease severity 3) does correlate with some other comorbidities etc21:30
de-factoso the point of such a publication is not to have a representative sample size at all (that would take way to much time), it is about investigating a suspected mechanism and reveal the details about it by staining cell cultures etc21:32
de-factoit is a bit like when police arrives at a crime scene and finds a dead body: pathological experts have to find causes and mechanisms for observed effects and underpin them with proof e.g. by samples and PCR tests etc.21:35
de-factoif they would wait with publishing those results to the investigators until they acquired a representative sample size the murder potentially already could have gotten away with killing many more victims21:36
de-factoforensic pathology would probably be the correct term in English for such a profession (i am not a native English speaker)21:43
Jigsy3>Boris Johnson is facing intense pressure to impose another national lockdown within days, as more than 40 countries banned arrivals from the UK in an effort to keep out a new fast-spreading variant of coronavirus.22:39
LjLJigsy, but then again, those countries did it because Boris Johnson's press conference scared them :P22:40
de-factohttps://offloop.net/covid19/?default=United%20Kingdom;Germany;South%20Africa;Netherlands;Czechia;Slovakia;Denmark&byPopulation=yes&cumulative=no&smooth=yes&miscType=Reff22:58
de-factointeresting all those started to have an increase since begin of December22:58
Jigsy3>Students yet to travel home exempt from English Tier 4 travel ban22:59
generadas paßt zu meiner These, daß es Agenten sind, die es zeitgleich ausstreuen ^^22:59
de-factomight be due to several reasons, e.g. lockdown ends at roughly synced but also sharing strains (hopefully not though)22:59
JigsyThe UK really doesn't grasp the concept of Lockdown.23:00
blkshpThe concept of lockdown is something that there is no agreement on throughout the world.23:02
LjLhttps://en.wikipedia.org/wiki/Lockdown#COVID-19_pandemic   i am not very happy with the labelling of South Africa's lockdown as "one of the strictest" based on the *headline* of a general news media article, same for the Philippines although that's got two23:19
de-factoPhilippines had military with weapons on the street to ensure lockdown already at a time where it just began to spread in Europe23:24
de-factoFriend of mine was there during that time, she barely could leave and said it was crazy strict23:25
LjLmaybe, i'm just saying that sourcing should be better than that23:25
LjL(especially for South Africa though)23:25
de-factoyeah of course, just telling what she told me (she said she was scared by them)23:26

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