libera/##covid-19/ Wednesday, 2021-06-02

BrainstormNew from Shane Crotty: @profshanecrotty: Long term vaccine side effects: @DrPaulOffit = In the history of vaccines, β€œThere are no long-term effects where you find that one year, two years, later your child or you develop some problem that wasn’t picked up initially. It has never happened.”https://bit.ly/3yR8zTs β†’ https://is.gd/x5S4sv00:08
BirossoHELLO!01:59
LjLBirosso, HI!02:43
aradeshthe UK cases look like they're going up again :<09:51
dTalYep. Sharply.10:39
dTalHello, Indiant variant - sorry, "variant delta"10:40
mrdata-so oxford vaccine isnt protecting from that variant so well?10:48
dTalnot after one dose, no10:52
dTalbetter after two, but still not quite as effective10:52
indoanon[m]https://assets.documentcloud.org/documents/20793561/leopold-nih-foia-anthony-fauci-emails.pdf11:13
pwr22dTal: could you link to the data on that?12:16
dTalI can't remember where I read it, it's pretty widely reported12:19
dTalI can google it if you'd like12:19
dTalit's something like 30% after one dose and 65-75% after two12:20
dTalhmm but now I'm seeing that figure for pfizer too so maybe it's not specific to AZ12:21
dTalhttps://pharmaceutical-journal.com/article/feature/everything-you-need-to-know-about-covid-19-vaccines12:21
dTalsearch on the page for B.1.61712:22
pwr22Ah ok, that's what I thought (i.e. we don't have good data on all the vaccines but we do fear that it resists them better)12:22
pwr22Thanks for the link12:25
pwr22Doesn't look too bad12:25
dTalhttps://thebulletin.org/2021/05/the-origin-of-covid-did-people-or-nature-open-pandoras-box-at-wuhan/14:39
dTaltl;dr - 0 evidence for natural origin, bucketloads of circumstantial evidence for lab leak14:54
JuerdI'll just throw https://www.microbe.tv/twiv/twiv-762/ into the discussion15:43
pwr22The way I see it, we have had several scares with novel human infecting coronaviruses with significant mortality, SARs and MERS, over the last decades16:11
pwr22So I kind of see that as writing on the wall16:11
pwr22The one that causes covid-19 is possibly just the straw that broke the camels back16:12
Thomond%cases ireland16:22
BrainstormDBRunRecoveryError: (-30973, 'BDB0087 DB_RUNRECOVERY: Fatal error, run database recovery -- BDB0060 PANIC: fatal region error detected; run recovery') (file "/usr/lib/python2.7/bsddb/__init__.py", line 270, in <lambda>)16:22
de-factoLjL16:30
pwr22That doesn't sound good 😧16:32
* de-facto pities Brainstorm16:33
Brainstormde-facto: Do as you wish!16:33
* de-facto did as he wished16:33
binlol17:01
binfatal region error17:01
binoof17:01
binthat doesnt sound good for Ireland17:01
binlet's say a prayer for them17:01
de-factolol17:07
ingwer%cases de17:54
BrainstormDBRunRecoveryError: (-30973, 'BDB0087 DB_RUNRECOVERY: Fatal error, run database recovery -- BDB0060 PANIC: fatal region error detected; run recovery') (file "/usr/lib/python2.7/bsddb/__init__.py", line 270, in <lambda>)17:54
ingwer%cases germany17:54
BrainstormDBRunRecoveryError: (-30973, 'BDB0087 DB_RUNRECOVERY: Fatal error, run database recovery -- BDB0060 PANIC: fatal region error detected; run recovery') (file "/usr/lib/python2.7/bsddb/__init__.py", line 270, in <lambda>)17:54
de-factoingwer, currently broken, i guess will be fixed soon17:57
de-factoin case you dont know yet RKI got its own dashboard for Germany at https://corona.rki.de/17:59
de-factoWeekly incidence per 100k citizens is around 37 and falling for Germany so thats good news :)18:00
pwr22Sounds like something in the database it uses is corrupt18:02
de-factothe currently occupied ICU capacity for Germany can be seen at https://www.intensivregister.de/#/aktuelle-lage/zeitreihen18:02
de-factoit also looks like those 2143 ICU beds got a good downwards trend, hopefully it continues like that18:03
pwr22Gah, its like 26C in my flat right now18:04
de-factoGot mRNA-1273 yesterday noon, expected some fever or such, but nothing so far, only a bit tired and my arm hurts18:05
de-factowell actually only the injection site in the deltroid muscle18:06
LjLde-facto, pwr22: whoops! no that doesn't sound good indeed, but it's probably not tragic. a couple of days ago i spawned a new instance of the bot for OFTC because F-Droid had the bright idea to move there, and initially it was running a bunch of modules it shouldn't have, including COVID, so it must have messed up the database. i'll delete the file and then it will probably work again, except it'll start again giving numbers for all possible countries until it18:17
LjLhas settled down a bit18:17
LjLde-facto, may not get any fever, my sister never got any fever with Pfizer... first injection she got nothing, second injection all her muscles were aching for a few hours, but still no fever18:18
LjL%cases Ireland18:19
BrainstormLjL: In Ireland, there have been 259972 confirmed cases (5.3% of the population) and 4941 deaths (1.9% of cases) as of 7 seconds ago. 4.7 million tests were performed (5.5% positive). See https://offloop.net/covid19/?default=Ireland for time series data.18:19
pwr22de-facto: what's mRNA-1273? Pfizer?18:24
LjLModerna18:24
pwr22Ah ok18:24
pwr22Why the cryptic name?18:24
pwr22Why don't we start giving the vaccines greek letters πŸ˜›18:25
jacklswscientific name18:31
LjLvaccines already have so many names that i try to specify them all in every entry in my github list to facilitate search via %links but just the other day i was thinking i might hardcode a list of "synonyms" (for vaccines, and also variants) in the bot's code18:32
binyay de-facto glad you got shot :D18:35
pwr22We are all glad de-facto has been shot πŸ˜›18:36
pwr22Hopefully he will get shot again soon πŸ˜€18:36
binbut not TOO soon18:36
de-factothank you :)18:41
de-factoi think maybe 1273 is the RNA sequence length or such18:42
de-factoerm amino acids of course18:45
de-factotrying to eat and live extra healthy, yet silly me i am an insomniac, so still working on optimizing that part18:52
* de-facto goes for a small hike enjoying some sun in the evening :)18:55
pwr22Enjoy18:55
LjLmy sleep-wake rhythm is basically inverted and i'm getting the vaccine in three days so...19:03
LjL<Brainstorm> New from EuroNews: Brussels unveils plans to reform borderless Schengen Area: The European Commission wants to improve the management of the external borders and also strengthen cooperation among Schengen states.  #BrusselsBureau β†’ https://is.gd/DgS30020:20
LjLWhen it comes to internal measures inside the passport-free space, the Commission recommends the introduction of a EU-wide police cooperation code and an upgrade to the exchange of information on DNA, fingerprints and vehicle registration.20:20
LjLThe executive suggests the advance passenger information (API) system, which currently gathers data on passengers that enter the Schengen space, also be used for intra-Schengen flights.20:20
BrainstormUpdates for Peru: +115165 deaths (now 184507) since 2 hours ago β€” Sri Lanka: +738 cases (now 192547), +39 deaths (now 1566) since 2 hours ago β€” Namibia: +452 cases (now 56264), +11 deaths (now 865) since 2 hours ago β€” Moldova: +44 cases (now 255285), +6 deaths (now 6120) since 2 hours ago20:42
BrainstormUpdates for Maldives: +704 cases (now 65868) since 3 hours ago β€” Liberia: +9 cases (now 2219) since 3 hours ago β€” Sierra Leone: +8 cases (now 4156) since 3 hours ago β€” Israel: +2 cases (now 839517), +2 deaths (now 6415) since 3 hours ago21:31
pwr22<LjL "my sleep-wake rhythm is basicall"> Mine is pretty sketchy too21:32
pwr22Hey, Brainstorm is alive again21:33
LjLpwr22, yeah it'll actually be very chatty about case numbers for a while now, since i wiped the databse21:45
pwr22Ah ok21:45
* de-facto congratulates Brainstorm to getting a shiny new and clean database!21:48
* Brainstorm starts to filigree de-facto with some graphic pomp 21:49
de-factoloOL21:49
pwr22How come it only responds to you on mentions de-facto ?21:51
* pwr22 says hello to Brainstorm21:51
Brainstormpwr22: Do as you wish!21:51
pwr22Ah, has to be in a /me?21:51
de-facto:D21:53
* pwr22 starts to filigree Brainstorm with some graphic pomp21:56
* Brainstorm starts to gruntle pwr22 with some cognoscible longanimity 21:56
pwr22I've never been gruntled before that I know of21:57
de-factoLMAO :D22:00
* de-facto pets Brainstorm22:01
* Brainstorm starts to exaggerate de-facto with some agog moralization 22:01
de-factohaha Brainstorm22:02
BrainstormUpdates for India: +35999 cases (now 28.3 million), +841 deaths (now 335003) since 3 hours ago22:08
BrainstormUpdates for Pennsylvania, United States: +3012 cases (now 1.2 million), +10 deaths (now 27214) since 4 hours ago β€” Kuwait: +1345 cases (now 311846), +4 deaths (now 1779) since 4 hours ago β€” Mauritius: +11 cases (now 1418) since 4 hours ago β€” Curacao: +1 cases (now 12274) since 4 hours ago22:33
ReGiStRaSSo is the COVID-19 vaccination really effective in protection us against COVID-19 at all?23:02
de-factovery much so, e.g. look at this paper23:03
de-facto.title https://www.nejm.org/doi/full/10.1056/nejmoa210176523:03
Brainstormde-facto: From www.nejm.org: BNT162b2 mRNA Covid-19 Vaccine in a Nationwide Mass Vaccination Setting | NEJM23:03
qubert49[m]As effective as anything can be against something that mutates and affects different people in different ways23:04
BrainstormUpdates for Eritrea: +28 cases (now 4145) since 4 hours ago β€” Eswatini: +17 cases (now 18618) since 4 hours ago β€” Aruba: +13 cases (now 11006) since 4 hours ago β€” Mali: +10 cases (now 14281) since 4 hours ago23:04
de-factowell yeah antigenic drift is natural with any virus, yet cellular immunity is more broad than humoral immunity, hence probably also effective against variants23:04
darsieReGiStRaS: Case rates declined a lot in Austria. We had a "lockdown" and vaccines.23:04
ReGiStRaSI don't think so. Look at this Definition of Terms for the word Vaccine:23:05
ReGiStRaShttps://www.cdc.gov/vaccines/vac-gen/imz-basics.htm23:05
ReGiStRaSVaccine: A product that stimulates a person’s immune system to produce immunity to a specific disease, protecting the person from that disease.23:05
de-factoalso looking at the numbers for Israel really makes hope23:05
LjLoh lord i'm starting to always know what it means when someone come in with "hints" on what page to look at without specifying what they have in mind23:06
ReGiStRaSimmunity it says. But we are still seeing vaccinated people getting infected with COVID-19!23:06
ReGiStRaSwhy?23:07
de-factoefficacy measures how much the *probability* for symptomatic SARS-CoV-2 infection of a vaccinated group is lowered compared to a non-vaccinated control group under same conditions (hence double blinded study)23:07
darsieSome get infected before the vaccine is fully effective. Some vaccines don't protect from some strains.23:08
ReGiStRaSagain that does not equate to immunity23:08
darsieTell the CDC to improve that page, then.23:08
de-factothere is no vaccine, worldwide that gives 100% efficacy against any disease23:08
de-factofor example 95% is extremely good in comparison23:09
ReGiStRaSthen the word immunity shouldn't be used at all23:09
darsieTell the CDC to improve that page, then.23:09
de-factothere is no 100% protection by immunity against any disease23:09
LjLthe word immunity is used because it's both the scientifically and popularly appropriate word to use.23:09
de-factoits the nature of probability23:09
LjLit's like after COVID suddenly people realized that 95% is not 100% while before, they took it for granted that the measles vaccine was virtually 100% (which it isn't, none is), while the flu vaccine was like 60%, and neither was a big deal23:10
ReGiStRaSimmunity: the ability of an organism to resist a particular infection or toxin by the action of specific antibodies or sensitized white blood cells.23:10
LjLyes, resist doesn't necessarily mean beat, overcome, eradicate...23:10
darsieSome people have weak immune systems.23:10
LjLthe antibodies etc certainly do resist23:10
LjLhow effective that is will depend23:10
de-factoi think the term immunity refers to a bodies immune system as reaction to already having been exposed to an antigen and doing its best to protect from infection against it. that is the "normal" case, i have no idea why one would want to refer to something else when talking about immunity23:11
darsieReGiStRaS: You could come up with a new word instead of 'immune' system, too.23:11
darsieWhile you're at it, please say tom instead of atom. Atom means unsplittable from tomos=split and a=not. Toms can be split.23:13
de-facto:D23:13
ReGiStRaSso if a person who have received both doses of vaccine and then got infected with COVID-19 (assuming another strain) 3 months after 2nd does, the person would be asymptomatic usually, right?23:14
LjL%addpoint darsie23:14
Brainstormdarsie: +1/-0, 123:14
darsie:)23:14
LjLReGiStRaS, if it's a different strain from the one the vaccine is "made for", it's hard to say what will happen, tbh23:15
LjLthere are some studies on how effective vaccines are with variants, but really vaccines are important to be deployed quickly because we really don't want variants so much as possible23:15
ReGiStRaSok let's assume the person is asymptomatic. THat means during they asymptomatic period, they can still spread COVID-19 right?23:16
de-factoReGiStRaS, well its always a probability game, the immunity has a whole spectrum: sterilizing immunity (preventing any infection from going on, very rare actually), immunity against asymptomatic infeciton, against symptomatic infection (endpoint of vaccine studies), immunity against more severe progressions (and hospitalizations), immunity against fatal outcome23:16
LjLReGiStRaS, if they're asymptomatic *and* vaccinated it's very likely there are much lower chances of spreading, but it's still theoretically possible. but also, "variants" aside, with an effective vaccine a majority of cases are likely not going to even be asymptomatic, they're just going to not happen.23:19
de-factowith the highest level of immunity (freshly vaccinated against exactly the same variant) it would start for most at preventing symptomatic infections (or even asymptomatic infections for some), then slowly waning off (and also antigenic drift, mutations selected and having an advantage if they gain some immuno-evasive capabilities) hence immunity against hospitalizations and fatal outcomes would vanish last23:19
LjLde-facto, i strongly feel that with mRNA vaccine, most people will actually get something that is effectively at least equivalent to sterilizing immunity (i.e. they won't get symptoms AND they won't be contagious)23:20
de-factoits never a black and white game, there always are all levels of gray in between and things are always in constant state of change, e.g. immunity drifts as well as virus mutations23:20
LjLi'm not so sure about that with other types of vaccine though23:20
de-factoLjL, yeah i think there were studies from Moderna, almost a year ago, that showed that at the peak level of their vaccine induced immunity they could prevent viral replication also in the nasal mucus (was it a challenge study in primates?), but who knows how long that lasts and if that even is possible with a Wuhan style s-protein vaccination and now having pre-selected, partly immuo-evasive VoCs circulating such as SA Mutant B.1.351 et al23:22
LjLgranted, there are many variables at play, and variants are certainly one of the scariest23:22
de-factoanyhow protection against severe progressions or fatal outcomes by *far* is better than protection against (a)symptomatic infections for any of the vaccines23:23
de-factofortunately23:23
de-factoalso the efficacy numbers cant be directly compared because studies have been done at different times, with different variants, in different populations etc23:25
de-factoquite a good explanatory video (about the generic ideas) is the following23:25
de-facto.title https://www.youtube.com/watch?v=K3odScka55A23:25
Brainstormde-facto: From www.youtube.com: Prima di continuare su YouTube23:26
de-facto"Why you can't compare Covid-19 vaccines"23:26
BrainstormUpdates for Ecuador: +1175 cases (now 428865), +61 deaths (now 20681) since 5 hours ago β€” Ethiopia: +246 cases (now 272036), +7 deaths (now 4178) since 5 hours ago β€” Cabo Verde: +171 cases (now 30694), +2 deaths (now 266) since 5 hours ago β€” Rwanda: +41 cases (now 27064), +1 deaths (now 358) since 5 hours ago23:35

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