libera/##covid-19/ Sunday, 2021-10-03

BrainstormUpdates for Bahrain: +45 cases (now 275175), +14852 tests (now 6.5 million) since a day ago00:06
BrainstormNew from r/WorldNews: worldnews: Merck pill seen as 'huge advance,' raises hope of preventing COVID-19 deaths → https://is.gd/nSR1yH00:07
nixonix.title https://www.medrxiv.org/content/10.1101/2021.09.29.21263145v1.article-info00:24
Brainstormnixonix: From www.medrxiv.org: COVID-19 in twins: What can we learn from them | medRxiv00:24
BrainstormNew from COVID tweets: Roland Baker (@RolandBakerIII): Well this sucks!Viral replication in human macrophages enhances an inflammatory cascade and interferon driven chronic COVID-19 in humanized mice: Demonstration of SARS-CoV-2 replication in Macrophages enhanced by virus specific antibodies.biorxiv.org/content/10.110… → https://is.gd/utDUhC00:28
BrainstormUpdates for Netherlands: +1800 cases (now 2.0 million) since 21 hours ago00:31
nixonixnot the same dr baker in pic with dr greger?00:31
nixonixanyways, mice lie. not similar cascade in humans, and didnt find replication (maybe didnt look hard enough, who knows)00:32
* LjL is not sure if he should show the twin study to a twin00:36
LjLbit low number of people sampled though i think00:37
nixonixyeah. well theres some correlation. some and perhaps most of those interferon defects may be because of previous infections, genetic defects due to aging etc, but there are some genetic traits causing it for younger too00:43
nixonix.title https://www.medrxiv.org/content/10.1101/2021.09.30.21264363v100:44
Brainstormnixonix: From www.medrxiv.org: SARS-CoV-2 infections elicit higher levels of original antigenic sin antibodies compared to SARS-CoV-2 mRNA vaccinations | medRxiv00:44
nixonixseems natural infection has more cross-reactive abs, but vax induces more specific against sars2 (compared to other ronaviruses)00:47
nixonixs/reactive/binding (reactivity is about cells, which can produce abs, but anyway)00:49
BrainstormNew from COVID tweets: Eric Topol (@EricTopol): Linear RNA is big, as in mRNA vaccinesIs circular RNA next ?bloomberg.com/news/articles/… pic.twitter.com/cDHzZ5xtgD → https://is.gd/Xj3XLq00:49
nixonixor maybe not quite that, but natural infection induced more abs that binded well to S2 of oc43, but poorly to sars2. and vax had less S2 cross-reactive abs, but high quality and cross-reactive (they use cross-reactivity for abs too in the paper)00:54
nixonix"recent study suggested that the recall of OC43-reactive antibodies is associated with a compromised de novo SARS-CoV-2 response in individuals with fatal COVID-19" - meaning natural infection would protect worse vs severe01:01
BrainstormUpdates for Faroe Is.: +32 cases (now 1210), +2972 tests (now 433972) since 2 days ago01:08
nixonixIt is possible that memory B cells elicited by prior β-hCoV infections are recalled by both SARS-CoV-2 infections and vaccinations, and that long-lived germinal centers elicited by mRNA vaccinations50 are required to allow for somatic hypermutations that promote the formation of cross-reactive S2 antibodies that bind efficiently to the spike01:09
nixonixproteins of both β-hCoVs and SARS-CoV-201:09
nixonixidk, because IL-17 or CXCL13 isnt found after mrna vaccination (and apparently some after some types of flu vaxes, depending on adjuvant used)01:10
nixonix"Consistent with this, a recent study found that S2-specific B cells with a memory phenotype are quickly recruited following primary immunization of humans01:11
nixonixi think i accidentally wrote IL-17 day or two ago when we discussed about germinal centers, meaning cxcl13 secreted by follicular dendritic cells, that attracts both memory b-cells and t-cells to germinal centers01:12
nixonixIL-17A is thought to promote formation of new germinal centers after infection or vaxing, and its produced by many types of immune cells. too bad that mrna vaxes dont induce it, so natural infection (and some other types of vaxes) have advantage with it01:14
nixonixbut who knows, maybe vax that induces IL-17A (and possibly other cytokines needed for activating follicular dendritic cells in germinal centers), also causes that phenomenom in the paper, so that neut abs would be less specific and suspectible to OAS (while good for b-cell affinity maturing)01:18
BrainstormNew from r/Science: science: Study finds a statistically significant positive association between COVID-19 mortality and the proportion of the overweight in adult populations spanning 154 countries.This association holds across countries after controlling for age, gender, and income. → https://is.gd/IhrzNs01:22
nixonix.title https://www.medrxiv.org/content/10.1101/2021.09.29.21264199v101:24
Brainstormnixonix: From www.medrxiv.org: Effectiveness of mRNA-1273 against Delta, Mu, and other emerging variants | medRxiv01:24
nixonix.title https://www.sciencedirect.com/science/article/abs/pii/S0022283621005179  no access...01:32
Brainstormnixonix: From www.sciencedirect.com: The mechanism and consequences of SARS-CoV-2 spike-mediated fusion and syncytia formation - ScienceDirect01:32
BrainstormNew from r/WorldNews: worldnews: Mass protests in Brazil call for Jair Bolsonaro’s impeachment. Huge crowds paraded through downtown Rio on Saturday to voice their outrage at Bolsonaro’s response to a Covid outbreak that has killed nearly 600,000 people and dealt a heavy blow to the South American country’s economy. → https://is.gd/4NpaES01:33
nixonixwhich is pity, because: "Several interferon-stimulated genes, including IFITMs and LY6E act as barriers to S protein-mediated fusion by altering the composition or biophysical properties of the target membrane. We also summarize the effect that the mutations associated with the variants of concern have on S protein fusogenicity01:33
BrainstormUpdates for Colombia: +1497 cases (now 5.0 million), +36 deaths (now 126372), +45313 tests (now 25.6 million) since a day ago — Barbados: +183 cases (now 8792), +1 deaths (now 79), +2199 tests (now 322476) since a day ago — Uruguay: +99 cases (now 389124), +1 deaths (now 6057), +6862 tests (now 3.6 million) since 23 hours ago01:33
nixonix.title https://www.biorxiv.org/content/10.1101/2021.09.27.462006v1.full01:40
Brainstormnixonix: From www.biorxiv.org: The BNT162b2 mRNA vaccine induces polyfunctional T cell responses with features of longevity | bioRxiv01:40
nixonix"Production of high levels of IFNγ and IL-2 was confirmed, whereas IL-17 and IL-4 were barely detectable (<5 pg/ml), confirming the Th1 differentiation profile of S-specific cells01:41
nixonix"High antibody titers induced by influenza vaccination have been shown to correlate positively with the frequency of T cells expressing follicular helper molecules, including CXCR5 and ICOS" - yup, cxcr5 is a receptor for cxcl13, but the latter is missing with mrna vaxes, so no migration to germinal centers, it seems (or its limited)01:45
nixonix"Relevant to infection with SARS-CoV-2, an interesting study has shown the absence of germinal centers and a block in the differentiation of Tfh cells in post-mortem tissues from COVID-19 patients (42), with loss of both transitional and follicular B cells in severe disease01:47
nixonixand loss of germinal centers in severe disease, according to another paper (apparently more than typical with other viruses because they mentioned it)01:48
nixonix"These findings show that vaccination with BNT162b2 appropriately induces the differentiation of the T cell subset specialized in providing B cell help and thus in sustaining the generation of high-affinity antibodies in germinal centers, and that these cells persist in the periphery for at least 6 months" well, maybe they know better. they01:49
nixonixshould...01:49
BrainstormNew from COVID tweets: Marc Veldhoen (@Marc_Veld): mRNA vaccination elicited S1 and S2-reactive antibodies, while 2nd vaccination boosted mostly S1 antibodies. SARS-CoV-2 infections > large proportion of original antigenic sin-like antibodies that bound efficiently to common seasonal human coronaviruses but poorly to SARS-CoV-2. pic.twitter.com/l3Nj4aThuy → https://is.gd/4CdPO501:54
nixonix^ good find01:56
nixonix"Reinfection by SARS-CoV-2 under endemic conditions would likely occur between 3 months and 5·1 years after peak antibody response, with a median of 16 months. This protection is less than half the duration revealed for the endemic coronaviruses circulating among humans (5–95% quantiles 15 months to 10 years for HCoV-OC43, 31 months to 12 years01:57
nixonixfor HCoV-NL63, and 16 months to 12 years for HCoV-229E).01:57
nixonix"For SARS-CoV, the 5–95% quantiles were 4 months to 6 years, whereas the 95% quantiles for MERS-CoV were inconsistent by dataset01:57
nixonix.title https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(21)00219-6/fulltext01:57
Brainstormnixonix: From www.thelancet.com: The Lancet | The best science for better lives01:57
nixonix* The durability of immunity against reinfection by SARS-CoV-2: a comparative evolutionary study01:58
nixonixhard to say how they estimated things like vaccinations, different vax types, delta etc in their model02:04
nixonixthose seasonal hcov immunities dont last long, but the frequency of reinfections is also limited by exposure, and they are more or less seasonal so they are not always around, unlike rona02:05
nixonixand they or some of them tend to have biannual nature, which shows up in some of the the surveillance datas, but not in all of them. also at least some of them tend to be asymptomatic every other time, so they go unnoticed easily then02:07
nixonixwhich may explain biennial looking nature perhaps02:07
nixonixand i meant biennial, not biannual (the latter would be every half year)02:08
LjLi don't understand this statement: "SARS-CoV-2 infections > large proportion of original antigenic sin-like antibodies that bound efficiently to common seasonal human coronaviruses but poorly to SARS-CoV-2."02:14
nixonixhopefully some discussion will follow. dissapointed to not see any, following that tweet02:15
BrainstormNew from r/WorldNews: worldnews: Tragic milestone as Covid-19 deaths eclipse 700,000 in U.S. → https://is.gd/P69hsH02:16
nixonixits because natural infection seems to strengthen abs binding to conserved and common sites, instead of rona-specific (and vise versa, better, with ronavax)02:16
nixonixwhich look like OAS, instead of getting protection to new antigen, you get stronger protection to old one02:17
nixonixbut its different sites, so not sure if its exactly what OAS means, i thought it was about the same sites, which are somewhat different with another strain (like with deng), or variant02:18
nixonixbut the whole concept of OAS isnt that well understood, and with dengue i think they are not sure if its OAS or some type of ADE (which was caused by that dengue vax of sanofi, for some of the younger kids)02:20
nixonixand also reinfection by another strain of dengue02:20
nixonixbugger that one paper that isnt open access02:21
nixonixdo they start to do that now, reduce open access ronapapers?02:22
nixonixits about polyclonality prob rather than quality of abs, i think, because quality improving needs b-cell maturing and time02:23
BrainstormNew from r/WorldNews: worldnews: Greater Sydney hits 100 days in lockdown as residents look forward to simple things once its over → https://is.gd/7JKfHy02:26
nixonixpolyclonality and maturing are both about energy conserving imo, evolution has tried to optimize our immune response as efficient as possibly so that as little energy for stuff like maintaining immune cells, making them go through things like expansion, differentiation, class-switching etc02:27
nixonixso if theres no evidence how something happens in the body, if you solve it how it would be most energy efficient, that gives the clue how it likely goes. it seems lots of things are not understood well, or theres no concensus. i see alternative theories mentioned in the papers etc02:29
BrainstormUpdates for Papua New Guinea: +217 cases (now 20672), +2863 tests (now 191130) since a day ago — India: +21498 cases (now 33.8 million), +241 deaths (now 448846) since 19 hours ago — Guinea: +14 cases (now 30434), +1110 tests (now 558693) since 23 hours ago — Netherlands: +1790 cases (now 2.0 million) since 23 hours ago02:35
nixonixalso those non-neutralizing abs with natural infection, towards conserved S2 sites similar with other hcovs, could be bad because:02:57
nixonix<yuriwho>  Nixonix. The idea is that antibodies to a related coronavirus may bind to SARS-CoV-2 but not neutralize it, your immune cells can then 'eat' these antibody coated particles intending to process them for an immune response but instead the immune cells become infected themselves because the virus was never neutralized. In this way, prior02:57
nixonixrelated infections/antibody responses can influence how your immune system02:57
nixonix<yuriwho>  handles a new variant. This is also why vaccines need so much testing as they can cause ADE is not designed correctly. This is also part of the 'second' wave theory. However SARS-CoV-2 mutates very slowly compared with other viruses and I do not believe the second wave will come.02:58
LjLwell, he wasn't quite on spot about the slow mutation and no second wave thing ;(02:59
nixonixit then picked up speed, especially S1 but also N, mutations around year ago (possibly in bodies of reinfected people)02:59
BrainstormUpdates for Panama: +227 cases (now 467565), +6 deaths (now 7236), +7280 tests (now 3.9 million) since 21 hours ago — Bermuda: +92 cases (now 5336), +3 deaths (now 75), +4158 tests (now 545465) since 2 days ago — St. Kitts and Nevis: +29 cases (now 1994), +798 tests (now 42866) since a day ago03:00
nixonixyeah, those forecasts have gone wrong many times prob for all. while im just a diletant, i list a few of my guesses where i was wrong: i didnt see those permanent damages from mild cases that may be way too common03:00
nixonixi didnt think delta would be faster spreading than alpha, before it started to gain in uk in early may. and i thought starting from the summer we would handle this with vaccines, which i also thought wouldnt fade as fast03:01
nixonixbut i saw the 2nd wave coming when i saw it happening in spain in july (and probably never believed it would be done before good vax coverage, despite cases going down after lockdowns, towards the summer)03:12
nixonixthat was in april 2 2020 though03:12
nixonixnext summer we will be thinking, looks like its done, time to reopen03:16
BrainstormNew from Reddit (test): CoronaVirus_2019_nCoV: How I got a school mask mandate in my rural West Virginia community → https://is.gd/0XpIQH03:19
nixonixbut who guessed this, over 1.5 years and we arent further in beating it. link me if somebody saw this and theres evidence left03:20
nixonix.title https://www.cnbc.com/2020/05/01/coronavirus-pandemic-likely-to-last-for-two-years-scientists-predict.html03:22
Brainstormnixonix: From www.cnbc.com: Coronavirus pandemic likely to last for two years, scientists predict03:22
nixonix.title https://twitter.com/TWenseleers/status/143390268708769382403:29
Brainstormnixonix: From twitter.com: Tom Wenseleers (@TWenseleers): "The timing of the end of the pandemic was influenced massively by the emergence of the Alpha and Delta variants. Hard to see how statements like this can be made with [...]03:29
sdfgsdfg"The timing of the end of the pandemic was influenced massively by..."03:32
sdfgsdfgthe end of the pandemic ? see .. I've been telling you guys03:32
sdfgsdfgit's over !03:32
sdfgsdfgwe can get finally get rid of this channel and continue our lives03:32
sdfgsdfgs/get / /03:33
sdfgsdfgthat's the first get. how did you substitute for only the first regex03:33
sdfgsdfgnvm03:33
BrainstormUpdates for Paraguay: +25 cases (now 460022), +1796 tests (now 1.8 million) since a day ago03:37
nixonix.title https://twitter.com/SCOTTeHENSLEY/status/144431388764665446803:40
Brainstormnixonix: From twitter.com: Hensley Lab (@SCOTTeHENSLEY): "Check out our new preprint: SARS-CoV-2 infections elicit higher levels of original antigenic sin antibodies compared to SARS-CoV-2 mRNA vaccinations 1/ [...]03:40
nixonixokay, lets count what we have supporting the idea, that there is ADE in natural sars2 infection (instead than after vaccination): that mouse study, that found replicating human TR macrophages in humanized mice (with cytokine cascade), another human study that found them infecting but not replicating, that OAS paper which evidence that can also03:49
nixonixcause ADE, and also this:03:49
nixonix.title https://www.nature.com/articles/s41467-021-24938-403:49
Brainstormnixonix: From www.nature.com: SARS-CoV-2 specific T cell responses are lower in children and increase with age and time after infection | Nature Communications03:49
nixonixreplicating *virus in human tissue-resident macrophages, twas03:50
BrainstormNew from r/WorldNews: worldnews: Girl, 15, Dies of Covid On Day she was Due to get Vaccine → https://is.gd/TpNB5k03:51
nixonixi guessed it was uk, they tried to prevent and delay vaxing 12-17 yo03:52
nixonixEarlier this month, the UK's chief medical officers recommended a single Pfizer dose for all 12 to 15-year-olds .. The chief medical officers say that a second dose should not be considered before the spring term.03:54
BrainstormUpdates for South Korea: +2085 cases (now 318105), +3 deaths (now 2507), +30430 tests (now 14.7 million) since 22 hours ago — New Zealand: +32 cases (now 4352), +16915 tests (now 3.4 million) since 22 hours ago04:02
nixonix.title https://www.dailymail.co.uk/news/article-10051923/Russell-Crowe-gives-Gladys-Berejiklian-glowing-review-shock-departure-NSWs-job.html04:17
Brainstormnixonix: From www.dailymail.co.uk: Russell Crowe gives Gladys Berejiklian a glowing review after her shock departure from NSW's top job | Daily Mail Online04:17
BrainstormUpdates for United Kingdom: +29520 cases (now 7.9 million), +124 deaths (now 137295) since 22 hours ago04:40
BrainstormNew from The Indian Express: World: UK to open up more travel by scrapping hotel quarantine for dozens of countries: Telegraph → https://is.gd/IOcnDE05:57
BrainstormNew from This Week In Virology: TWiV 812: Bespoke capsids delivered: TWiV considers lessons learned from COVID-19 about emergency drug use during a pandemic, and selection of AAV capsids to produce vectors that efficiently deliver genes to muscle cells. → https://is.gd/fb1czV06:18
BrainstormUpdates for India: +20460 cases (now 33.8 million) since 13 hours ago07:09
BrainstormNew from r/WorldNews: worldnews: Home Health Nurse Kicked Out By A Couple For Being Unvaccinated → https://is.gd/jYj0oI07:11
BrainstormUpdates for Kelantan, Malaysia: +1288 cases (now 117454) since a day ago — Terengganu, Malaysia: +816 cases (now 57162) since a day ago — Negeri Sembilan, Malaysia: +210 cases (now 97652) since a day ago — Lombardy, Italy: +361 cases (now 884486), +1 deaths (now 34050) since a day ago07:34
nana_if you had covid, would you then take sinopharm or sinovax is that was the only choice?07:37
BrainstormNew from r/WorldNews: worldnews: Israeli scientists construct new model to determine optimal strategies for combining Vaccines and Social Distancing against COVID19 → https://is.gd/x8FRug08:03
BrainstormNew from r/WorldNews: worldnews: New Zealand tightens travel rules as COVID spreads → https://is.gd/kA7fSB08:14
BrainstormUpdates for St. Vin. and Gren.: +113 cases (now 3676), +2 deaths (now 28), +666 tests (now 77842) since a day ago08:36
BrainstormNew from r/WorldNews: worldnews: New Zealand widens Covid lockdown as Delta spreads outside Auckland → https://is.gd/4qRtxN08:46
BrainstormNew from r/Coronavirus: Daily Discussion Thread | October 03, 2021: 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://is.gd/HUfP8r09:06
BrainstormUpdates for Czechia: +556 cases (now 1.7 million), +1 deaths (now 30478), +46537 tests (now 38.4 million) since a day ago09:38
BrainstormUpdates for Armenia: +907 cases (now 264690), +18 deaths (now 5372), +13804 tests (now 1.7 million) since a day ago10:03
BrainstormNew from The Indian Express: World: Nicaragua authorises two Covid-19 vaccines from Cuba, Cuban firm says → https://is.gd/AKZwW410:10
BrainstormNew from Reddit (test): nCoV: Global COVID Cases For 03OCT21 → https://is.gd/AvJY1E10:20
BrainstormNew from COVID tweets: Marc Veldhoen (@Marc_Veld): Change in Symptoms and Immune Response in People with Post-Acute Sequelae of SARS-Cov-2 Infection (PASC) After SARS-Cov-2 Vaccinationmedrxiv.org/content/10.110… → https://is.gd/rAB7mx10:31
sdfgsdfgcovid is finally over10:36
BrainstormNew from Reddit (test): nCoV: New virus cases in 2,000s for 8th day; holiday-tied virus surge concerning | 03OCT21 → https://is.gd/o3meaj10:52
BrainstormUpdates for Israel: +1263 cases (now 1.3 million), +5 deaths (now 7783), +6088006 tests (now 26.9 million) since 14 hours ago — Slovakia: +977 cases (now 415993), +8 deaths (now 12668), +7308 tests (now 3.6 million) since 20 hours ago11:05
BrainstormNew from Reddit (test): nCoV: Covid-19 coronavirus: How to ask friends and family if they're vaccinated, and how to handle it if they say no | 02OCT21 → https://is.gd/2kFGZv11:13
BrainstormNew from r/WorldNews: worldnews: UK might not be over the worst, scientists warn, as Covid case numbers stay high → https://is.gd/IIhCKB11:23
BrainstormUpdates for Russia: +25769 cases (now 7.6 million), +890 deaths (now 209918), +1100000 tests (now 193.2 million) since 23 hours ago — Germany: +4698 cases (now 4.3 million) since 14 hours ago — France: +5003 cases (now 7.1 million) since 17 hours ago — St. Kitts and Nevis: +35 cases (now 2029), +2 deaths (now 15) since 8 hours ago11:30
BrainstormNew from r/WorldNews: worldnews: COVID-19: Jurgen Klopp says refusing vaccine is like drink-driving as it endangers others | UK News → https://is.gd/m76ERC11:34
BrainstormUpdates for Latvia: +1033 cases (now 161641), +10 deaths (now 2741), +9075 tests (now 4.4 million) since a day ago12:07
BrainstormNew from COVID tweets: Marc Veldhoen (@Marc_Veld): Singaporeans not all happy with reduced measures against SARS-COV-2, even requesting tough measures to be put back in place.ft.com/content/530258… → https://is.gd/7TRW1f12:16
BrainstormUpdates for Austria: +2445 cases (now 748825), +5 deaths (now 11026), +408724 tests (now 88.1 million) since 22 hours ago — United Kingdom: +29524 cases (now 7.9 million) since 21 hours ago12:32
BrainstormNew from r/Science: science: Research shows businesses that fully reopened during the height of the pandemic last fall saw more than a 10% rise in the COVID-19 infection rate in their first two weeks, nearly double the rise of establishments that only partially reopened, → https://is.gd/zraCxC12:58
BrainstormNew from The Indian Express: World: Dubai Expo revises worker fatalities to six after including COVID-related deaths → https://is.gd/Lycwpq13:09
BrainstormUpdates for Indonesia: +1142 cases (now 4.2 million), +58 deaths (now 142173), +905493 vaccines (now 93.1 million), +238058 tests (now 39.8 million) since 23 hours ago — UAE: +184 cases (now 736708), +2 deaths (now 2102), +311282 tests (now 84.9 million) since a day ago — Afghanistan: +23 cases (now 155286), +3425 tests (now 764673) since a day ago13:10
BrainstormUpdates for Romania: +8682 cases (now 1.3 million), +150 deaths (now 37544), +46075 tests (now 13.0 million) since 23 hours ago — Nepal: +574 cases (now 797192), +7 deaths (now 11164), +7070 tests (now 4.2 million) since 23 hours ago — Brunei: +148 cases (now 7716), +1 deaths (now 56), +4433 tests (now 369372) since 23 hours ago [... want %more?]13:34
lastshelllooks like delta is fading slowly but there is other variant (ohio dashboard) https://coronavirus.ohio.gov/wps/portal/gov/covid-19/dashboards/key-metrics/variants13:38
BrainstormNew from r/Science: science: People Can Change Their Minds About Vaccines. From January 6 to March 29 of 2021 the percentage of Americans who had received at least one vaccine dose or definitely intended to get the jab increased from 54.7% to 72.3%, → https://is.gd/uhEWVg13:51
BrainstormUpdates for Belarus: +1899 cases (now 543976), +14 deaths (now 4188), +39228 tests (now 8.6 million) since 21 hours ago — Senegal: +7 cases (now 73800), +1 deaths (now 1860), +1717 tests (now 804484) since 23 hours ago13:59
BrainstormUpdates for Laos: +301 cases (now 25217), +1 deaths (now 22), +5264 tests (now 513579) since 22 hours ago — Qatar: +79 cases (now 236913), +5825 tests (now 2.7 million) since 21 hours ago — Germany: +4699 cases (now 4.3 million) since 17 hours ago14:37
BrainstormNew from r/Science: science: No, vaccinated people do not carry a bigger COVID viral load than the unvaccinated → https://is.gd/n77B3m14:44
BrainstormUpdates for Bhutan: +7 cases (now 2608), +1505 tests (now 1.2 million) since 3 days ago15:08
de-factolastshell that link does not work from here, can you give deails?15:10
de-factohow is that new variant called?15:10
sdfgsdfgthey took the site down ?15:21
de-factoo rather think its geoblocked or such15:23
sdfgsdfgit doesn't look concerning15:24
de-factoyeah site only works with a US ip address15:31
sdfgsdfgI mean there's not much concerning with the charts or latest data on variants etc15:31
sdfgsdfglooks good15:32
BrainstormUpdates for Saudi Arabia: +41 cases (now 547262), +2 deaths (now 8724), +46499 tests (now 29.1 million) since 23 hours ago15:33
de-factoi does not look good to me, the "other" variant seems to overtake Delta there in Ohio15:34
de-factohow can that be good?15:34
sdfgsdfgnah it's just delta ratio going down15:36
sdfgsdfgthat makes other variants look higher15:37
de-factoyeah but that means something "other" is more reproductive than Delta, due to whatever reason15:37
de-factohttps://i.ibb.co/4jfKwzf/ohio-variants.png15:38
sdfgsdfg20 percent in just 10 days ?15:39
sdfgsdfgthat's insane15:39
sdfgsdfgwhoa15:39
de-factohttps://www.worldometers.info/coronavirus/usa/ohio/15:40
de-factoso that transition of the last two chart bars is at the increasing edge of their peak there15:41
de-factoi really wish their data was of better quality15:42
de-factohow are we supposed to know what "other" means?15:42
de-factoGamma is green, Iota is black so its neither of those15:44
de-factomaybe Lambda or Mu or such?15:44
sdfgsdfgwhy isn't this in the news though15:45
de-factomaybe the variant dashboard was created recently15:47
de-factoanyhow it looks like their peak is delta driven, yet i wonder what hides in that "other" category15:48
de-factoif they just would publish the sequences15:48
antepost[m]<de-facto> "how can that be good?" <- may its a weak variant15:48
sdfgsdfgthat would explain an unusually calm media15:49
sdfgsdfghttps://www.cleveland.com/open/2021/09/small-numbers-of-coronavirus-mu-variant-reach-ohio-early-research-shows-mu-may-be-vaccine-resistant.html15:51
de-factowell its of a fitness that competes with Delta in a way that allows it to increase more than Delta (hence increase its contribution to over all incidence)15:51
sdfgsdfgwhat if it's the mu ?15:51
sdfgsdfgmu could be the answer15:51
de-factoyeah possibly, but iirc neither Mu nor Lambda was that fit15:52
de-factoi guess we have to wait until we get better data15:53
sdfgsdfgmoo looks promising15:53
de-factoe.g. i dont even know how many sequences they use for that graph there15:53
sdfgsdfgmaybe in another 2 weeks ohio will be swamped by moo lol15:53
de-factothey reached the peak and case numbers are going down, so ...15:53
de-factoat least for now15:54
sdfgsdfgif the data is right about moo's potential, we need about 2 to 4 weeks to find out15:55
de-factoif incidence is a sum of two exponentials each with different reproduction number we should see incidence increasing in Ohio again soon15:56
de-factoe.g. if Rt(Delta)<1 and Rt(Other?)>115:56
sdfgsdfgit could be a diverse range of variants of interest15:57
de-factobut thats all speculation without better data we cant know15:57
sdfgsdfginstead of a variant rising15:57
de-factoyeah indeed15:57
de-factoalso possible15:57
BrainstormNew from The Indian Express: World: A few skeptical US hospital workers choose dismissal over vaccine → https://is.gd/lysfvK16:00
de-factoyeah we cant say much with that data its just not allowing a precise statement, if we see increase of incidence in Ohio soon this "other" variant(s) may be of interest/concern16:09
BrainstormUpdates for Bangladesh: +617 cases (now 1.6 million), +18 deaths (now 27573), +21246 tests (now 9.8 million) since a day ago16:10
de-factobtw they have (**) "Data for this date interval is preliminary"16:16
de-factoso maybe they will change ?16:16
sdfgsdfgthey already marked 30% of it as "other" variants16:24
sdfgsdfgI wonder how much that could change16:24
sdfgsdfghttps://www.deseret.com/coronavirus/2021/9/29/22700773/mu-covid-variant-new-cases-us-data-says16:26
sdfgsdfganother very recent article says no mo moo16:26
sdfgsdfgthis is all so confusing I think we're all gonna die16:27
de-factohttps://outbreak.info/location-reports?loc=USA_US-OH16:30
de-factoall those AY are subvariants of Delta16:31
BrainstormNew from r/WorldNews: worldnews: Fourth person charged in Ontario COVID-19 relief fund embezzlement scheme. → https://is.gd/IaNizd16:32
de-factohere is the Ohio Variants Tableau, i extracted it, it can be seen without proxy: https://tabsoft.co/3DbtPEC16:34
lastshellde-facto did you guys were able to enter the website ?16:43
BrainstormNew from r/Science: science: A new antiviral pill cuts COVID-19 hospitalization and death rates → https://is.gd/N12lvi16:43
lastshellyeah the other varian is slowly growing16:44
lastshellbut not sure what variant is it16:44
de-factoyeah the extracted tableau is not geoblocked, the rest of ohio dashboard requires an US IP address16:50
de-factolastshell, could it be that its just some artifact because of that (**) preliminary disclaimer?16:51
BrainstormNew from COVID tweets: Eric Topol (@EricTopol): Israel, where 3.4 million people have had a 3rd shot, required for its vaccine passport, is recovering from its 4th wave ft.com/content/a1b2fd… @MehulAtLarge @FT data for 60+ pic.twitter.com/aAYhb4V9xi → https://is.gd/Cm5An216:54
BrainstormUpdates for India: +23537 cases (now 33.8 million), +252 deaths (now 448888) since 23 hours ago17:00
BrainstormNew from COVID tweets: Charles C. Mann (@CharlesCMann): Intriguing look at why CDC/WHO fought the idea that COVID spread via air: "Resistance to the idea of airborne spread ... is not new. In fact, it has occurred repeatedly over the last century and greatly hampered understanding of how diseases transmit." papers.ssrn.com/sol3/papers.cf… → https://is.gd/JIQ8mB17:05
BrainstormNew from Reddit (test): Sunday 03 October 2021 Update: submitted by /u/HippolasCage to r/CoronavirusUK → https://is.gd/SxAAqS17:16
BrainstormNew from COVID tweets: Anthony J Leonardi, PhD, MS (@fitterhappierAJ): Yes, it's a straightforward SARSThese are published to become more severe and transmissible as the adapt following a species jumpAnd your (news) publications and essays all compare it to Influenza/ OC43Reflect it in your publications please :)twitter.com/zeynep/status/… [... want %more?] → https://is.gd/7fJo2T17:26
de-factolastshell, do you know it that variant subpage of the Ohio dashboard is new?17:31
BrainstormUpdates for Netherlands: +1632 cases (now 2.0 million), +2 deaths (now 18597) since 17 hours ago — Chile: +718 cases (now 1.7 million), +10 deaths (now 37494), +61648 tests (now 22.0 million) since a day ago — Canada: +1654 cases (now 1.6 million) since 22 hours ago17:37
BrainstormNew from Reddit (test): China_Flu: U.S. hits 700,000 COVID deaths just as cases begin to fall : NPR → https://is.gd/SrLAhu17:48
BrainstormNew from r/Science: science: Administering an influenza vaccine at the same time as a second dose of a covid-19 vaccine produced no safety concerns and preserves the immune response to both vaccines → https://is.gd/5YoQyX17:59
BrainstormUpdates for Italy: +2967 cases (now 4.7 million), +33 deaths (now 131031), +285960 tests (now 93.4 million) since a day ago — Greece: +1142 cases (now 661308), +31 deaths (now 14920), +150507 tests (now 20.7 million) since a day ago18:02
lastshellde-facto I don't know18:10
BrainstormNew from r/Science: science: New study shows universal masking of healthcare workers decreases occupational COVID-19 infection → https://is.gd/3T3HwQ18:20
BrainstormNew from COVID tweets: Deepti Gurdasani (@dgurdasani1): @zeynep @michaelmina_lab Infection, and damage of multiple organs. Neurotropism, neuro-degeneration even in people with mild illness. Long-term T cell dysregulation in people with long COVID. What other virus do you know that does that? → https://is.gd/HPLc5518:31
BrainstormNew from COVID tweets: Double Individual Speculator (@x2IndSpeculator): Come on, guys, @fitterhappierAJ and the rest, @zeynep is right, this is a straightforward textbook virus. Nothing to see here, you're just imagining that all communication about it is redacted.And all those #SARS2 studies published daily are just imaginary. Pure fantasies. [... want %more?] → https://is.gd/ZCtKm018:42
BrainstormNew from COVID tweets: Eric Topol (@EricTopol): Yet another reason why people with prior Covid should get a dose of vaccine "...reinfection after natural recovery from COVID-19 will become increasingly common as the pandemic progresses." @LancetMicrobe thelancet.com/journals/lanmi… pic.twitter.com/8pjqsQYRPr → https://is.gd/sIy0X319:04
BrainstormUpdates for United Kingdom: +29790 cases (now 7.9 million), +46 deaths (now 137338) since 23 hours ago19:29
nixonix.title https://twitter.com/feldman_gil/status/1444679272287854593/photo/1  full battery with a 3rd dose, och so vidare19:59
Brainstormnixonix, the URL could not be loaded19:59
nixonix.title https://twitter.com/feldman_gil/status/1444679272287854593/photo/119:59
Brainstormnixonix: From twitter.com: Gil Feldman (@feldman_gil): "Israel - where the data speaks for itself 👇" | 42l - nitter19:59
nixonix.title https://twitter.com/EricTopol/status/144443308641074790920:10
Brainstormnixonix: From twitter.com: Eric Topol (@EricTopol): "Linear RNA is big, as in mRNA vaccines Is circular RNA next ? https://www.bloomberg.com/news/articles/2021-10-01/can-rna-be-altered-scientists-could-bend-strands-into- [...]20:10
nixonixpossibly replacing CAR-T which costs 500k per single treatment20:12
nixonixcircular rna appears in nature, but they have patented it anyway. article doesnt use the word plasmid, but maybe the same thing20:15
LjLsuch patent nonsense20:16
nixonixin nature dna plasmids are separete from chromosomes, but also dna and rna plasmids are used in synthesis of dna or mrna, circular or linear20:16
nixonixcorporations are profit making machines. they dont have a soul. sometimes they do things that looks like philanthropic, but its when they think it could increase profits. not saying its bad or good, its just how it is20:20
nixonix(that original patent had applied by single person, though, but anyways)20:21
nixonixwas20:21
BrainstormNew from StatNews: STAT+: Pfizer loses a lawsuit alleging the U.S. illegally limits use of patient copay assistance programs: A federal judge ruled that programs Pfizer wanted to launch to provide copay assistance to Medicare patients would likely violate kickback laws, a controversial notion that has caused numerous drug… → https://is.gd/WOIo0P20:29
BrainstormUpdates for India: +21438 cases (now 33.8 million), +182 deaths (now 449028) since 17 hours ago — Germany: +6000 cases (now 4.3 million) since 23 hours ago20:31
nixonix.title https://www.ft.com/content/d88457da-6bbc-4f07-82a6-4738aa845492    https://archive.is/bplAG   BioNTech chief predicts need for updated Covid vaccines next year20:36
Brainstormnixonix: From www.ft.com: Subscribe to read | Financial Times20:36
Brainstormnixonix: From www.ft.com: Subscribe to read | Financial Times20:36
nixonix"This is a continuous evolution, and that evolution has just started.”20:37
LjLTwitter told me to look at this tweet https://twitter.com/michaelmina_lab/status/1444690897531179008 so i look and wonder, why exactly are some people convinced that rapid test positiveness correlates strongly with infectiousness? i guess it's a reasonable possibility, but has it actually been ascertained? are there studies about it, or it is just people repeating it as truth on twitter?20:42
LjLnixonix, just for the sake of argument, i'm not a convinced capitalist, but - like corporation "sometimes do things that look like philantropic, but it's when they think it could increase profits", evolution is arguably similar, as it has evolved altruism as a series of complex mechanism that ultimately benefit either the individual or the individual's genome (selfish gene theory)20:44
nixonixyeah, it likely does, because those lateral flow tests etc are not as sensitive, so they show positive when viral load is high enough (and sample taking was done properly). but if it was taken too early, viral load is rising, and it will be transmissible a bit later20:45
LjLnixonix, okay but who said "high enough" is the same for rapid tests as for infectiousness? have they been calibrated for that threshold?20:45
ublxwell that was the motivation in the design, so.. probably?20:46
nixonixi dont know. but roughly they can be used to show if the person is likely to be transmissible at that moment. the same could be done with pcr, with higher reliability (if there isnt delay for the result), checking the ct value, something like over 27 and not likely to infect people easily20:49
nixonixbut they can never be sure of the timing, if its rising or declining20:49
nixonixwell if its days after symptoms start, and confirmed previously it was the rona, then with high reliability20:51
nixonixhere rapid tests cost €6 or more. the importer got media time when they said, for better reliability use 3 tests20:51
LjLlol20:53
nixonixwe are just symbiotic collection of organisms, that communicate at distance with cytokines, or when in direct contact, with exchange of molecules or electrical signals. we have an illusion of being an individual person21:01
nixonixtheres kind of genetic altruism in cellular programs in it that they dont just try to replicate as fast as possible, unlike viruses21:01
nixonixevery once in a while somebody mentions, that perhaps not getting infected by some respiratory viruses regularly is a bad thing, because that would weaken the immune system21:04
nixoniximo its never a good idea for an adult to get infected by a virus, despite that after infection you have stronger immunity against a reinfection for awhile. couple of execptions:21:05
nixonixyou know you can infect by a weaker version, that still gives you immunity against the more potent version (vaccines mostly - but for kids chickenpox and couple other viruses, if vaccine isnt available)21:06
nixonixother types of viruses dont give good if any protection to some other viruses, and there may well be harmful interference instead of protection. yes, there is speculation of potective cross-immunity in some cases, but afaik, hard evidence is missing21:08
BrainstormUpdates for Dominican Rep.: +573 cases (now 360830), +4913 tests (now 2.1 million) since a day ago21:08
nixonixand afaik, there is no general immunity improving viral infection. on the contrary, your immune system doesnt like a new infection soon after recovering from previous. your immune cells might not have been recovered, some of them might still be in alert mode (that rona study where they sped up recovery of rona infected humanized mice with anti-cd821:11
nixonixantibodies)21:11
BrainstormNew from r/WorldNews: worldnews: Russia hits record number of daily COVID-19 deaths → https://is.gd/QxaY9x21:11
nixonixalso a viral infection depletes naive t-cell reservoir, and un-class-switched b-cells. in some cases like with rona possibly, that depleting effect can be huge21:12
nixonix.title https://twitter.com/fitterhappierAJ/status/1426736216360243201   because im just a rona nerd, maybe you believe an immunologist:21:13
Brainstormnixonix: From twitter.com: Anthony J Leonardi, PhD, MS (@fitterhappierAJ): "The only reason exposure to *some* pathogens may help in the future, is so the immune "memory" is able to deal with it faster when you are older and [...]21:13
LjLbut what if it's statistically inevitably that you'll get infected (maybe multiple times)? then we can probably talk about when it's best to get infected (by a virus in general, not just COVID)21:14
LjLi'm not sure "as late as possible" is always the optimal answer21:14
nixonixas a kid for a smallpox (if not vaccine available). for adults, you can come up with a hypothetical example, like i will likely get it as old anyway, and immunity would last for decades, but id like to see a real world example21:15
nixonixthe longer you postpone it, the better changes to avoid it, or vaccines and treatments to improve before it21:16
nixonix*chickenpox21:17
nixonixsome direct translations from finnish, shows that theres interference with translation errors i make: chickenpox - waterpox, smallpox - bigpox21:18
LjLwe call them varicella and vaiolo, i think varicella is originally a diminutive of vaiolo (variola in latin), but i don't immediately think of them as related things21:19
nixonixlots of english words come from french (almost all three or more syllable english words seem to come from latin, french etc). so french often write funny english, because the corresponding words have often slightly different meaning21:21
BrainstormNew from Reddit (test): CoronaVirus_ITALIA: Incredibile marea umana a Milano contro il Green Pass: solidarietà alla vice questore, offese a Mattarella e Draghi (Video) → https://is.gd/Jselmw21:22
LjLyes that's true of italians too, because even though the words come from french, they're also similar to italian ones21:22
LjL%wik false friend21:22
BrainstormLjL, from English Wikipedia: In linguistics, a false friend is either of a pair of words in different languages that look or sound similar, but differ significantly in meaning. An example is the English embarrassed and the Spanish embarazada (which means pregnant), the word parents and the Portuguese parentes and Italian parenti (both [... want %more?] → https://en.wikipedia.org/wiki/False_friend21:23
nixonixsome people think that they should try to get rona infection when they have had around 2 months from the last vax dose (protection still high, and imo 2-3 months would be better because more time for b-cell affinity maturation and recovering from the vax)21:32
nixonixi wouldnt risk it, unless i knew 3rd dose wont be available for a long time, and infection later is almost guaranteed (as it likely is... - but anyway, i still hope they will let us get the 3rd soon enough)21:33
BrainstormUpdates for France: +3799 cases (now 7.1 million) since 23 hours ago — Greenland: +7 cases (now 591), +309 tests (now 76800) since a day ago21:33
LjLi guess if you believe that you WILL inevitably get it eventually, that may make sense. but we still know so little about it, treatments are still in their infancy, we don't know how older variants will interact with future ones...21:33
LjLfor now, i prefer to keep thinking i won't necessarily get it21:34
LjLit may be wishful thinking, but hey i don't afford myself much wishful thinking, so let me have that21:34
nixonixyeah, treatment and knowledge improving point. also that knowledge would affect to govts decisions on 3rd and later doses21:35
nixonixalso along the epidemic i have thought (even when i wasnt aware of all the prospects of permanent organ damages that common), i thought very low case goal is the best, because besides vaccines, treatments and knowledge keep improving, so every delay for every infection is for good (dont mass infect the kids, you monsters)21:37
nixonixnot zero covid (we are not an island, so doesnt make sense, imo), but close to zero covid, for us. like in july of 2020. tight borders is the key, then trace the cases down, using regional measures21:40
nixonixchecking logs, the talk about second wave started around apr 10 202021:42
nixonix[Friday, April 24, 2020] [12:38:33 AM EEST] <nixonix>   a few weeks after they remove enough restrictions21:43
Arsaneritdoes vaccinating make tracing harder?  Vaccinating brings symptomatic infections down more than it does asymptomatic infections, which means a larger proportion of infected people don't know they're infected?21:44
ArsaneritEbola is easier to trace...21:44
nixonix[Monday, June 1, 2020] [6:00:55 PM EEST] <LjL>  "Zangrillo said some experts were too alarmist about the prospect of a second wave of infections and politicians needed to take into account the new reality. "21:46
nixonixi remember writing about worst case scenario with vaccines, but cant find from logs - maybe it was on some other channel. something like "typhoid marys walking around". luckily vaccines also reduce spreading21:52
BrainstormNew from Reddit (test): CoronaVirus_2019_nCoV: Millions have lost a loved one to COVID-19. Grief’s mental and physical burden is especially heavy on kids: An estimated 40,000 children in the U.S. have lost a parent... a 17% to 20% increase over the annual average... At least 2 million children lost grandparents → https://is.gd/4pEYVC21:54
nixonixjune 8 2020: <palasso>      Greece is having a second wave of the pandemic21:56
nixonixbelgium had a summer wave, that suppressed then, in july i think. it started in spain before belgium i think21:57
Arsaneritsummer 2020 or summer 2021?21:57
nixonixand in balkan, where there was not much 1st wave, when they had very tight lockdowns and epidemic got suppressed early (that was 2020, what palasso wrote)21:57
nixonixso they didnt take it seriously during the summer i guess, in balkan. and it started to spead to other europe in july and august from spain and balkan mostly, i think21:58
nixonix202021:58
LjLnixonix, Zangrillo is an idiot, for the record22:00
nixonixthis was early june 2020, with google translate error (coronary=covid): title: "I don't really think a big wave can come anymore" - Professor of Immunology estimates that vigilance prevents the second wave of coronary infections in Finland22:01
nixonixisrael had it early, in june 2020. i think in schools especially22:02
nixonixjuly 9 2020: <de-facto>   dang havent realized second waves are in so many countries already22:04
BrainstormUpdates for Kuwait: +72 cases (now 411803), +1 deaths (now 2452), +28538 tests (now 4.3 million) since 23 hours ago22:04
BrainstormNew from Reddit (test): nCoV: Lessons from how bats resist covid could inform new treatments in humans Using bats’ responses to SARS-CoV-2 may provide key insights into therapies for COVID-19 → https://is.gd/UgaoxX22:04
nixonixjuly 17 2020: <LeoBodnar>   I never thought the second wave is going to be a thing, but with sharp relaxation of measures it seems inevitable now22:06
nixonixleo bought an immunology book recommended by yuri22:07
nixonixsomebody should write huge, 10-part book about this pandemic. maybe 2022:12
nixonixwill buy, if its good22:12
Arsaneritthey're probably working on it already22:13
Arsanerithave you searched if it might already exist?22:13
nixonix"lets pick one expert first, then do as he recommends. he may be wrong and even bastard, but he is OUR bastard"22:13
nixonixwith quick look, there are some books out. i thought something like describing the different events and social aspects during the whole epidemic, in many countries. and to do it comprehensively would require many books, and new parts coming out every few months, with newest events and some retrospective look on previous events22:19
nixonixgood rona books will be great christmas presents, that you can then borrow... pro tip: give a different book to different people, so you can read many. dont forget some immunology text books!22:29
nixonix.title https://twitter.com/alisonannyoung/status/144469891056022733322:37
Brainstormnixonix, the URL could not be loaded22:37
nixonix.title https://twitter.com/alisonannyoung/status/144469891056022733322:37
Brainstormnixonix: From twitter.com: Alison Young (@alisonannyoung): "Transparency is a cornerstone of public confidence. Yet both the U.S. and British governments are keeping secret key details of a 2/1/2020 meeting where top [...]22:37
nixonix"The lines left intact include a demand for the discussions, involving 13 participants around the world, to be conducted in ‘total confidence’, and an intriguing email line suggesting ‘we need to talk about the backbone too, not just the insert’. That was possibly sent by Dutch virologist Marion Koopmans, a member of the World Health22:38
nixonixOrganisation team that produced a widely criticised report into Covid’s origins22:38
nixonixthere was discussion about herd immunity plan between vallance, dutch chief epidemiologist, tegnell and finnish mika salminen. not sure if they were all among those 13, though22:40
nixonix.title https://twitter.com/ChristosArgyrop/status/144432320215131341322:42
Brainstormnixonix: From twitter.com: ChristosArgyropoulos MD, PhD (Green Chili Check) (@ChristosArgyrop): "I will elevate my level of concern about the mutagenic potential of molnupiravir from "aspartame-level" (none) -> moderate. Dose [...]22:42
BrainstormNew from COVID tweets: Prof Francois Balloux (@BallouxFrancois): I'm personally concerned about the political aftermath of the pandemic. We're facing a difficult situation sociologically, culturally, economically and geopolitically, and I can see a genuine risk for the emergence of more authoritarian societies, which some seem to welcome.2/ → https://is.gd/a0busK22:47
BrainstormNew from COVID tweets: Kimberly Prather, Ph.D. (@kprather88): We have added one more key layer of protection @UCSanDiego. As part of our Return to Learn program, we upgraded mask recommendations to KN95 which we supply to anyone who needs an upgrade while on campus. → https://is.gd/SjRTA323:19
nixonix.title https://twitter.com/kchr_grr_krch__/status/144472648521497396523:19
Brainstormnixonix: From twitter.com: 🔴 alleswirdgut...alsovielleicht | HE (@kchr_grr_krch__): "Dear @fitterhappierAJ, in Germany there is a ongoing discussion if - after reaching a certain threshold in vaccinated / infected people and [...]23:19
nixonix(yes, its a lottery, especially with permanent organ damages)23:22
BrainstormUpdates for Burkina Faso: +45 cases (now 14335), +750 tests (now 218512) since a day ago — Chad: +2 cases (now 5044), +85 tests (now 146983) since 2 days ago23:31

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