libera/##covid-19/ Thursday, 2022-02-10

BrainstormNew from WebMD: Omicron Death Rate Higher Than During Delta Surge: With the Omicron variant now accounting for almost 100% of COVID-19 cases in the United States, the seven-day average of daily COVID-related deaths hit 2,600 recently, the highest rate in about a year. → https://www.webmd.com/lung/news/20220209/omicron-death-rate-higher-than-during-delta-surge00:02
de-factoyeah exactly what we expected at the time it became public how contagious it was.00:05
de-factonext wave probably we be even worse00:06
BrainstormUpdates for India: +67070 cases, +1241 deaths since 23 hours ago — France: +4322 cases, +3 deaths since 12 hours ago — Netherlands: +86667 cases since 23 hours ago00:06
xxyou think something is coming after BA.2?00:06
de-factoof course, BA.2 is just one variants in the sequence of many to come00:08
xxdo you think we already sequenced the one that'll make a big wave?00:08
de-factonew variants will continue to emerge, just as long as such high incidence of new infections is tolerated to continue00:08
xxit should be in the db then, and we could bet on it00:08
de-factonot sure, i dont think that we have seen the new VoC, otherwise it probably would have got attention due to having new alarming properties00:09
de-factoOmicron is an immuno-evasive variant, but its not so fit actually, so maybe the next VoC will combine that, be immuno-evasive but even more fit than Omicron00:10
xxBA.1 was identified a month before it even became a VoI (or VoC?)00:10
de-factowith Omicron the WHO was very fast with classifying it a VoC00:11
de-factoBA.2 is too similar to BA.1, its only a slight optimization, not a major new VoC or such00:12
de-factoso if the assumption holds that the next VoC also needs immuno-evasive properties, it needs to evade Omicron induced immunity, hence would need to have quite different surface features to evade antibodies raised against Omicron00:13
de-factoso it must have some significantly different mutations in its S-protein, compared to Omicron00:14
de-factomaybe it restores TMPRSS2 functionality and becomes more lethal again?00:14
xxis there any pressure on it that would make that likely?00:22
de-factowell the necessity for evading Omicron induced immunity emerges from the gigantic prevalence of Omicron recoveries, so anything spreading must be able to deal with that in a population00:24
de-factothe TMPRSS2 functionality may be a fitness advantage, but maybe it also may have other fitness advantages, as every variant before it probably will surprise us with some new properties00:25
OksanaaSoooo, question on booster: does it provide additional protection from the virus, when compared against just-double-vaccination? If yes, then does it mean a fourth dose will be needed later? If fourth dose will not be needed later, then why is third dose needed? I don't want to live my whole life getting booster vaccine shots every few months or so - sounds like vitamin/mineral supplements, artificial replacement for healthy immune system.00:26
de-factoyes a third shot increases protection (against Omicron) by a lot00:26
xxand so does a fourth shot, if it has been a few months since the 3rd00:27
OksanaaSoooo, protection from the 3rd shot decreases with time. To what level? Does it ever get down to pre-3rd-shot levels? Or even lower than that?00:28
de-factosource for that claim i just made (that booster is of big benefit against Omicron)00:28
xxrough estimate would be 50% protection after 6-9 months00:28
de-factohttps://www.gov.uk/government/publications/covid-19-vaccine-weekly-surveillance-reports00:28
de-facto.title00:28
Brainstormde-facto: From www.gov.uk: COVID-19 vaccine weekly surveillance reports (weeks 39 to 5, 2021 to 2022) - GOV.UK00:28
de-facto.title https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1052353/Vaccine_surveillance_report_-_week_5.pdf00:29
Brainstormde-facto: From assets.publishing.service.gov.uk: COVID-19 vaccine surveillance report - week 5 (UKHSA)00:29
xxbut we have no idea what variants are coming00:29
de-facto"Vaccine effectiveness against hospitalisation with the Omicron variant has been estimated using a test-negative case control study design (Figure 2).00:30
de-factoTwo doses of either AstraZeneca (ChAdOx1-S) or Pfizer (BNT162b2) vaccines was associated with a vaccine effectiveness of approximately 25 to 35% against hospitalisation following infection with the Omicron variant, after 25+ weeks."00:30
de-facto"After a Pfizer booster (after either primary vaccination course), vaccine effectiveness against hospitalisation started at around 90% dropping to around 75% after 10 to 14 weeks. After a Moderna booster (mRNA-1273) (after either primary vaccination course), vaccine effectiveness against hospitalisation was 90 to 95% up to 9 weeks after vaccination."00:30
BrainstormNew from COVID on Twitter: Marc Veldhoen (@Marc_Veld): Prior SARS-CoV-2 infection provides limited protection against OmicronProtection against the Omicron Variant from Previous SARS-CoV-2 Infectionnejm.org/doi/full/10.10… → https://twitter.com/Marc_Veld/status/149155458406152602600:31
de-factoOksanaa, yes of course vaccine protection wanes off with immune contraction. its a falling exponential function with time, e.g. breakthrough infections may double each 50-70 days or such00:31
de-factoprotection from severe progressions may last longer though00:32
BrainstormNew from COVID on Twitter: Marc Veldhoen (@Marc_Veld): "Among individuals with prior COVID-19, one dose of BNT162b2 and two doses of CoronaVac could induce detectable serum Omicron NAb" A vaccine to protect against Omicron is required after infection with any previous variant. pic.twitter.com/LA1tPXDiOj → https://twitter.com/Marc_Veld/status/149155657422102937700:40
OksanaaQuestion is: I am already double-vaccinated (that seems to be quite enough, where legalities/access-to-places are concerned, in NSW, Australia), and I have booster appointment for tomorrow (Pfizer for everything - Moderna isn't quite as commonly available). I do not quite understand why I am getting booster.00:46
OksanaaAlright, so booster will increase protection (and from Omicron variant, too) significantly, which is important, because NSW is getting new cases every day *and* re-opening, which is a volatile combination.00:46
OksanaaBut will number of new-cases-per-day ever get down to zero, or will the pandemic continue - providing sort-of motivation for fourth dose? Will another variant arrive?00:48
OksanaaAnd, if I allow vaccine protection to fade after 3rd shot, will I still have better-than-before-3rd-shot protection in a few years, or will the protection decrease to practically zero?00:49
xxignoring the whole covid thing, "I do not understand why I am getting booster" is a very scary statement...00:50
xxpeople doing stuff they don't understand...00:50
Oksanaaxx: Exactly. On one hand, I already had Pfizer twice, getting a third one is not likely to have negative after-effects. And, with university re-opening, international students returning, and plan for staff to return to campus (instead of working from home), it would be preferable to have as much protection as possible.00:54
OksanaaOn another hand, if these vaccines are that bad at providing long-term protection, shouldn't somebody figure out a better vaccine that doesn't need boosters, for five years at least?00:55
BrainstormNew from COVID on Twitter: Marc Veldhoen (@Marc_Veld): A new study confirms this, with similar observation; people infected with COVID-19 had more than three times the risk of dying over the following year:Long-Term Mortality Following COVID-19 Infection: A National Cohort Study From Estoniapapers.ssrn.com/sol3/papers.cf… → https://twitter.com/Marc_Veld/status/149156036767529369801:00
BrainstormUpdates for Hong Kong: +1161 cases, +2 deaths since 23 hours ago01:09
BrainstormNew from COVID on Twitter: Gunhild Alvik Nyborg (@GANyborg): This piece from 2010 on long term symptoms after infection with SARS1 is scary - like hearing those w long Covid now. Unfortunately, for many the condition deteriorated over time for several years after they fell ill in 2003. What is ahead of us now? [... want %more?] → https://twitter.com/GANyborg/status/149156333156349953301:10
de-factothere wont be long lasting immunity with SARS-CoV-2, neither by recovery from infections (as reinfections, e.g. with Omicron demonstrate) nor by vaccination (as vaccine breakthrough infections demonstrate)01:11
de-factothese vaccines already provide much better protection that many other vaccines against respiratory diseases, e.g. Influenza or such01:11
de-factoso they already are very good, but there is room from improvement01:11
de-factoyet i doubt that there ever will be long lasting immunity (years or such)01:11
de-factoso if the pandemic will continue, necessity for protection from severe progressions continue01:12
de-factothank the AU government for opening up, thereby letting in the pathogen01:12
BrainstormNew from COVID on Twitter: Eric Topol (@EricTopol): In the large J&J vaccine trial, pre-Omicron:"Previous infection alone, in an analysis involving seropositive and seronegative placebo recipients, was found to provide 90.4% (95% CI, 83.2 to 95.1) protection against moderate to severe–criticalCovid-19."nejm.org/doi/full/10.10… → https://twitter.com/EricTopol/status/149156904688972185701:29
Oksanaade-facto: I didn't do the annual flu shots, and I didn't worry about influenza. I reckoned that my immune system can fend off flu on its own, and if I get sick, I can just stay at home and wait for it to pass. With COVID-19, the problems are both higher danger of hospitalization, and apparently high possibility of being an asymptomatic carrier of the virus to other people.01:34
de-factoI just mentioned it as one example for vaccinations available against a respiratory disease01:35
de-factoinfluenza vaccines have efficacy as low as 20%-60% or such01:35
de-facto.title https://www.cdc.gov/flu/vaccines-work/effectiveness-studies.htm01:36
Brainstormde-facto: From www.cdc.gov: CDC Seasonal Flu Vaccine Effectiveness Studies | CDC01:36
OksanaaI know of no other vaccine shots that have to be done annually. And even at that, I used to think that it is merely because of new variants of flu arising every year.01:36
de-factowhat i try to say is that i doubt that there ever will be any long lasting immunity against COVID01:37
de-factoas long as the virus is in circulation, there will be the necessity to mitigate probability for severe progressions01:37
de-factosome mutants may cause milder disease, others may cause more severe disease01:37
de-factoout immune systems will become more competent with dealing with them, but the virus also will become more optimized hence more fit01:38
de-factoso how much of a problem emerges from the hydra of new COVID mutants depends on how competent our immune systems can become in terms of dealing with an optimization of the pathogen variants (both in evasion and fitness)01:41
de-factobecause the bruteforce for finding new mutations that optimize SARS-CoV-2 continues with the magnitude of new infections happening, it basically means "computing power" in trying out new mutations in reality01:42
de-factothats the reason why i think its a mistake to open and let it "rip through" the population (ignoring all the damage to populations health and even claiming human life)01:43
de-factovaccination at least can reduce the duration the virus can replicate inside one carrier, and thereby decrease the possible amount of mutations it can try out in that one step of an infection chain01:44
de-factobut much better would be to cut down transmission paths and thereby unconditionally decrease daily number of new infections (hence possibilities for the virus to find new advantageous mutations)01:45
de-factoinstead everyone cries out for opening up, "freedom day" etc and such nonsense, not realizing that this really means asking for giving the virus the opportunity to optimize further01:46
de-factoof waving the "white flag" claiming its impossible to contain it, also nonsense, countries like China, Australia and NZ demonstrated that it is possible01:47
de-factothen probably acting surprised when the next mutant after Omicron emerges and claims even more life. "Oh wow, noone could have seen that one coming". Well look at all the variants before it, ask why it would be different this time.01:48
de-facto.title https://www.worldometers.info/coronavirus/country/us/ <-- 2500 people die every single day from Omicron, only in USA01:51
Brainstormde-facto: From www.worldometers.info: United States COVID - Coronavirus Statistics - Worldometer01:51
de-factothats one COVID death from Omicron every 35 seconds in USA01:52
de-factoCOVID death rate of Omicron is now already at 70% of all time peak in USA01:53
de-factoimho that is not a good strategy, its not mild, it kills too many people, unacceptable to open up01:54
de-factobut it seems many see that differently, i stay with my opinion: the only sane way to deal with this pathogen is strict ZERO-COVID.01:55
xxand the only sure way is ZERO-HUMANS01:56
xxand mink I guess01:56
BrainstormNew from COVID on Twitter: Eric Topol (@EricTopol): New @BMJ_latestAfter Covid, in people age 65+, 1 in 3 had a new medical sequelae/diagnosis, compared with 1 in 5 matched controls. Specific difference in respiratory failure and dementiabmj.com/content/376/bm… pic.twitter.com/11VLV7PpCK → https://twitter.com/EricTopol/status/149157568857853542501:57
de-factothat does not really make sense to me, why would we care about ZERO-COVID if there were no humans that could be infected?01:58
xxbecause we want to eradicate covid?01:58
Tuvixxx: Please stop with the 'humans are better of not existing' trope. It's tired here, and it seems to be your fallback rebuttal. It doesn't help the discussion of this channel, and if your "solution" to COVID is genocide as that logic appears to be, it doesn't belong here.01:59
de-factowhy would we if humans were not there anymore as price for that?01:59
Tuvix"Hopefully the channel can also provide opportunities to feel more informed, more in control to the extent it's possible, and less stressed and anxious about events; every person talking should try to keep this in mind, even though it can be hard." (last line from the channel rules.)01:59
xxTuvix: I just really want covid to be gone01:59
xxI don't like covid02:00
de-factoimho it makes sense to use this opportunity to learn how to control transmission paths and thereby force down SARS-CoV-2 by constantly holding Rt<102:00
de-factothat way it could not increase the number of carriers and would slowly fade away02:00
MerlinMp[m]Well if most of the covid research is based on simple statistical correlation - why you reject covid incidences correlation with people alive?02:00
de-factowhile humans would of course stay and acquired the ability to force down pathogens with transmission paths similar to those that SARS-CoV-2 uses02:01
de-factothat way we would maximize our freedom in a global society while not paying a too high price of sacrificing biosecurity for that, as we obviously suffer from right now02:01
Tuvixde-facto: You were musing about German trends a day or so ago, but as you just noted with the Omicron-death peak vs. the pre-vaccination Alpha-peak, the US is doing notably worse than most other countries, Germany included this time around.02:02
de-factowe would have to find a balanced way to prevent such an outbreak in the future, and imho the best way to do that is gaining competence in controlling transmission paths02:02
MerlinMp[m]We already had that unreal idea- zero bacterias, with multitude of antibiotics prescribed every day to evaporate them02:03
OksanaaI am looking at https://en.wikipedia.org/wiki/2009_swine_flu_pandemic#Comparisons_to_other_pandemics_and_epidemics . If case fatality ratio for COVID-19 pandemic is 1.44% , then the pandemic severity index is 4, just behind Spanish flu pandemic - centenary edition?02:03
MerlinMp[m]I thought we have a lesson learned from this battle02:03
Tuvixde-facto: Sure, and I think we can (and frankly, need to) do better in the future, but it *is* still a balancing act as the goal at a leadership / political level is to get results while limiting side-effects.02:04
xxMerlinMp[m]: and yet we manage zero-bacterias through irradiation and other methods in preparing food for transport and storage02:04
MerlinMp[m]So why there are scientists who believe alergies are caused by lack of contact with bacterias?02:05
TuvixMerlinMp[m]: You're moving between topics too rapid to really even bother to deal with, so I won't. On one had you demonstrate a pretty poor understanding of the science of COVID to day, much of which is more than "simple [c]orrelation" and then you compare it to a bacteria, which is itself much differnet than a virus.02:05
de-factoTuvix, of course, and the most effective way of controlling transmission paths will also require the least impact on daily life, hence the real goal should be to increase the effectiveness of containment measures02:05
MerlinMp[m]Tuvix: Maybe you can find some similarities in human approach02:06
de-factoe.g. if there is a way to target the containment efforts at the scenarios and transmission paths with the highest probability for actually resulting in new infections, the rest in form of the very majority of potential transmission paths that actually never will result in infection may not be affected by the measures02:06
de-factosimplest example: if we just knew the carriers we could isolate them, and not the rest of the population02:07
de-facto(an idealized case of course)02:07
xxa safe bet is that the carriers are people who fly on planes - they are the ones who brought it across continents02:07
TuvixWell, Hong Kong is trying, although I argue that their solution is too invasive to be practical for use in other countries.02:07
MerlinMp[m]xx: Why not people who goes out grom home?02:08
TuvixThe recent NY Times article on this was an intersting read, because if you're trying to come up with functional containment, it needs to be something that the majority of air-travel enabled countries can do reasonably, otherwise it really doesn't matter.02:08
de-factobut thats why i think we need to have as goal to increase the effective of controlling transmission paths: the better we become at this the more we can lower reproduction number with the less impact on majorities02:08
xxMerlinMp[m]: I don't know what that is02:08
MerlinMp[m]xx: Whats the difference between lockdown for planes and home lockdown?02:09
xxMerlinMp[m]: containing it to a city/country/continent02:09
de-factoplanes bring mutants from far locations, hence import02:09
xxevery single variant has been spread through air travel02:10
xxinstead of possibly dying out in its place of origin02:10
TuvixNot everywhere.02:10
MerlinMp[m]No big difference. Bats are not flying in planes02:10
xxMerlinMp[m]: people are02:10
TuvixTongo effectively imported COVID by sea-vessle, not air-travel. "every single varient" has been spread _by_ air travel, yes, but not necessarily the preveailing method *everywhere.* Frankly, the real problem is a lack of consistent containment framework and enforcement of it.02:11
BrainstormUpdates for France: +35104 cases, +37 deaths since 15 hours ago — Canada: +10312 cases, +131 deaths, +342703 tests (0.7% positive) since 22 hours ago — Tonga: +20 cases since a day ago — Kiribati: +1 deaths since 10 hours ago02:11
xxtongo is an edge case02:11
TuvixEvery jurisdiction has its own idea of how, when, to what level, and with what exceptions to introduce various restrictions.02:11
de-factohuh? if Omicron would not have spread from SA (and heh, it was not bats spreading it from there, it was stubborn tourists), it probably would not have reached Europe and spread from there to all across the world02:11
TuvixThese could be restrictions on movement within a country, its own citizens returning or moving within a country, foreign nationals entering or moving within a country, how essential workers are allowed to do their jobs if/when they require physical movement.02:12
de-factoand it did not even last long there, so as xx said it probably would have caused a local peak, then incidence would have gone down again, and it would not have become a global VoC02:12
TuvixThis is a very complex set of variables, and declaring that "nobody can move across <these> borders" is really not viable without a well-structured framework, and in the global case, coordinated with fully independent governments.02:12
MerlinMp[m]Tuvix: The real problem is preventive containment. Until were sure something is not deadly02:12
TuvixSo, 3 month containment? It took a while for us to realze how deadly COVID would be back in 2019.02:13
OksanaaPoor minks... https://en.wikipedia.org/wiki/Variants_of_SARS-CoV-2#Cross-species_transmission02:13
oerhekscontainment is an illusion.02:13
xxOksanaa: https://en.wikipedia.org/wiki/List_of_animals_that_can_get_SARS-CoV-2 read the references for details of each case02:14
TuvixSure, I'll go get the world informed that all international travellers will have to contain in strict, medical-grade military-controlled containment. I'm sure everyone will accept this! https://xkcd.com/59202:14
xxTuvix: well all the ecologists have already been talking for decades that something has to be done about air travel02:14
xxthere's no *essential* air travel02:14
MerlinMp[m]Im still curious when we gonna finally know how many people are really vulnerable to covid or its descendants02:14
Tuvixxx: Mouseover on that caption is doubly relevant to your rebuttal.02:15
xxor at least no *essential* air travel between countries02:15
xxMerlinMp[m]: ignoring outliers, it's basically all sick and old people02:16
TuvixHow do you explain absolutely no country stopping air-travel then? Even Australia / New Zealand didn't do that, and they had very strict rules.02:16
xxwell I haven't seen a VoC come from north korea02:16
TuvixIt's *not* viable to do that. The pandemic could have been 10 times worse and we still wouldn't have done that.02:16
MerlinMp[m]xx: We also have no guarantee flu, hiv or any other virus will not mutate into something lethal02:16
OksanaaOn 8 December 2021, Pfizer and BioNTech reported that preliminary data indicated that a third dose of the vaccine would provide a similar level of neutralizing antibodies against the Omicron variant as seen against other variants after two doses.02:17
xxMerlinMp[m]: not sure what point you're making there02:17
xxlike yeah, every virus can get worse02:17
xxthat's why we should be working against viruses02:18
MerlinMp[m]xx: That too much preventive actions is dead end02:18
TuvixAt some point it's not the same virus. Influenza would have to be both significantly more lethal and mutate so significantly to become as bad as SARS-CoV-2 to the point that it would no longer be "the flu" anymore.02:18
xxor it would become "THE FLU"02:19
TuvixInfluenza is also over an order of magnitude less leathal (as measured in annual deaths per capita) compard to COVID, and on top of that has nowhere near the side-effectis COVID does.02:19
MerlinMp[m]The Millenium Flu02:19
de-facto(I did not specify how, because that is exactly what we would need to investigate, model, try out, and improve by feedback from real world trials)02:20
TuvixGiving it a clever name changes nothing of the science. 'A rose by any other name…'02:20
de-facto.title https://investors.biontech.de/static-files/47b4131a-0545-4a0b-a353-49b3a1d01789 from https://investors.biontech.de/events/event-details/press-conference-provide-update-omicron-variant02:20
Brainstormde-facto: From investors.biontech.de: PowerPoint-Präsentation02:20
de-factoOksanaa, yes this here02:20
de-factoyeah Influenza is a completely different virus, but it shares similar transmission paths02:20
de-factohence containment efforts for SARS_CoV-2 brought down Influenza in the last two winter seasons to almost no cases at all02:20
de-factoone strain of Influenza even may have became extinct due to this02:21
MerlinMp[m]I would say we havent noticed any flu, but might be due to covid focus02:22
xxeveryone who wore proper masks all the time (and properly), washed hands, avoided contact with others and maintained larger physical distance when unavoidable, has managed to avoid *all* infectious respiratory diseases02:22
OksanaaDr. Monica Gandhi, an infectious diseases specialist with the University of California, San Francisco, told Healthline that although these lab studies show that antibodies can wane over time or be affected by mutations along the virus’s spike protein, vaccines were able to bring about generation of other types of immune cells to fight off infection.02:22
Oksanaa“We know now that T cells from the vaccines still work against Omicron, and B cells generated by the vaccines adapt the new antibodies they produce to work against variants. So, I think the clinical scenarios we are seeing in those with prior immunity, vaccinated, and even boosted individuals [show that] the vaccines are likely still protecting Omicron-infected individuals from severe disease,” she said.02:22
* Oksanaa grimaces - B cells were generated by human body in response to vaccination. B cells were not generated directly by the vaccines.02:22
TuvixSure, the vaccines are what induce the long-term cell memory useful to fight off a future infection.02:23
MerlinMp[m]I felt sick about 15-20 times during   last 2 years but have no proof if this was flu, others virus or bacteria02:23
xxthat number looks excessive02:24
xxyou sure you're ok?02:24
MerlinMp[m]So I wouldnt argue if flu was gone, because I have no medical proof for it02:24
Tuvix"gone?"02:25
MerlinMp[m]"Brought down to almost no casas"02:25
TuvixVery differnet from gone I will point out, but there is a very robust influenza tracking network and it indeed showed a vast reduction in case incidence that coincided with the COVID-related restrictions.02:26
de-factoremember, the flu is not a "simple" cold, its influenza, hence you will know if it hits you02:27
TuvixThis is not just correlation, since the influenza tracking process is refined enough to be very good at facotring in a great many causes of typical under-counts, and modern country's health deparmtnets are in fact quite open about how they do this.02:27
de-factofor sure you did not have influenza 20 times in 2 years02:27
xxde-facto: some people can still have light symptoms02:27
MerlinMp[m]xx: I have small kids in kindergarden, so have another pandemic every 3 weeks02:27
xxwell you wouldn't have that problem if you wouldn't have kids02:27
de-factothose are the common cold viruses, such as Adenoviruses, Parainfluenza, human Coronaviruses etc02:27
TuvixTo say that you doubt the science here either means you have some VERY good evidence to bring to the discusison, or are talking about something you don't actually know much about. If the latter case, I can recommended some introduction reading to you on how the influenza is tracked and you can begin to have the proof you just claimed not to have.02:28
de-factolots of Rhinoviruses02:28
de-factosuch things02:28
MerlinMp[m]Yep, but until you run specific test you cannot deny it was not flu02:29
de-factothe flu is not as mild as those upper respiratory tract infections "common cold"02:29
TuvixThankfully, the influenza tracking network runs lots of tests combined with very wildely understood analysis based on decades of epidemiology.02:29
MerlinMp[m]And who had a flu test recently?02:29
TuvixAs aforementioned, this is all very well documented.02:29
de-factoyou cant just call every respiratory disease "flu"02:29
de-facto"flu" is short for Influenza02:30
OksanaaAh. I personally think that before COVID-19 pandemic, I got a cough every year around August, I think - I remember at least two times in a row (a year apart from each other) when I went to GP about the cough, had X-Ray done, and lungs were clear. During the pandemic, I don't recall having such a cough.02:30
de-factothere are surveillance programs, monitoring for any respiratory disease outbreaks02:30
de-factoif people get ill from something, its investigated and sequenced02:30
MerlinMp[m]de-facto: Not if the symptoms are mild02:31
MerlinMp[m]Same as with covid02:31
de-factoif there is the signal for increasing outbreaks and it can not be determined by which pathogen, experts begin to raise eyebrows on it and investigate with more resources02:31
TuvixAnd thankfully, the flu-tracking network KNOWS how to deal with this.02:31
de-factoyes if the symptoms are mild too02:31
oerhekssewage is a good indicator02:32
de-factoone example https://influenza.rki.de/02:32
MerlinMp[m]You probably have different physicians than mine02:32
TuvixMerlinMp[m]: This is not "just" something you do in a clinic. As Aforementioned by me before, there is an entier science around this and it's *NOT* just based on a clinical test to estimate burden.02:33
TuvixMerlinMp[m]: An introduction: https://www.cdc.gov/flu/about/burden/how-cdc-estimates.htm02:33
de-facto.tr <de Im Nationalen Referenzzentrum (NRZ) für Influenzaviren wurden in der 5. KW 2022 in insgesamt 88 (65 %) der 135 eingesandten Sentinelproben respiratorische Viren identifiziert, darunter 31 (23 %) Proben mit SARS-CoV-2, 20 (15 %) mit humanen Metapneumoviren (hMPV), 19 (14 %) mit Rhinoviren, elf (8 %) mit humanen saisonalen Coronaviren (hCoV) des Typs OC43, 229E oder NL63, sieben (5 %) mit Influenza A(H3N2)-Viren, sechs (4 %) mit02:33
de-facto Respiratorischen Synzytialviren (RSV) und eine (1 %) Probe mit Parainfluenzaviren (PIV).02:33
Brainstormde-facto, German to English: At the National Reference Centre (NRZ) for Influenza Viruses, respiratory viruses were identified in a total of 88 (65%) of the 135 sentinel samples submitted in the 5th week of 2022, including 31 (23%) samples with SARS-CoV-2, 20 (15%) with human metapneumoviruses (hMPV), 19 (14%) with rhinoviruses, eleven (8%) with human seasonal coronaviruses [... want %more?]02:33
de-factooops sorry02:33
TuvixMerlinMp[m]: If you really want more information, please ask and I have a far more scientific reference I can dig up for you. But your claims are utter nonsense, blaming "different physicians" and claiming that because you don't know about it that it must not exist.02:33
de-facto"In the National Reference Center (NRZ) for influenza viruses, respiratory viruses were identified in a total of 88 (65%) of the 135 sentinel samples in the 5th week of 2022, including 31 (23%) samples with SARS-CoV-2, 20 (15%) with human metapneumovirus (hMPV), 19 (14%) with rhinoviruses, eleven (8%) with human seasonal coronaviruses (hCoV) types OC43, 229E or NL63, seven (5%) with influenza A(H3N2) viruses, six ( 4%) with respiratory syncytial02:34
de-factovirus (RSV) and one (1%) sample with parainfluenza virus (PIV)."02:34
de-factobtw that is the original reason for GISAID02:35
OksanaaTuvix: Yes, I just don't like when scientists use words carelessly thinking "the listeners will get the gist of it" and mangle the details meanwhile, as if they cannot find the right words to describe exactly what is happening. T cells are not part of a vaccine (at least, mRNA one - cannot say about those vaccines that are made from body fluids extracted from people who have an immune response).02:35
TuvixMerlinMp[m]: 'eh. I pulled it up anyway as it was in my recent borwser history: https://www.cdc.gov/mmwr/preview/mmwrhtml/mm6349a2.htm?s_cid=mm6349a2_w02:35
TuvixThis is how we can estimate case, hospitalization, and death burden even *WITHOUT* the benefit of every sick, injured, or dead individual being tested personally.02:36
TuvixIt's quite impractical for a modern country to test every individual for every clicnically possible cause of death.02:36
MerlinMp[m]Tuvix: I think you overestimate research of cases which are very mild. Unless you dig in sewage02:36
TuvixAnd you're basing this on what part of the information I linked you not even 1 minute before that comment?02:37
de-factoOksanaa, oh T-cell responses to provocation with the vaccine-induced antigen (the SARS-CoV-2 spike protein produced by the cells that are instructed to do so by the vaccine mRNA) are a very important part of the vaccine protection from severe progression02:37
de-factothe vaccine trains the immune systems "soldiers" in competence to fight with the real enemy in form of wild type pathogen on contamination02:37
MerlinMp[m]Im not blaming anyone, just know people who visit doctor once per 10 years and Im pretty sure any estimation about their health might be very innacurate02:38
de-factothat includes many branches of the immune system, not only B-cells (producing antibodies) or T-cells (killing off infected cells) but many more mechanisms, also making it much more difficult for the virus to replicate "incognito" once it contaminated a new host02:39
TuvixMerlinMp[m]: That's now how burden esetimation works. Clealy you haven't read any of the information I've linked, which is frankly insulting, but this seems to be your intention. That's a shame :\02:39
Tuvixnot now*02:39
de-factobtw that sewage sampling is a very smart thing to do, we should have more of that02:39
Tuvix"The reported numbers of hospitalizations are used to calculate hospitalization rates and the rates are adjusted to correct for under-detection of influenza.  This adjustment is done by using the percent of persons hospitalized with respiratory illness who were tested for influenza and the average sensitivity of influenza tests used in the participating FluSurv-NET hospitals. The data on influenza02:40
Tuvixtesting can lag up to two years after the end of the season, so for more recent seasons, testing data from prior seasons is used"02:40
TuvixDid you even *READ* the material I linked which includes that?02:40
TuvixDid you realize this is more than clinical data driving the burden estimation?02:40
TuvixDo you have any attempt at a rebuttal that demonstrates even a basic undersatnding fo the epidemiological processes being applied here?02:40
MerlinMp[m]de-facto: But prior you need to make sure everyone have access to public sewer sysyem02:41
Tuvixunderstanding of* (time to switch to a decent keyboard, or ignore people arguing things they don't understand from my laptop I guess)02:41
Tuvix.title https://doi.org/10.1111/irv.1248602:43
BrainstormTuvix: From doi.org: Annual estimates of the burden of seasonal influenza in the United States: A tool for strengthening influenza surveillance and preparedness - Rolfes - 2018 - Influenza and Other Respiratory Viruses - [...]02:43
de-factothere should be PCR primers on a constantly updated list for investigation derived by the surveillance of symptomatic infections (and identification of potentially circulating pathogens)02:43
MerlinMp[m]Yes. I understand you are basing on hospital data, and if something happening without hospitalization youre just ignoring it02:43
TuvixThis is used as a reference in the summary link I gave you above, which includes the case (not hospital or death incidence) quote of, "The methods used to calculate the burden of influenza have been described previously (1-2). More recently, the same model was adopted to estimate influenza-associated deaths in the United States. This methodology has been used to retroactively calculate influenza burden,02:43
Tuvixincluding deaths, going back to 2010."02:44
MerlinMp[m]This is called bias right?02:44
TuvixMerlinMp[m]: No, I've specifically explained how things other than hospital data are used.02:44
TuvixWhich you've ignored. You're either here to troll me or intentionally refuse to read any of the material I've provided to show how right you are. I refuse to play, and think you're a fool.02:44
MerlinMp[m]Which proves your bias again02:45
MerlinMp[m]Im not ignoring youre statement just verifying if they can be applied in all cases02:46
Tuvixlmao, your not reading material before rebuttals shows how I'm not familiar with this. Keep that head burried in the sand; it suits you.02:46
xxhead buried in sand might work against covid transmission02:48
MerlinMp[m]Your material does not explain how to measure such cases. Multiplicating by 2.1 is not an explanation02:52
BrainstormNew from Reddit (test): Covid2019: NIAID issues new awards to fund “pan-coronavirus” vaccines → https://old.reddit.com/r/Covid2019/comments/sou5l6/niaid_issues_new_awards_to_fund_pancoronavirus/02:55
MerlinMp[m]<xx> "head buried in sand might work..." <- If there are anal tests for covid it means you can infect others with head buried in sand02:59
BrainstormUpdates for Germany: +72091 cases since 20 hours ago03:01
xxMerlinMp[m]: head in sand, mask on butt03:04
r3mall set general powerline 003:04
xxmandate it worldwide03:04
BrainstormNew from Reddit (test): CoronaVirus_2019_nCoV: NIH: Broad neutralization of pandemic threat coronaviruses - ROCKEFELLER UNIVERSITY → https://old.reddit.com/r/CoronaVirus_2019_nCoV/comments/souawz/nih_broad_neutralization_of_pandemic_threat/03:04
MerlinMp[m]I just doubt if this is the right way but whatever03:05
OksanaaTable 4 in https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1045619/Technical-Briefing-31-Dec-2021-Omicron_severity_update.pdf is confusing.03:41
OksanaaWhere Omicron is concerned, is it better to be Unvaccinated/<28 days since first vaccine dose than ≥28 days since first vaccine dose?03:42
OksanaaFigure 2 is very helpful, thank you. But negative values for vaccine effectiveness 20+ weeks after two doses, where Omicron is concerned, are... annoying. Even though it's AZ vaccine, so not that relevant for me personally. How can vaccine effectiveness be negative?03:49
OksanaaFigure 2(B) makes me wish I got Moderna booster after two doses of Pfizer. Also, I wish there was more data shown/available on vaccine effectiveness without booster - this hook is mysterious.03:50
gryhello de-facto03:51
gryany clue about the above?03:51
OksanaaTable 6 is confusing. VE against hospitalization or vaccine effectiveness against symptomatic disease?03:57
gryI'm trying to figure out whether this (larger) channel is more dead than ##coronavirus because there is a newbie fooling around there, who would be quite unhelpful to leading a civilized conversation, or because this channel is just asleep, or because this channel usually likes to be silent in general.03:58
gryIt's hard to tell.03:58
de-factoHR 1.02 (0.72-1.44)03:58
de-factothats both, more and less03:59
Oksanaade-facto: Probably because they lumped together those not vaccinated yet, and those who had first dose within the last four weeks?04:01
BrainstormNew from Reddit (test): CoronaVirus_2019_nCoV: Almost 1 in 3 older adults develop new conditions after COVID-19 infection → https://old.reddit.com/r/CoronaVirus_2019_nCoV/comments/sovoat/almost_1_in_3_older_adults_develop_new_conditions/04:02
de-factoalso there are cofounding effects included, for example vaccinated may take less care of preventing contamination, some even go in clubs etc, hence will have higher contamination rates04:02
de-factovery hard to estimate how much effect that got04:02
de-factobecause people know their status04:02
de-factobtw they explain HR and OR on page 1004:04
de-factoindeed a bit confusing at first, but its just the ratio of probabilities compared04:05
LjL%title https://newatlas.com/health-wellbeing/heart-cardiovascular-long-covid-disease/04:05
BrainstormLjL: From newatlas.com: Heart problems surge in COVID patients up to 12 months after infection04:05
de-factoooof04:05
LjL%title https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4025054 this is the study involved04:07
BrainstormLjL: From papers.ssrn.com: Complications Following SARS-CoV-2 Infection in Victoria, Australia: A Record Linkage Study by Stacey L. Rowe, Karin Leder, Kylie Dyson, Lalitha Sundaresan, Dennis Wollersheim, Brigid M. Lynch, Ifrah [...]04:07
LjL%title https://www.nature.com/articles/s41591-022-01689-3 also this, actually04:08
BrainstormLjL: From www.nature.com: Long-term cardiovascular outcomes of COVID-19 | Nature Medicine04:08
LjLi recall i also saw earlier that in the UK something like 1/4th of employers are saying Long COVID is the leading cause of work absences, but i was half asleep, not sure where i saw that04:08
OksanaaFigure 10 in https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1043807/technical-briefing-33.pdf is same as in briefing 31, no new points?04:09
BrainstormNew from Reddit (test): CoronaVirus_2019_nCoV: Nasal Spray Booster Keeps COVID-19 at Bay: In mice, a vaccination strategy that uses an mRNA coronavirus vaccine injection followed by a nasal spray booster generates immune protection in the airways → https://old.reddit.com/r/CoronaVirus_2019_nCoV/comments/sovxo6/nasal_spray_booster_keeps_covid19_at_bay_in_mice/04:12
LjLOksanaa, that's briefing 33, but 34 and 35 are also out, isn't figure 11 at https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1050236/technical-briefing-34-14-january-2022.pdf an update of that?04:14
LjL%title https://twitter.com/erictopol/status/1491423306922496001 heh this tweet about UK dropping quarantine04:20
BrainstormLjL: From twitter.com: Eric Topol (@EricTopol): "The data that supports abandonment of self-isolation after a positive test, announced by Boris Johnson today for the UK https://www.ft.com/content/0f84d942-ddaf-4e9b-869d- [...]04:20
OksanaaLjL: Thank you, didn't see it before. Didn't show up in search results, and I don't know how to navigate the website to the list of briefings. Still no points after 25+ weeks, but at least I am not that jealous of Moderna anymore. Just a tiny bit.04:21
LjLOksanaa, you can find the briefings here https://www.gov.uk/government/publications/investigation-of-sars-cov-2-variants-technical-briefings04:26
LjLthe Zotero page in the channel topic also has them under "Reports → Rolling"04:26
LjLde-facto, have you seen https://covglobe.org/ (got it from https://twitter.com/theosanderson/status/1491154395597512704 )?04:27
de-factooh nice, have not seen that one before04:29
de-factothats pretty cool, should save the link04:30
de-factoa bit like sanger but global04:30
LjLit uses the same backend as sanger yeah04:30
de-factooh they share code, no wonder it reminds me of them04:31
BrainstormNew from ##covid-19 Zotero group: CovGlobe: Type Web Page URL https://covglobe.org/ Accessed 2022-02-10 03:28:16 Abstract  displays GISAID data on pango lineages on a spatiotemporal map → https://www.zotero.org/groups/covid_links/items/UXXWUC8M04:32
LjLgry, i, for one, was literally half asleep04:40
LjLi wouldn't necessarily ascribe a collective will to a channel04:40
BrainstormNew from ##covid-19 Zotero group: Protection against the Omicron Variant from Previous SARS-CoV-2 Infection: Type Journal Article Author Heba N. Altarawneh Author Hiam Chemaitelly Author Mohammad R. Hasan Author Houssein H. Ayoub Author Suelen Qassim Author Sawsan AlMukdad Author Peter Coyle Author Hadi M. Yassine [... want %more?] → https://www.zotero.org/groups/covid_links/items/8M29TTEH04:41
OksanaaWhat is your take on driving 24 hours after booster shot? My sister is asking, wondering if she should postpone booster appointment because of that.04:57
LjLOksanaa, if you're feeling fine, then it should be fine, but i suppose you can't know in advance :P04:58
LjLdid she feel bad after the prior two shots?04:58
BrainstormNew from ##covid-19 Zotero group: Risk of persistent and new clinical sequelae among adults aged 65 years and older during the post-acute phase of SARS-CoV-2 infection: retrospective cohort study: Type Journal Article Author Ken Cohen Author Sheng Ren Author Kevin Heath Author Micah C. Dasmariñas Author Karol [... want %more?] → https://www.zotero.org/groups/covid_links/items/7AIGAR2T05:00
BrainstormNew from Reddit (test): China_Flu: Clots | Blood Vessel Damage - This Is The Most Important Lecture for COVID (Dr. Syed) → https://old.reddit.com/r/China_Flu/comments/sox1ko/clots_blood_vessel_damage_this_is_the_most/05:10
TuvixMerlinMp[m]: I stepped away because our conversation wasn't going anywhere. If you're honestly interested in learning how it works, feel free to reach out directly again. There are about a dozen footnotes between the 2018 DOI burden estimation (regarding well-practice surveillance methods) and the 2014 vaccination prevention methods. Given you wished to refute them not even a minute after I posted them,05:40
TuvixI presumed you weren't interested in understanding them.05:40
TuvixMerlinMp[m]: If I've mistaken your rebuke of the material without apparent review for not noticing the continunity with the original claim of case-incidence and specifically *avoiding* both bias and under-counting of cases, please feel free to review my prior material and reach out again; I have more references, but opted not to continue the discussion without focus on the materials I'd offered05:41
Tuvixpreviously.05:41
Tuvix"On the other hand, estimates of the number of symptomatic community illnesses, for which medical care is not sought but may still result in missed school or work, and outpatient medical visits due to influenza underscore the frequency of influenza illness and its widespread societal impact. We estimate that for every influenza-related hospitalization, between 11 and 365 more non-hospitalized cases occur05:45
Tuvixin the community, depending on the age group.4, 8"05:45
TuvixSource: https://doi.org/10.1111/irv.12486 . This seems to be directly on-point with the earlier discussion, and indiciates the methods are specifically aware of and attempt to factor in both bias for clinical-only data and use all available resources to produce a burden estimation as accurate as possible.05:46
BrainstormUpdates for Belgium: +22333 cases, +68 deaths, +70390 tests (31.7% positive) since 23 hours ago — India: +67084 cases, +1511321 tests (0.1% positive) since 23 hours ago — Netherlands: +189 cases, +2 deaths since 8 hours ago — United Kingdom: +558 cases since 8 hours ago06:09
BrainstormNew from Science-Based Medicine: State legislators dispense with standard of care for COVID treatment and encourage medical misinformation: State legislatures are considering bills that protect doctors and other health care providers [... want %more?] → https://sciencebasedmedicine.org/state-legislators-dispense-with-standard-of-care-for-covid-treatment-and-encourage-medical-misinformation/07:04
BrainstormUpdates for Germany: +247453 cases since 16 hours ago — Atacama, Chile: +1049 cases since a day ago — British Virgin Islands, United Kingdom: +7 deaths since 6 days ago — Jilin, China: +2 cases since 8 days ago07:11
BrainstormNew from COVID on Twitter: Tulio de Oliveira (@Tuliodna): Lots of preparation but very excited to get a visit of WHO DG @DrTedros tomorrow. We will showcase the strong scientific infrastructure of SA that is working together with @WHO to build mRNA vaccines in Africa. Press release @PresidencyZA website [... want %more?] → https://twitter.com/Tuliodna/status/149165508358244761707:13
BrainstormNew from MedicineNet: (news): Strokes Triggered by COVID-19 Could Be More Disabling → http://www.medicinenet.com/script/main/art.asp08:39
BrainstormNew from BMJ: Seven days in medicine: 2-8 February 2022: Covid-19Government writes off £10bn spent on PPEThe UK government has written off almost £10bn (€11.9bn; $13.6bn) of spending on personal protective equipment that was unusable, above market price,... → http://www.bmj.com/content/376/bmj.o330.short08:59
BrainstormNew from r/Coronavirus: Daily Discussion Thread | February 10, 2022: Please refer to our Wiki for more information on COVID-19 and our sub. You can find answers to frequently asked questions in our FAQ , where there is valuable information such as our: → https://old.reddit.com/r/Coronavirus/comments/sp18y2/daily_discussion_thread_february_10_2022/09:08
BrainstormNew from EMA: Human medicine assessment reports: (news): Human medicines European public assessment report (EPAR): Fluenz Tetra, influenza vaccine (live attenuated, nasal), Influenza, Human, Date of authorisation: 04/12/2013, Revision: 22, Status: Authorised → https://www.ema.europa.eu/en/medicines/human/EPAR/fluenz-tetra09:36
BrainstormNew from EMA: What's new: Document: Consideration on core requirements for RMPs of COVID-19 vaccines → https://www.ema.europa.eu/documents/other/consideration-core-requirements-rmps-covid-19-vaccines_en.pdf09:46
BrainstormNew from Politico: Coronavirus: Paris police ban ‘freedom convoy’ COVID protest → https://www.politico.eu/article/paris-police-bans-freedom-convoy-protest-covid19-coronavirus/10:05
BrainstormNew from Politico: Brussels sees stronger growth in 2023 despite slowdown this year: Omicron, surging energy prices and supply-chain bottlenecks caused the Commission to downgrade its 2022 growth forecast. → https://www.politico.eu/article/brussels-sees-stronger-growth-in-2023-despite-slowdown-this-year/11:14
pwr22I've had a couple of covid symptoms since yesterday was was negative on lft11:51
pwr22My brother and his gf though who have COVID ATM were symptomatic for two days before they became positive on their LFTs though11:51
pwr22So I guess I will give it another day then test again11:52
darsiepwr22: my sis was pcr positive, but lft negative. I was lft positive after noticing my symptoms.12:41
dudzpwr22: the test you really need to squint at it12:42
dudzyou gotta get right up close with the uv light and squint to see if your possitive in the early stages12:42
dudzthis was something i learnt12:43
pwr22Ah, couldn't see anything at all on mine yesterday, will do another one tomorrow12:43
dudzthen as you are further in the marking is clearer and its more obvious12:43
dudzand make sure you get a good amount of liquid out of your nose to mix12:43
dudzdoesnt ahve to go in deep in the nose12:44
dudzturn it around a few times12:44
pwr22I think I got that bit covered ok 😀12:45
dudz:)12:45
* de-facto gives pwr22 a hot cup of delicious Lady Grey :)13:22
pwr22I shall drink some Genmaicha 😉13:22
de-factoalso a good idea indeed :)13:23
de-factospread it over long duration, so its always present in the throat13:24
de-factoand let the leaves in so its becomes extra bitter13:25
pwr22Na, I'm not gonna probably do either of those 😛13:28
pwr22The second one would be a ruining of good Genmaicha 😉13:28
pwr22I'm not that committed 😆13:29
de-factoi always slice Ginger, put it in a glass-can together with Sencha and then pour boiling water on it, i let it like that until its empty (pour it in my mug over a sieve)13:30
pwr22👍️13:31
de-factoanyhow it probably is beneficial to always have a thin film of that on the mucus, so drink it over long duration in small sips13:31
de-factojust doing an antigen test myself too13:32
de-factoi always sneeze like hell when taking the sample13:32
de-factoLjL-Matrix, your ZNC is offline?13:36
de-factowhere is Brainstorm?13:37
de-factopwr22, out of curiosity, what symptoms did you experience?13:42
pwr22de-facto: sore throat, tiredness (I slept a lot), no energy, generally feeling unwell, some headache13:52
pwr22Yeah taking the samples in my nose makes me sleep and in my throat gives me a combination of gagging and coughing fits13:53
pwr22Maybe LjL's internet is out13:53
de-factothe tea definitely will help with the sore throat, sleeping a lot also is a great idea, it will support the immune reaction13:55
de-factohope you feel better soon13:56
pwr22Thank you13:56
BrainstormUpdates for France: +177542 cases, +280 deaths since 17 hours ago — Switzerland: +26334 cases, +17 deaths, +81447 tests (32.3% positive) since 15 hours ago — Germany: +234918 cases since 22 hours ago — Tonga: +31 cases since 15 hours ago17:45
BrainstormNew from ClinicalTrials.gov: (news): MiVacunaLA: an Intervention to Improve COVID-19 Vaccination Behaviors Among Latinos → https://clinicaltrials.gov/ct2/show/NCT0523437217:47
LjL-Matrixdudz: you suggest looking at rapid tests with a UV light? First time I heard of that, does that affect the incidence of false positives?17:47
LjL-Matrixde-facto: my Ethernet cable was unplugged :p17:48
LjL-Matrixpwr22: nasal probes make you sleep? O.o17:55
pwr22Lol, I meant sneeze18:00
BrainstormNew from COVID on Twitter: Marc Veldhoen (@Marc_Veld): Africa transitioning out of pandemic phase of Covid, WHO saystheguardian.com/world/2022/feb… → https://twitter.com/Marc_Veld/status/149182024108463309618:07
BrainstormUpdates for Canada: +4629 cases, +53 deaths since 22 hours ago18:09
BrainstormNew from BBC Health: Covid: Lack of hospital beds makes spread 'inevitable': A doctor says it is "inevitable" Covid patients will come into contact with others amid shortages. → https://www.bbc.co.uk/news/uk-wales-6032019918:16
xx^ there's no need for covid patients to come into contact with not-covid patients18:27
BrainstormNew from Virology.ws: Trial By Error: My Exchange of Letters on Amygdala Retraining; That Undead Lightning Process Study: By David Tuller, DrPH Earlier this week, I wrote to Helena Liira of the Helsinki University Central Hospital about a new [... want %more?] → https://www.virology.ws/2022/02/10/trial-by-error-my-exchange-of-letters-on-amygdala-retraining-that-undead-lightning-process-study/18:35
BrainstormUpdates for Netherlands: +86968 cases, +17 deaths since 22 hours ago — Italy: +76195 cases, +325 deaths, +683715 tests (11.1% positive) since 23 hours ago19:11
BrainstormNew from COVID on Twitter: Eric Topol (@EricTopol): Booster vaccine % in countries for age 60+(% total population of the age group)@OurWorldInData Denmark 93%Ireland 93%Spain 89%Portugal 90%------------United States, age 65+58% → https://twitter.com/EricTopol/status/149183733518436762319:14
BrainstormNew from COVID on Twitter: Tulio de Oliveira (@Tuliodna): Spot the difference? UK royalty yesterday, a day before tested COVID-19 positive. Our SA president today with his key advisors preparing the speech for the nation... pic.twitter.com/gZATQZxtJ9 → https://twitter.com/Tuliodna/status/149183932889237504819:24
BrainstormUpdates for United Kingdom: +687 cases since 22 hours ago20:02
BrainstormUpdates for France: +191442 cases since 20 hours ago21:04
BrainstormNew from COVID on Twitter: Marc Veldhoen (@Marc_Veld): Particular enzymes add the RNA-cap, these enzymes can be targeted. SARS-CoV-2 has a 7MeGpppA2′-O-Me-RNA cap. pic.twitter.com/EXSAGjA5jj → https://twitter.com/Marc_Veld/status/149186366188287590921:05
BrainstormNew from CIDRAP: News Scan for Feb 10, 2022: Previous COVID infection and Omicron New symptoms after COVID-19 Nipah vaccine trial launch CDC on H5N1 avian flu threat → https://www.cidrap.umn.edu/news-perspective/2022/02/news-scan-feb-10-202221:15
TuvixPoking at this week's CDC provisonal US deaths update (with about 86% of expected deaths reported for Jan 2022) it looks like the 18-29, & 30-39 age groups each generally died in almost equal numbers to the Winter 2020-21 (Alpha) surge, and the <18 group experiencd slightly more death. All 3 of these age-groups had notably more (around 2 to 2.5 times as much) death during Delta as compared to Alpha.21:43
TuvixThat's just really sad considering the similar-looking Omicron deaths (as compared to Alpha a year ago) are months into vaccines being available for all but the under-5 group :\21:43
BrainstormNew from Contagion Live: Lower Vaccinated US Counties Saw Greater Incidence Rates During the Delta Surge: A study looked at COVID-19 vaccination rates and new COVID-19 infections across US counties during the Delta surge last summer. Many of the highly [... want %more?] → https://www.contagionlive.com/view/lower-vaccinated-us-counties-saw-greater-incidence-rates-during-the-delta-surge21:45
BrainstormNew from r/COVID19: COVID19: Predicted impact of the viral mutational landscape on the cytotoxic response against SARS-CoV-2 → https://www.reddit.com/r/COVID19/comments/spfx85/predicted_impact_of_the_viral_mutational/21:55
BrainstormNew from Novavax: (news): Novavax Announces Positive Results of COVID-19 Vaccine in Pediatric Population of PREVENT-19 Phase 3 Clinical Trial → https://ir.novavax.com/2022-02-10-Novavax-Announces-Positive-Results-of-COVID-19-Vaccine-in-Pediatric-Population-of-PREVENT-19-Phase-3-Clinical-Trial22:05
BrainstormUpdates for Germany: +262 deaths since 23 hours ago22:07
ArsaneritHow many of those deaths are due to the virus?22:21
TuvixFrom the CDC dataset I was using? All of them: https://data.cdc.gov/NCHS/Provisional-COVID-19-Deaths-by-Sex-and-Age/9bhg-hcku22:22
ArsaneritHow do they tell the difference between dying due to the virus and dying with the virus?22:22
TuvixDetailed analysis of the patient case data; great care is taken to avoid counting deaths from another primary cause.22:23
ArsaneritThere are now so many people infected, that just statistically, it should be likely that many people die with the virus even if they were asymptomatic.  How are such people counted in the analysis?22:23
ArsaneritOk.22:23
ArsaneritI wonder if all countries take such care.22:23
ArsaneritHere deaths are often reported as "due to OR with".22:23
TuvixNote that some deaths were "due to COVID" if COVID was the *primary* cause of death, even if the incident was "technically" something else. In other words, a condition that is all likelyhood would not have resulted in a death except for COVID.22:23
TuvixAnd, we also know the *true* impact of COVID-19 on the death rate is actually a fair bit higher than officially reported in the US by the CDC.22:24
TuvixThis is a fairly easy claim to make looking at the value of Excess Deaths, which are abnormal deaths that fall outside of expected year-to-year changes.22:24
BrainstormNew from Ars Technica: Science: Why covering anti-evolution laws has me worried about the future of vaccines → https://arstechnica.com/22:24
TuvixTypically the metric if Excess Deaths is used when there is a major disaster, such as war, natural disaster, or in this case, a pandemic. Since the 2020-2021 calendar years had no such major national-sized event in the US of similar magnitude besides the pandemic, it's quite easy to attribute the majority of those excess deaths to the pandemic as a primary cause.22:25
TuvixNote that some of *those* Excess Deaths may not at all be "by COVID", but for example someone who died to due lack of healthcare access, or someone who overdosed on drugs as a result of higher stress of the pandemic, and so on.22:26
ArsaneritYes, but excess death rate is usually only available quite a bit later.22:26
ArsaneritOr is excess death rate available with relatively small delay in the USA?22:26
Tuvixhttps://www.cdc.gov/nchs/nvss/vsrr/covid19/excess_deaths.htm (let's see)22:27
TuvixLooks like there's provisional data as up to date as the 3rd week of Jan, 2022.22:28
ArsaneritAbout one month then.22:28
ArsaneritBit late to base policy on during the omicron wave.22:29
TuvixRight, and really it's a fairly consistent number throughout the whole pandemic, obviously a lot more than the expected deaths, and slightly more than even the official "death by COVID" counts.22:29
TuvixA number of doctors in hospitals an ERs have been talking about the whole political issue of "from" vs. "with" COVID, but most of them stand firmly by the official records their own hospitals are reporting.22:30
TuvixSuch hospitals track these things quite closely; one childrens-focused hospital had a doctor I heard on an interview segment, and he cited some data that showed the increased stress this winter in pediatric patients was unlike anything he'd ever seen.22:31
TuvixNot just COVID directly, but the impact on related diseases we're learning are either made worse or produce a far earlier onset of symptoms due to sometimes even mild cases of COVID.22:32
BrainstormNew from CIDRAP: NCAA athletics not linked to increased COVID-19, data suggest: Mary Van Beusekom | News Writer | CIDRAP News Feb 10, 2022 Division 1 student athletes had about half the risk of testing positive in 2020-21. → https://www.cidrap.umn.edu/news-perspective/2022/02/ncaa-athletics-not-linked-increased-covid-19-data-suggest22:34
ArsaneritGermany excess death rate appears to be at 3% or so22:35
Arsaneritoh, that's old data22:35
TuvixKeep in mind in some specific ways, excess deaths would have decreased due to the pandemic, just obviously not by enough to make up for pandemic-related rises. For instance, during the somewhat limited movement restrictions we had, driving deaths were much lower due to far fewer people on the roads22:35
ArsaneritI was looking at https://www.ft.com/content/a2901ce8-5eb7-4633-b89c-cbdf5b38693822:35
Arsaneritthere was less air pollution too22:36
TuvixYea, I saw at least one article about the measurable change in air quality for a couple months when traffic was at an all-time low.22:36
TuvixThat's largely gone back to normal now that people, at least in the US, have largely been back to business as usual for 6+ months now.22:36
TuvixFrankly, I suspect even the official CDC Deaths due to COVID are still an undercount; some cases may simply not have been tested or tested negative due to time delay yet had conditions made worse or brought on by the disease. Still, using official fatality data is a decent way to compare trends across the waves here and draw comparisons between age-groups.22:38
dudzLjL-Matrix: the tests we buy here in Australia come packaged with UV lights i thought that was the normal.22:39
TuvixIt'll be interesting to see where Germany lands for a peak-fatality rate as cases tick up now due to Omicron. I don't see how it could be worse than the US (doing about 70% or so of the Alpha peak last winter) but that too is an intersting comparison between countries.22:41
LjLdudz, can't say i'm an expert on rapid tests, but i've always seen people here just talking about looking at red lines22:42
TuvixVaccination plays a big role, but also other mitigations like mask compliance (enforced or just largely-accepted by a population), restrictions, and so on.22:42
LjL(okay not necessarly red)22:42
ArsaneritThe German hospital association no longer expects an overloaded healthcare system in the omicron wave.22:45
ArsaneritIn the absence of an overloaded healthcare system, is it still justified to have restrictions to protect (primarily) the unvaccinated from getting seriously sick and die?22:46
LjLclearly the UK's answer is "no"22:47
ArsaneritI thought the NHS was already overloaded before the pandemic even started.22:47
ArsaneritOr at least overloaded with a regular pre-pandemic winter flu wave.22:48
LjLis it possible that the healthcare system isn't overloaded at least partly *thanks* to the restrictions?22:48
TuvixIt's not entierly an all-or-nothing approach; guidelines matter too, even if not enforced or carrying any legal weight. Obviously there are some that would only follow guidance if it's a requirement, and some that won't do it in any case (facing fines or other fallout, like the PM as an example)22:49
DisconsentedI suspect its too early to know but, we're started pushing up (pfizer) boosters from 6m after second shot to 3m. Does there happen to be any information on the efficacy of (pfizer) boosters based on when the last vaccine was given?22:50
ArsaneritLjL: That's certainly possible.22:51
ArsaneritTuvix: Ok, more specifically, I doubt if it's still justified to deny unvaccinated people access to "non-essential" shops and outside areas in restaurants.22:52
TuvixI don't have data handy offhand, but from reading & listening to a number of interviews with various doctors and health experts, the booster seems to give a similar rise in antibodies (the best way we have to measure its effect at this point) any time after about 4 to 5 months. Getting a boost less than 3 month sout after your initial 2x Pfizer (or Moderna) sequence seems to be generally not recommended.22:52
ArsaneritLjL: Without a control run of history, we can never be sure of that.22:52
TuvixA lot of the purpose of a boost is to counter the waning impact seen after the 5 to 6 month mark, especially in light of Omicron since it requires more antibodies to get the same effect of allowing the body to fight off the infection when compared to pre-Omicron varients.22:53
LjLDisconsented, https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1050236/technical-briefing-34-14-january-2022.pdf  figure 11 is about all i know, although it's possible there is longer-term information from Israel22:54
TuvixNow antibodies in the blood aren't really the goal; the goal is a robust immune response which has more to do with how effective the body can produce antibodies. Yes, having them in the bloodstream is helpful if they're effective, but the long-term cell memory to produce useful results is the true goal. The trouble is the best way we have to measure that is watch for outcomes in a larger population and22:55
Tuvixmodel how effective the vaccines remain.22:55
LjLthis is not very meaningful i guess as it's against symptomatic disease, where efficacy is kinda low anyway22:55
DisconsentedOh huh if I am reading this correct, it appears its better to get the booster sooner rather than later22:57
TuvixThat's generally true, although I'd not do it any earlier than 4 months. In the US the recommendation is now 2nd dose + 5 months (except for the immunocompromised, which can get it as early as 3 I believe)22:57
LjLDisconsented, you mean because the efficacy goes down a fair bit after dose 2? that's kinda why they've been moved from 6m to 3m as you say22:58
LjLbut again this is efficacy against symptomatic disease, and at risk of exaggerating, i'd say that ship has mostly sailed22:59
LjLwe should probably looked at efficacy against hospitalization and death, efficacy against death is sometimes quited as up to 98% (although i've heard all sorts of numbers and am "a bit confused" at this point)22:59
TuvixYup, I'd not read too much into either case rates, case-incidence, or VE against symptomatic or asymptomatic disease.22:59
LjLi'm so confused i can't even write the right verb tenses22:59
DisconsentedI was working on the understanding we were doing it primarily to keep the health system standing, I was happy to be a hermit for an extra 3 months for 5% efficacy or whatever23:00
DisconsentedOh well time to get the booster sooner then, thanks LjL23:00
LjLDisconsented, it's quite possible 2 doses give virtually no protection against omicron, so, yes, i'd say so23:00
LjLunless we want to make a "the rest of the world needs it more" but WHO'd make that argument23:01
TuvixAn individual deciding not to get it won't really help the rest of the world though.23:01
TuvixIt's not like if I'd not scheduled my booster dose earlier this winter that it could have ended up in some poorer country instead; it would have just gone to whoever signed up for the vaccination slot I got.23:02
LjLDisconsented, https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3949410 for two-dose efficacy against severe disease (and disease in general), with perhaps lower numbers than other studies23:03
BrainstormNew from Contagion Live: us: Novavax Announces Positive Results of its Investigational COVID-19 Vaccine in Pediatric Population → https://www.contagionlive.com/view/novavax-announces-positive-results-of-its-investigational-covid-19-vaccine-in-pediatric-population23:03
TuvixArsanerit: As to your point on restrictions and their value, it really depends what you're trying to do. Somewhere like the US, the goal might still be to get more vaccinated since at least during Omicron our hospitals/ICUs were hit quite hard, largely by the unvaccinated, and deaths were far higher compared to other countries of similar economic standing. But the catch is that you need results, and23:07
Tuvixfrankly none of the weak rules here, often with little-to-no enforcement and countless exceptions, do any good.23:07
ArsaneritTuvix: I think that those people who were pushed to get the vaccine by the restrictins have gotten it by now, and the ones who still don't want the vaccine aren't going to get it due to these restrictions.23:08
ArsaneritI can see how soft pressure can be a motivation, but only if that pressure is actually effective.23:08
TuvixRight; we'd either need far more involved vaccine requirements (likely to be fought very hard at political level and by public protest) or need some major social shift to get vaccination rates up. Just check out the CDC newly fully-vaccinated rate as co-plotted with deaths: https://covid.cdc.gov/covid-data-tracker/#trends_dailydeaths_7daypeoplefullyvaccinated23:09
BrainstormUpdates for Spain: +53055 cases, +393 deaths since a day ago23:09
TuvixBoth Delta and the announcement of Omicron cased a small, fairly short-lived jump in new 1st time vaccine recipients, and quickly returned to prior trends.23:10
TuvixI suspect all this largely-inaccurate talk of Omicron being 'more mild' (by death counts it's now notably worse than Delta) may have discouraged more possible vaccine recipients from acting, unless/until there's a new varient or wave of death to manifest.23:12
ArsaneritDelta overloaded German ICUs, unlike Omicron.  But Delta came before vaccines.  Even if too many people are unvaccinated (12% of 60+ have not been fully vaccinated), it would seem the vaccines are the main reason we in Germany have been spared from ICU overloading in the omicron wave.23:14
ArsaneritNot many children are vaccinated, but fortunately they're very unlikely to get to ICU23:14
TuvixYup, that's largely my conclusion at well comparing the US to nearly any other EU country in aggregate.23:14
ArsaneritMeaning that even if all children get the virus at the same time it still won't overload hospitals.  I just hope they won't suffer from long covid much.23:15
TuvixThat trend seems more pronounced in the US when you break down the fatalities by age-group; the younger groups are dying less comapred to their *older* counterparts, but they're doing more compared to their *own* age-group in Delta as compared to Alpha, while the older group actually did much better.23:15
TuvixThat's another big difference; the age-gap here in the States is still quite bad for the under-18 group, and even worse for the 5 to 11 year olds.23:16
TuvixThis also comes as many states are looking at removing mask requirements in schools, leaving it up to local school districts and/or individual familes to decide what to do.23:17
TuvixIt'd be one thing if vaccination rates were generally higher, but they aren't, and we've already seen the impact of this more-transmissible Omicron varient on the youth. The under-18's are showing more death now than pre-vaccines, although not suprising considering the low percentage vaccinated.23:18
ArsaneritIs there a measurable excess death rate in children during the coronavirus pandemic?23:18
TuvixBest is probably to use the provisional COVID death counts and break it down by age: https://data.cdc.gov/NCHS/Provisional-COVID-19-Deaths-by-Sex-and-Age/9bhg-hcku23:18
TuvixIf you go to visualize, you can pick just that age grop by plotting a column chart in the 'End Date' dimension, a Measure of 'COVID-19 Deaths' and adding filters for 'Group: By Month', 'Sex: All Sexes', 'State: United States', 'Age Group: 0-17 years'23:19
TuvixNote that it's crucial to set those first 3 filters and a non overlapping age-selection, otherwise you'll get double-counts.23:20
TuvixJan '22 dat (and Feb obviously) is incomplete, but Jan '22 is only missing about 14% by my calculation against CDC-aggregate data. For the <18 year olds, the peak of Alpha was 51 deaths (Jan 2021) vs. 58 (Jan 2022) and keep in mind the 2022 value is likely to go up slightly in the coming weeks due to data lags.23:21
TuvixA similar trend is seen if you limit to the 5-14 year age group, so that largely rules out that it's skewed due to the 0-4 ages not being eligible for vaccination (they have a lower incidence rate to begin with)23:22
BrainstormNew from The Atlantic: How to Reclaim Normal Life Without Being ‘Done’: In many ways, the pandemic has never felt quite so paradoxical. In the United States, cases and hospitalizations are falling, and millions of people are as vaccinated as they can be. A rash of [... want %more?] → https://www.theatlantic.com/health/archive/2022/02/covid-normal-life-grace-period-done/622051/23:23
lastshellhi guys I been overload with work last days/weeks23:27
lastshellI saw some places are lifting masks mandates23:28
lastshellbut hospitalization continue to be high23:28
lastshelldo we know where we a re heading now ?23:28
xxwe're heading into an even crappier future, best to do all you can to prepare for it23:29
lastshellxx can you provide more extra context23:29
lastshellI think even fauci say that pandemic was over23:29
TuvixThis is US-specific? There's been a trend for that in the states, yes, including in some school districts state-wide. Cases have indeed dropped notably from the Omicron-peak, although in the K-12 schools, youth remain far less vaccinated in the US as compared to many other comperable nations.23:29
lastshellyes sorry forgot to clarify in US wise Tuvix23:30
TuvixJust before you joined I was discussing the fact that the under-18 group is actually seeing a higher peak rate of death during Omicron than seen during the prior winter Alpha-wave, and this is with the benefit of vaccines now which are highly effective.23:30
TuvixSlightly higher, to be clear; it's somewhat similar, though notably more death leading into Omicron, yet substantially, over twice as much, death seen in Delta (vs. Alpha) although that was before vaccines in under-18's were generally available.23:31
ecksso what's the absolute risk ratio for under-18s mortality when comparing omicron with delta? a relative risk increase of 100% doesn't mean much if the baseline risk was low to begin with23:33
lastshellso is omicron worst for yonger polulations than delta ?23:33
Tuvixlastshell: No, Omicron, in terms of death, is about on-part and slightly worse than Alpha. I've got a chart of this, just a sec, based on data plotted from this source: https://data.cdc.gov/NCHS/Provisional-COVID-19-Deaths-by-Sex-and-Age/9bhg-hcku23:34
Tuvixlastshell: https://imgur.com/JSCTXpP23:35
Tuvixecks: Right, incidence rate is much lower, I think CDC has info there too broken down by vaccination status, but the data lags longer. The source for that is here: https://data.cdc.gov/Public-Health-Surveillance/Rates-of-COVID-19-Cases-or-Deaths-by-Age-Group-and/3rge-nu2a23:36
ArsaneritWhy are deaths in many European countries going up, but in Germany they're going down?23:39
xxa disclaim should probably be given that we still don't know (and won't know for a long time) what the effects of even a mild covid infection are in 10 years time for the current 18 year olds23:39
ArsaneritUp in France, Sweden, Spain, Denmark, UK.  Down in Germany, Switzerland, Netherlands.23:39
TuvixIsn't the wave in Germany only really starting in the past couple of weeks? It'll take about 3 weeks for that to be refelcted in fatalities.23:40
TuvixEach area is getting hit at different times, so you have to compare the uptick of death relative to the wave's start, peak, & end.23:40
ArsaneritMaybe that's all there is to it.23:41
TuvixThis applies in a different way to something lik the US where the very different state travel & culture result in pockets of virus outbreak.23:41
ArsaneritThe countries with death rates going up actually have cases going down.23:41
ArsaneritNetherlands and Germany still have sharply rising cases23:41
TuvixFor instance, our death rate is largley falling in the areas hit hard earlier by Omicron, yet our national death-rate has remained fairly flat right near the peak death rates, mostly becuase the disease is now peaking or just about to in largely under-vaccinated states.23:41
ArsaneritOk23:42
TuvixThe real quesiton will be what kind of a rise Germany, Netherlands, and other countries just going into their peaks see.23:42
ecksso 50 deaths across the entire US population 0-17 years during the omicron wave so far? or is that per 100k or whatever?23:42
lastshellTuvix why now goverments are more lax and lifting mandates or covid meassures ?23:43
Arsaneritecks: per million I think?23:44
ArsaneritTuvix: True.  I guess that when the hospital association in Germany says they don't expect overloaded ICUs, they have some data-driven models they predict that on.23:44
TuvixNo, those are raw detah rates; you need to use the incidence rate in the 2nd link I supplied, I'll upload an incidence chart through Nov 2021 (latest that chart goes due to longer data lag)23:45
TuvixSorry, raw deaths; it's not a rate in that chart.23:45
Arsanerit50 in total is not many23:47
ecksfrom a cursory googling there are about 60 million people ages 0-17 in the US and around 57 deaths in January according to your graph... so a monthly mortality rate of 0.0000833%23:47
ArsaneritI think it helps to put such numbers in covid.  How many children die from cancer, traffic, air pollution, crime, other diseases, etc.?23:47
Arsanerits/covid/context23:48
Tuvixecks: https://imgur.com/t3aUSaX23:48
eckssorry, 0.000095%23:48
Arsaneritgn23:48
ecksthat doesn't sound like a very high risk23:49
TuvixThose IRR values are rates per 100k population, so your percentages don't seem to match. But further, the difference between unvaccinated (light blue) and vaccinated (dark blue) is stark.23:49
TuvixAnd you're also forgetting the impact of hospitalizations and non-fatal outcomes. The whole point is to compare the risks involved. The risk of heart inflamation alone is worse in the unvaccinated, and thanks to Omicron (and it would be made worse by removing mitigations, like masks which do have value if worn properly by everyone) the disease spread will rise.23:50
TuvixFor vaccines to be a bad thing in aggregate, you'd have to have more risk from taking the vaccine than from relative risk to going without it. One of the most often-cited reasons is myocarditis, except the risk of that is quite a bit worse from catching COVID as an unvaccianted immune-naive individual than from the vaccine, by an order of magnitude.23:51
ecksthat's another question, of course, but the number of deaths seems very unconcerning23:52
LjLTuvix, for people below 30 that is not really so clear imo23:52
xxecks: different people become concerned at different number of deaths23:52
ecksyes and at some number you gotta admit it's irrational23:53
xxso there'll be a natural variation between all the countries23:53
Tuvixecks: Not really. Let's say instead of the 106 deaths in youth peak (Sept 2021) that instead a lone gunman went to all 50 states and shot 2 children, at random. Yes, I realize this is a different cause of death, but it would be an outrage. The majority of deaths are prevented with vaccination, so again, by saying "it's such a small number" largely misses the point that these are nearly all preventable23:54
Tuvixdeaths.23:54
TuvixNow sure, we can debate the risk factor vs. the side-effects, but then let's be honest about the comparison. The comparision isn't "oh those deaths are acceptable." If they were shot at random they'd be very *unacceptable* , at least I think that's true. Why are deaths that could be trivially prevented by action upfront any less concerning?23:55
ecksthose crude numbers mean nothing if you don't put them in context23:55
xxa 9/11 every 2 days23:55
TuvixSure, which is why the IRR unvax. vs. vax. rates are also important. OWID has that for various countries too, although only down to 18 years.23:56
Alex1138[m]9 million+ dead in the US :/23:57
TuvixErm, official CDC counts are  900k, not 9M, if we're talking COVID.23:57
TuvixExcess deaths are around 1.3M, give or take depending on the model used, as a more accurate representation of the "true cost" of the pandemic in lives.23:58
Alex1138[m]sorry, i'm dumb af23:58
Alex1138[m]900k is still a lot23:58
TuvixNah, 9 followed by "too many zeros" is close enough. Just one too many zeros earlier…23:58
ecksquick googling shows that the overall mortality of teens aged 15-19 is 49/100 000/year in the US23:59
eckswhat's another 0.5/100 000/year23:59
BrainstormUpdates for India: +57926 cases, +659 deaths since 23 hours ago — Canada: +11622 cases, +118 deaths since 23 hours ago23:59
ecksyeah it sounds harsh but that's the truth23:59

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