libera/##covid-19/ Friday, 2020-06-19

kreyren_%cases USA00:01
Brainstormkreyren_: In US, there have been 2.3 million confirmed cases (0.7% of the population) and 120531 deaths (5.3% of cases) as of 13 minutes ago. 26.2 million tests were performed (8.6% positive). Fatality can be broadly expected to lie between 1.8% (assuming deaths/cases with ⅔ undetected), and less than 11.5% (considering only deaths and recoveries). See https://offloop.net/covid19/?default=US for time series data.00:01
Arsanerit%cases world00:07
BrainstormArsanerit: In World, there have been 8.6 million confirmed cases (0.1% of the population) and 455393 deaths (5.3% of cases) as of 14 minutes ago. 132.2 million tests were performed (6.5% positive). Fatality can be broadly expected to lie between 1.8% (assuming deaths/cases with ⅔ undetected), and less than 9.6% (considering only deaths and recoveries). See https://offloop.net/covid19/?default=World for time series data.00:07
Arsanerit%cases Navajo Nation00:08
BrainstormArsanerit: Sorry, Navajo Nation not found. Either there aren't cases, or it's under a different name.00:08
CoronaBot04/r/coronavirus: Fauci says "anti-science bias" is a problem in the US (10818 votes) | https://www.cnn.com/world/live-news/coronavirus-pandemic-06-18-20-intl/h_fcadb4e9f7cc9f3461c4a20c8074596a | https://redd.it/hbhjig00:20
BrainstormUpdates for Oklahoma, US: +450 cases (now 9354), +2 deaths (now 366) since 23 hours ago — Hawaii, US: +18 cases (now 762) since 23 hours ago — Peru: +3480 cases (now 244388), +204 deaths (now 7461) since 23 hours ago — Colorado, US: +228 cases (now 29901), +7 deaths (now 1638) since 23 hours ago00:20
ap4lmtreehi00:38
ap4lmtreei dont want to see my doctor until i get a vaccien00:38
ap4lmtreebut i need a refill on some of my blood pressure medication in october00:39
BrainstormUpdates for Nigeria: +745 cases (now 18480), +6 deaths (now 475) since a day ago — Brazil: +5217 cases (now 983359), +121 deaths (now 47869) since an hour ago — Gabon: +111 cases (now 4340), +2 deaths (now 32) since 22 hours ago — US: +1744 cases (now 2.3 million), +25 deaths (now 120567) since 48 minutes ago01:06
bin_bashap4lmtree: call them and tell them you want to do the appointment over the phone or over video01:09
dTalOctober's a long time away01:20
BrainstormUpdates for Colombia: +3171 cases (now 60217), +63 deaths (now 1950) since 6 hours ago — California, US: +1044 cases (now 166368), +36 deaths (now 5356) since an hour ago — US: +1205 cases (now 2.3 million), +37 deaths (now 120604) since 17 minutes ago — World: +4386 cases (now 8.6 million), +100 deaths (now 455661) since 17 minutes ago01:21
BrainstormUpdates for Idaho, US: +111 cases (now 3743), +1 deaths (now 89) since a day ago — Nebraska, US: +189 cases (now 17415), +6 deaths (now 240) since 7 hours ago — US: +591 cases (now 2.3 million), +19 deaths (now 120623) since 17 minutes ago — California, US: +158 cases (now 166526), +1 deaths (now 5357) since 17 minutes ago01:36
DianaSunnyhi01:44
LjL%title https://translate.google.com/translate?sl=it&tl=en&u=https%3A%2F%2Fwww.punto-informatico.it%2Fuk-contact-tracing-decentralizzato%2F01:46
BrainstormLjL: From translate.google.com: Google Translate01:46
LjLthat's a useful title as usual, thanks01:47
LjLDianaSunny, hi01:47
nixonix%date egypt01:47
nixonix%data egypt01:47
Brainstormnixonix: In Egypt, there have been 50437 confirmed cases (0.1% of the population) and 1938 deaths (3.8% of cases) as of 3 hours ago. 141002 tests were performed (35.8% positive). Fatality can be broadly expected to lie between 1.3% (assuming deaths/cases with ⅔ undetected), and less than 12.5% (considering only deaths and recoveries). See https://offloop.net/covid19/?default=Egypt for time series data.01:47
nixonixthey are arresting doctors who criticize govt response there, according to that cnn link above. i wonder whats going on there01:48
nixonixhttps://www.theguardian.com/world/2020/jun/17/argentina-president-enters-voluntary-isolation-amid-coronavirus-surge01:51
ryoumanew york, arizona, italy, egypt: http://www.offloop.net/covid19/?default=Egypt;Italy;Arizona;New%20York&byPopulation=yes&cumulative=no&smooth=yes&miscType=Rate01:51
nixonix^ ^ Argentina's president enters voluntary isolation amid coronavirus surge01:51
LjLnixonix, well in Russia they just fall from windows01:51
ryouma:/01:52
ryoumawhat is up with that01:52
LjLa longstanding tradition01:52
DianaSunnyhe hides?01:52
ryoumahow do they even get defestration squads into a room without being noticed?01:52
ryouman*01:52
ryoumadefenestration*01:52
ryoumaeven polonium seems more discreet01:53
LjLwell if i knew i'd be either employed by them, or in the curb01:53
nixonixtil a new word01:53
DianaSunnyljl sorry i don't know how to work this, it's my first day01:53
LjLDianaSunny, i didn't say anything01:54
LjLwho hides though?01:54
nixonixof course, fönster/fenster01:54
DianaSunnyi saw a bubble with my name on it ?01:54
ryoumalatin fenestra maybe01:54
nixonixmore likely yeah01:54
DianaSunnyphysics experts must be in here.01:55
LjLnixonix, fenestra in latin, i think the germanic words are loanwords from that01:55
DianaSunny=# 01:56
LjLDianaSunny, i just said hi01:56
LjLyou said hi, i said hi. that's not particularly specific to this!01:57
DianaSunnyhi01:57
DianaSunnyi think they kicked me out of physics?01:57
DianaSunnymy words won't go on there, i don't know why01:58
LjLhave no idea, i'm not in there01:58
DianaSunnyok01:58
DianaSunnyi'm happy there are mods.01:58
LjLhere's something we've known for a while now https://www.scientificamerican.com/article/coronavirus-antibody-tests-have-a-mathematical-pitfall/ but it comes with graphs that maybe help explaining it to others02:02
nixonixtemporary muting perhaps there02:02
DianaSunnydo u think there'll be a 2nd wave?02:02
LjLthere has already been in some places02:02
DianaSunnyi think they blew it out of proportion to shut down the cities.02:03
LjLchances are there will be in other places02:03
LjL"they"?02:03
DianaSunnythe gov02:03
LjL%cases lombardy02:03
BrainstormLjL: In Lombardy, Italy, there have been 92302 confirmed cases (0.9% of the population) and 16480 deaths (17.9% of cases) as of 18 hours ago. 196302 tests were performed (47.0% positive). See https://offloop.net/covid19/?default=Lombardy for time series data.02:03
DianaSunnyaround here they say everything is covid02:03
LjLthis is where i live. 16480 deaths means we had as many deaths as a big earthquake, every single day, for weeks02:03
DianaSunnyheart attack,, stroke etc02:03
LjLi suspect my gov isn't your gov02:03
DianaSunnyn02:03
LjLno, they don't02:03
DianaSunnyno02:03
DianaSunnyyes they did02:04
LjLif anything the other way around02:04
DianaSunnyhere they did.02:04
DianaSunnythat's why the # of the other diseases all went down02:04
DianaSunnydrs even said it.02:04
LjLhave you looked at excess mortality data?02:04
DianaSunnyit's less than 1% mortality rate.02:04
DianaSunnynice talking to you, take care02:05
LjLi can't imagine why they've muted her in ##physics02:06
nixonixthat made me curious, but then sudden quit02:06
LjLnixonix, "Between March 15th (the week New York passed 50 official fatalities) and May 23rd, the city recorded 21,300 official covid-19 deaths, according to the revised estimate. This figure is 84% as high as the 25,300 excess deaths from all causes registered in the same period."02:06
LjLhttps://www.economist.com/graphic-detail/2020/04/16/tracking-covid-19-excess-deaths-across-countries02:06
LjLso however you shuffle the death cases, NYC suffered many more deaths than normal02:06
LjLcauses*02:07
LjLat least that was my guess as to the location02:07
LjL%wa cpe-24-193-166-40.nyc.res.rr.com02:07
BrainstormLjL, failed to get any hits! 02:08
LjLstill a better guess than Brainstorm's02:08
ryoumaLjL: what is up with this http://www.offloop.net/covid19/?default=Lombardy;Arizona;New%20York&byPopulation=yes&cumulative=no&smooth=yes&miscType=Rate02:12
LjLryouma, my guess is it doesn't have the population of lombardy available02:13
LjLi'll check02:14
LjLactually it does have it02:14
LjLbut earlier tinwhiskers was discussing something about population having issues, not sure if this is related02:15
tinwhiskers Most countries don't have regional populations, but Italy is an exception.02:16
LjLtinwhiskers, but it doesn't seem to work, with "by population" selected, Lombardy's graph is flat02:18
BrainstormUpdates for Argentina: +1958 cases (now 37510), +19 deaths (now 948) since 7 hours ago — Panama: +754 cases (now 23351), +5 deaths (now 475) since a day ago — North Carolina, US: +502 cases (now 48690), +54 deaths (now 1235) since 7 hours ago — Texas, US: +461 cases (now 102661), +2 deaths (now 2142) since 47 minutes ago02:21
LjLtinwhiskers, also, two other inquiries: how do you compute R_eff (it seems to end up a fair bit higher than the way our authorities estimate it, since it's hovering below *and above* 1.0 in Italy now, while we're reassured it's staying well below), and secondly could you expose it in the data (current, or better yesterday's since current sometimes has quirks, would be enough, i don't need historical)?02:24
Kyros54 deaths in 7 hours?02:24
LjLKyros, they have been added to the tally in the past 7 hours, i have no way to determine that they *occurred* in the past 7 hours (they probably didn't)02:25
Kyrostheir daily number of cases is accelerating quite quickly02:26
LjLyes it's one of the states that's doing badly right now02:27
LjLtogether with South Carolina, Arizona, and others02:27
Kyrosi live on the other side of the mountains from them in tn02:27
LjLCalifornia is steadily increasing but not quite exponential02:27
LjLuhm, India is doing *very* badly with deaths02:30
LjLthe new cases are growing more than linearly but the deaths just spiked horribly in the past couple of days02:30
Kyroswow yeah02:30
Kyrosi wonder if they changed the way they were reporting them02:31
LjLor in some state, healthcare collapsed completely02:31
LjLit's also possible some state has failed to report them for a while02:31
LjLand is reporting them all at a time now02:32
LjLhttp://www.offloop.net/covid19/?default=Delhi&smooth=yes me no like02:32
nixonixwhats the latest on temp and humidity correlating infections? that study they used for metropolitan areas could have used those too. in usa would be perfect, because filtering other factors is easier than between different countries (where also data can be incorrect in different ways)02:40
LjLnixonix, i was wondering about that, the only such study i saw was very coarse, taking a limited number of countries and not looking at regional units. there are countries now, especially in south america, that are being hit badly but where the weather conditions are likely to vary dramatically depending on the region (Brazil, Chile, Argentina)02:41
ryoumawell arizona would be a countertrend for heat02:42
LjLin some parts of them it coule be fully winter while others may be mildly affected by seasons02:42
LjLi think now we should have data for enough countries to re-run some statistics on this02:42
BrainstormUpdates for Mexico: +5662 cases (now 165455), +667 deaths (now 19747) since a day ago — Guatemala: +617 cases (now 11868), +17 deaths (now 449) since a day ago — Jamaica: +12 cases (now 638) since 23 hours ago — World: +6625 cases (now 8.6 million), +688 deaths (now 456453) since an hour ago03:21
nixonixTegnell said Tuesday that "a fair amount of the population is immune" to the coronavirus now, adding that a study on the level of immunity now seen in Sweden is due to be published in the next few days. He told CNBC back in April that the capital Stockholm was starting to "see the effects of herd immunity." 03:59
redlanternnixonix: who is tegnell04:00
redlanternI heard antibodies are protective for 2 months04:00
nixonixswedens head epidemiologist anders tegnell:04:00
nixonixWe are better prepared in many ways, health care is better prepared. We'd be up and running a bit more with contact tracing and we also have the immunity in the population which will make things a lot easier in a lot of ways," he told CNBC Tuesday.04:00
nixonixhttps://www.cnbc.com/2020/06/17/swedens-plan-if-theres-a-second-wave-of-coronavirus.html04:00
ryoumathen consider the long term effects04:00
redlanternnixonix: aren't they still on the 1st wave?04:01
redlanternisn't everyone?04:01
redlanternexcept maybe new zealand04:02
nixonixif you look at offloop graph, it seems the second wave is starting in sweden now. so their herd immunity will be useful04:03
LjLno, there are places with a definite second peak04:03
ryoumany is not on the first wave04:03
ryoumaaz is04:03
ryoumasweden and az look similar actually04:06
nixonixbut you dont have herd immunity in az04:07
ryoumathe ny rate of increase chart is interesting04:07
ryoumaidk what the second wave will look like politically in theus04:07
ryoumai'm not sure americans know how to not be cantankerous04:07
nixonixthey are doing antibody survey in the highest prevalence area in stockholm, that is rinkeby. maybe tegnells herd immunity study will be based on that04:10
nixonixi wonder how it goes, when later they find out, it was just pipe dreams. will tegnell say something like, it was supposed to be 70%, but we had a decimal point error in calculations04:12
PlanckWalkSweden doesn't have anywhere near herd immunity04:17
nixonixa few days, and they will present the proof04:18
PlanckWalkIt wouldn't surprise me if some particular localities had much higher infections than others04:35
PlanckWalk(and please, let this not be yet another antibody study with shit sampling methods)04:36
BrainstormUpdates for Myanmar: +23 cases (now 286) since 21 hours ago — Bolivia: +814 cases (now 21499), +18 deaths (now 697) since a day ago — Honduras: +440 cases (now 10739), +7 deaths (now 343) since a day ago — World: +1296 cases (now 8.6 million), +22 deaths (now 456475) since an hour ago04:37
PlanckWalk"Facebook recruits" or "supermarket volunteers" or "health system employees" with conclusions generalized to the whole population.04:37
tinwhiskersLjL: the R(eff) is being calculated using a very crude approximation that I got from DocScrutinizer. It's basically uses a smoothing algorithm then gets the ratio of cases today over cases from 4 days ago. I'm surprised it works as well as it does but am looking for a better method. If you have/see/find any methods that don't rely on numbers we have no idea about please let me know!04:45
tinwhiskersas for exposing the data, I'm not quite sure what you mean. You can export the values to csv using the icon at the top right of the graph.04:46
tinwhiskersthe only reliable methods for R(eff) I've seen require detailed case-specific data which we don't have. If nothing else you can use this R(eff) value as a comparative index between countries but you shouldn't consider it to be an accurate value. A value over 1 does mean *confirmed* cases are increasing so it has that going for it.04:49
tinwhiskers(or confirmed deaths if you choose that option)04:50
LjLtinwhiskers, exposing i mean for he bot, in the data csv05:00
LjLexposing the R_eff05:00
tinwhiskersah. ok. 05:00
LjLtinwhiskers, i assume our authorities also are using "naive" R_eff estimation, naive as in based on the official data05:01
tinwhiskersthey tend to have case tracking data that allows them to put a much more accurate figure on it05:02
CoronaBot04/r/coronavirus: Arnold Schwarzenegger backs California face-mask order: ‘Anyone making it a political issue is an absolute moron’ (10952 votes) | https://www.marketwatch.com/story/arnold-schwarzenegger-says-to-wear-a-mask-anyone-making-it-a-political-issue-is-an-absolute-moron-2020-06-18 | https://redd.it/hbraa505:10
Trippy72394I hear from friends in India that the lockdown is only in name, and that people are all going to work and are out and about. Does anyone know for sure?05:44
ryoumare the ca order, what is available now?  surgical masks available now?  n95 not yet?05:48
ryoumaor are face masks a lower grade of surgical masks?  or are they any face covering?05:48
redlanternryouma: can wear bandana, won't be enforced much06:03
redlanternmy area started this months ago, just goes to show you how totally stupid US is06:04
ryoumano i mean what are the most useful masks available. like actually certified surgical maskis?06:18
ryoumawell it's nice to see public figures making sense every ocne in a while06:21
ryoumai was floored by cuomo making sense back when, and now floored by the clickbait above.  is the current gov same party?06:21
CoronaBot04/r/covid19: Challenges of “Return to Work” in an Ongoing Pandemic (80 votes) | https://www.nejm.org/doi/pdf/10.1056/NEJMsr2019953?articleTools=true | https://redd.it/hbi4n806:47
BrainstormUpdates for Kyrgyzstan: +132 cases (now 2789), +1 deaths (now 32) since a day ago — Pakistan: +4944 cases (now 165062), +136 deaths (now 3229) since a day ago — Kazakhstan: +474 cases (now 16351), +5 deaths (now 105) since 12 hours ago — Haiti: +228 cases (now 4916), +2 deaths (now 84) since a day ago06:53
BrainstormUpdates for Ukraine: +770 cases (now 34833), +10 deaths (now 976) since 12 hours ago — Ontario, Canada: +192 cases (now 34574), +6 deaths (now 2613) since a day ago — Quebec, Canada: +120 cases (now 54383), +42 deaths (now 5340) since a day ago — Alberta, Canada: +49 cases (now 7579), +1 deaths (now 152) since a day ago07:08
BrainstormUpdates for Norrbotten, Sweden: +66 cases (now 853), +1 deaths (now 60) since a day ago — Atlantico, Colombia: +804 cases (now 12228), +33 deaths (now 500) since a day ago — Goias, Brazil: +1068 cases (now 13304), +12 deaths (now 264) since a day ago — Parana, Brazil: +834 cases (now 11919), +20 deaths (now 406) since a day ago07:53
BrainstormUpdates for Cameroon: +774 cases (now 10638), +6 deaths (now 282) since 3 days ago — World: +1266 cases (now 8.6 million), +7 deaths (now 456649) since 31 minutes ago — India: +394 cases (now 381485), +1 deaths (now 12605) since 10 hours ago — Iowa, US: +98 cases (now 24959) since 6 hours ago08:08
BrainstormUpdates for Slovakia: +14 cases (now 1576) since 15 hours ago — Russia: +7972 cases (now 569063), +181 deaths (now 7841) since 15 hours ago — Armenia: +459 cases (now 19157), +10 deaths (now 319) since 15 hours ago — World: +9111 cases (now 8.6 million), +201 deaths (now 456850) since 2 hours ago10:23
DocScrutinizer05tinwhiskers: http://reisenweber.net/et_al/covid/covid19_statistics.htm still works :-)10:45
DocScrutinizer05plus a new "faster" d/d-1 calculation10:46
tinwhiskersHi DocScrutinizer05. I don't follow10:46
DocScrutinizer05actually (d/d-1)^410:46
DocScrutinizer05we had d(d-410:47
DocScrutinizer05>> [1d] is diff from yesterday to today ^4<<10:48
tinwhiskersok. But I'm not sure what you're getting at10:51
DocScrutinizer05well, https://i.imgur.com/D5kBzMD.png the light green curve is "faster response" to changes10:52
tinwhiskerswell, I certainly don't disagree, but I'10:54
tinwhiskersm wondering what the relevance of the point you're making is, or what the topic is...10:54
tinwhiskerscould you start at the beginning for me?10:54
tinwhiskersI'm assuming it's something to do with me mentioning earlier the R_eff method I'm using that I got from you, but I'm just not understanding where you're going with this sorry10:56
DocScrutinizer05reply rto a highlight I noticed ;-) 11:00
DocScrutinizer05>>[19 Jun 2020 04:45:51] <tinwhiskers> LjL: the R(eff) is being calculated using a very crude approximation that I got from DocScrutinizer. It's basically uses a smoothing algorithm then gets the ratio of cases today over cases from 4 days ago. I'm surprised it works as well as it does but am looking for a better method. If you have/see/find any methods that don't rely on numbers we have no idea about please let me know!<<11:00
DocScrutinizer05I now adoped/developed a new R_eff algo11:01
tinwhiskersyeah, ok. I guessed that part correctly then. :-)11:01
tinwhiskersso, what are you saying about it? Are you suggesting I should change the method?11:01
DocScrutinizer05depends on the sensitivity to noise you want11:02
tinwhiskersok. thanks for the heads-up. I'll check out that site and see if anything there looks better.11:03
DocScrutinizer05(d[o]/d[-4])^1 is what RKI does as well, (d[0](d[-1])^4 is the faster equivalent11:04
tinwhiskersah. ok11:04
tinwhiskersthanks. I'll play with that tomorrow.11:05
tinwhiskersHow you been? Haven't seen you around for a while.11:05
DocScrutinizer05the pub lockdown caused complete true social isolation and I'm breeding a covid-alike cough since mid of November already, so...11:08
tinwhiskers:-(11:08
tinwhiskerswhy is there a ^1 in there?11:09
DocScrutinizer05just to explain the systematic. 4 is the serial length as of RKI, you could also do a (d[0]/d[-2])^2 or (d[0](d[-8])^0.511:11
tinwhiskersoh, ok11:12
tinwhiskersDo you happen to have a reference to the RKI saying the generation time is 4 days? That seems low to me. I tried playing around with the sensitivity of that and it made very little difference, but it still seems worth getting right.11:15
tinwhiskersI would have expected the generation time to be something like 6-8 days (the average time until people start shedding virions)11:16
PlanckWalkhttps://wwwnc.cdc.gov/eid/article/26/6/20-0357_article11:18
PlanckWalkThere was also a South Korean one reporting ~4 days11:18
tinwhiskersoh. thanks!11:18
DocScrutinizer05the reference... lemme see11:20
PlanckWalkHowever, mean serial intervals can be shortened by public health interventions11:20
PlanckWalk(By preventing transmissions later in the course of illness)11:21
DocScrutinizer05the generic formula I came up (verified by petschge[studied epidemiology]) anyway is (d[0]/d[4*N])^(1/N)11:23
tinwhiskerscool. What's N?11:23
DocScrutinizer05well -4 but you know what I mean11:23
BrainstormUpdates for Morocco: +206 cases (now 9280) since 13 hours ago — Bangladesh: +3243 cases (now 105535), +45 deaths (now 1388) since 16 hours ago — Philippines: +660 cases (now 28459), +14 deaths (now 1130) since 16 hours ago — Indonesia: +1041 cases (now 43803), +34 deaths (now 2373) since 16 hours ago11:24
DocScrutinizer05N is an arbitrary factor to adjust the actual observed timespan and thus the applied "smoothing"11:24
DocScrutinizer05RKI works with N=111:24
DocScrutinizer05I added a curve N=0.2511:25
tinwhiskersCool. Those are good things for me to look at tomorrow. And it's good to get some info about the basis for the equation, which reassures me a great deal.11:28
tinwhiskersThat makes me fairly happy to keep using it I think. If you happen to find a ref to RKI using it that I could link to that would be even better11:29
tinwhiskersbut it's bed time for me now.11:29
tinwhiskersthanks very much DocScrutinizer05 and PlanckWalk11:30
DocScrutinizer05tinwhiskers: somewhere nearby https://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Situationsberichte/2020-06-17-en.html - I'll try to find the spot where I once found it11:37
DocScrutinizer05maybe https://www.rki.de/SharedDocs/FAQ/NCOV2019/FAQ_Liste_Epidemiologie.html#FAQId13985854    or actually https://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Situationsberichte/2020-05-05-de.pdf?__blob=publicationFile  >> Die im Rahmen des Nowcastings geschätzte Anzahl der COVID-19-Neuerkrankungen wird als gleitendes 4-Tage-Mittel dargestellt, um Zufallseffekte einzelner Tage auszugleichen (Abbildung 8). Damit ergibt sich 11:42
DocScrutinizer05die Berechnung des Punktschätzers von R für einen bestimmten Tag als einfacher Quotient der Anzahl von Neuerkrankungen für diesen Tag geteilt durch die Anzahl von Neuerkrankungen 4 Tage davor<<11:42
DocScrutinizer05the last part says verbatim >>R_0 = d[0]/d[-4]<<11:43
tinwhiskersOh, cool. 11:46
DocScrutinizer05there's always an english report as well, I hope it has same info11:48
DocScrutinizer05yep  https://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Situationsberichte/2020-06-17-en.html  >> The sensitive R-value reported can be estimated by using a 4-day moving average of the number of new cases estimated by nowcasting. This 4-day value reflects the infection situation about one to two weeks ago. This value reacts sensitively to short-term changes in case numbers, such as those caused by individual outbreaks. This 11:51
DocScrutinizer05can lead to relatively large fluctuations, especially if the total number of new cases is small. The current estimate of the 4-day-R-value is 0.86 (95%-prediction interval: 0.73 – 1.02) and is based on electronically notified cases as of 17/06/2020, 12:00 AM.<<11:51
DocScrutinizer05RKI due to nowcasting gets significantly different numbers than I do, for *today*, while for older values they converge with mine11:53
tinwhiskersthanks DocScrutinizer05. I'll check that out tomorrow. Appreciate the info.11:54
tinwhiskersTranslated I get, "The number of COVID-19 new cases estimated as part of the nowcasting is shown as a 4-day moving average to compensate for the random effects of individual days (Figure 8), which means that the calculation of the point estimate of R for a specific day is a simple quotient of the number of new cases for this day divided by the number of new cases 4 days before. As of 06.05.20200: 00 o'clock, the number of reproductions 11:56
tinwhiskersis estimated at R = 0.71 (95% prediction interval: 0.59-0.82)." which is very clear (and not repeated in the English version).11:56
CoronaBot04/r/covid19: Remdesivir but not famotidine inhibits SARS-CoV-2 replication in human pluripotent stem cell-derived intestinal organoids (80 votes) | https://www.biorxiv.org/content/10.1101/2020.06.10.144816v1?rss=1 | https://redd.it/hbr3uu12:01
tinwhiskersah, here's the english version that spells it out: https://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Situationsberichte/2020-05-05-en.pdf?__blob=publicationFile12:01
DocScrutinizer05yeah in fact RKI does nowcasting -> 4day-average -> d[0]/d[-4]; I do 7day-average -> (d[0]/d[-4*N])^(1/N)12:01
tinwhiskersyeah, I noticed that12:01
DocScrutinizer05no nowcasting12:01
tinwhiskersI'm currently following your method (7 day)12:01
DocScrutinizer05it's an empirical method that yields good results12:02
tinwhiskers== 7 day moving average then d[0]/d[-4]12:03
DocScrutinizer05a little "slow" but then the nowcasting seems rather arbitrary, that's why I deliberately refuse to use it12:03
DocScrutinizer05actually it was the reason why I created http://reisenweber.net/et_al/covid/covid19_statistics.htm12:04
tinwhiskersok. bed. thanks12:04
DocScrutinizer05o/ yw12:04
CoronaBot04/r/covid19: Identifying airborne transmission as the dominant route for the spread of COVID-19 (81 votes) | https://ncrc.jhsph.edu/research/identifying-airborne-transmission-as-the-dominant-route-for-the-spread-of-covid-19/ | https://redd.it/hbje7812:37
BrainstormUpdates for Qatar: +1021 cases (now 85462), +7 deaths (now 93) since 18 hours ago — Oman: +852 cases (now 27670), +6 deaths (now 125) since 18 hours ago — United Arab Emirates: +393 cases (now 44145), +2 deaths (now 300) since 18 hours ago — Romania: +320 cases (now 23400), +11 deaths (now 1484) since 18 hours ago12:39
CoronaBot04/r/covid19: Prevalence of SARS-CoV-2 specific neutralising antibodies in blood donors from the Lodi Red Zone in Lombardy, Italy, as at 06 April 2020 (81 votes) | https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.24.2001031?#abstract_content | https://redd.it/hbkiqg12:43
CoronaBot04/r/covid19: 39/2020 Study ISS on Wastewater, in Milan and Turin SARS-CoV-2 already present in December (84 votes) | https://www.iss.it/en/primo-piano/-/asset_publisher/o4oGR9qmvUz9/content/id/5422725 | https://redd.it/hbxwzh13:49
BrainstormUpdates for Ethiopia: +116 cases (now 4070), +7 deaths (now 72) since 20 hours ago — Kuwait: +604 cases (now 38678), +5 deaths (now 313) since 20 hours ago — Iran: +2615 cases (now 200262), +120 deaths (now 9392) since 20 hours ago — Belarus: +676 cases (now 57333), +6 deaths (now 337) since 20 hours ago14:40
ubLIXmeta-9 /buffer *1014:55
blkshpSo I guess now the UK has lowered from '4' to '3' they will be reducing the 2metre rule. I wonder how much money has been spent on signs and painting "keep 2 metres" signage that's going to have to come down. I know this is not the most important thing but its just gone through my brain16:11
pwr22<blkshp "So I guess now the UK has lowere"> It doesn't mean we didn't need those signs before so it's a sunk cost thing16:12
blkshpmost of them went up last week16:12
pwr22Infact, even if we didn't need the signs it'd still be a sunk cost 😁 16:12
blkshpI don't know what a "sunk cost" i16:13
blkshpos16:13
blkshpis16:13
pwr22Ah, not been my experience16:13
pwr22But I have avoided going out as much as possible so maybe there's a lot more around here now16:13
blkshpI am out of the city but there have not been many signs around here but since the relaxation of the shopping closures which happened monday, all the shopping centres and individual shops have put floor signs, lamp post signage, etc There was some before but nothing like what's appeared in the last 7 days16:14
Jigsy%cases UK16:16
BrainstormJigsy: In United Kingdom, there have been 300469 confirmed cases (0.5% of the population) and 42288 deaths (14.1% of cases) as of 21 hours ago. 7.3 million tests were performed (4.1% positive). See https://offloop.net/covid19/?default=United%20Kingdom for time series data.16:16
LjLblkshp: 4 to 3 what?16:21
blkshpWe have a US DEFCON style alert system16:21
blkshphttps://www.bbc.co.uk/news/uk-5310667316:22
LjLblkshp: Italy has a better situation than the UK at the moment but masks are compulsory indoors (and outdoors in Lombardy, or wherever you can't keep the distance), and stores are still limiting the amount of people who can be inside at a time, with queues outside. Needless to say public transport also has and enforces all the signage. If the UK is smart (big if) they won't relax any of that16:23
blkshpSo masks are now required on public transport and 2m rules still required everwhere else. definitely limiting the number of people inside shops, queues outside yes.16:24
pwr22<blkshp "So masks are now required on pub"> There hasn't been any limiting in supermarkets where I am for a while :(16:33
blkshpReally :O16:33
blkshpI only shop and Sainsburys and Tesco, I'm not ure if it's managers discretion but there's still people filtering people16:34
BrainstormUpdates for Botswana: +10 cases (now 89) since a day ago — Saudi Arabia: +4301 cases (now 150292), +45 deaths (now 1184) since 22 hours ago — Virginia, US: +555 cases (now 56793), +16 deaths (now 1602) since 22 hours ago — United Kingdom: +1346 cases (now 301815), +173 deaths (now 42461) since 22 hours ago16:35
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CoronaBot04/r/covid19: Detection of antibodies to the SARS-CoV-2 spike glycoprotein in both serum and saliva enhances detection of infection (80 votes) | https://www.medrxiv.org/content/10.1101/2020.06.16.20133025v1 | https://redd.it/hbiqfe18:21
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CoronaBot04/r/coronavirus: American Airlines bans conservative activist who refused to wear a mask (10731 votes) | https://www.nytimes.com/2020/06/18/us/american-airlines-mask-brandon-straka.html | https://redd.it/hc0fw818:46
LjLquick note before i leave for a walk (!): today the new cases in Italy are going *down* in number, which may make some graphs funky (tinwhiskers), because apparently Sicily realized they had overcounted by some 300 cases18:56
LjLalso, discuss: https://translate.google.com/translate?sl=it&tl=en&u=https%3A%2F%2Fwww.corriere.it%2Fcronache%2F20_giugno_19%2Fcoronavirus-remuzzi-nuovi-positivi-non-sono-contagiosi-stop-paura-bf24c59c-b199-11ea-842e-6a88f68d3e0a.shtml (if the translated page loads because it doesn't for me)18:57
nixonixThe results, confirmed in two different laboratories by two different methods, showed the presence of SARS-Cov-2 in samples taken in Milan and Turin on December 18th, 2019 and in Bologna on January 29th, 2020. Samples from October and November 2019 were negative, showing the virus had yet to arrive, La Rosa said.19:01
nixonixMeanwhile, in Spain, a study found the trace virus in the wastewater collected in mid-January in Barcelona, ​​about 40 days before the first case was discovered.19:04
nixonixFrench scientists said tests on samples from drainage in May showed a patient treated for suspected pneumonia near Paris on 27 December actually had the coronavirus.19:04
nixonixThe findings echo similar discoveries elsewhere in Europe suggesting the coronavirus was circulating globally well before Chinese authorities flagged the new infection on December 31.19:05
nixonixwhen were those strange pneumonia cases in italy?19:05
xrogaanChinese authorities are still preventing any kind of foreign taskforce to enter and study the virus.19:14
nixonixhttps://www.reuters.com/article/us-health-coronavirus-italy-timing/italian-scientists-investigate-possible-earlier-emergence-of-coronavirus-idUSKBN21D2IG19:14
nixonix%title19:14
Brainstormnixonix: From www.reuters.com: Italian scientists investigate possible earlier emergence of coronavirus - Reuters19:14
nixonixit was from march, that news19:14
nixonixbut it will take a while to spread, until it shows up in sewer samples19:15
generahow do they do those tests?19:19
BrainstormUpdates for Morocco: +333 cases (now 9613) since 8 hours ago — Brazil: +25384 cases (now 1.0 million), +530 deaths (now 48427) since 2 hours ago — World: +29427 cases (now 8.7 million), +667 deaths (now 458860) since 47 minutes ago — Dominican Rep.: +423 cases (now 25068), +12 deaths (now 647) since an hour ago19:21
JoeLlamaEEEEPPP!!!19:29
LjLnixonix: not sure if same thing (I'm walking) but I heard today they analyzed sewage water dating from back in December, in Milan and in Turin (which they keep... for some reason), and they found covid RNA in it19:37
LjLWorth noting that as far as we knew until now, the Turin outbreak was "late"19:39
CoronaBot04/r/covid19: Divergent SARS-CoV-2-specific T and B cell responses in severe but not mild COVID-19 (80 votes) | https://www.biorxiv.org/content/10.1101/2020.06.18.159202v1 | https://redd.it/hbq84o19:46
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user.19:57
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CoronaBot04/r/covid19: Genes, Blood Type Tied to Risk of Severe COVID-19. (81 votes) | https://directorsblog.nih.gov/2020/06/18/genes-blood-type-tied-to-covid-19-risk-of-severe-disease/ | https://redd.it/hbvt2x20:16
LjL<nixonix> when were those strange pneumonia cases in italy? ← "december", from what i remember, don't have details20:17
User1231Not spam, need support. Please put "thumbs up": https://www.youtube.com/watch?v=sUt6HIgfQgo20:20
User1231Not spam, need support. Please put "thumbs up": https://www.youtube.com/watch?v=sUt6HIgfQgo20:20
nixonixi linked an article from march (pneumonia) above. also quotes about these recent sewer findings20:22
nixonix"Adriano Decarli, an epidemiologist and medical statistics professor at the University of Milan, said there had been a “significant” increase in the number of people hospitalized for pneumonia and flu in the areas of Milan and Lodi between October and December last year. He told Reuters he could not give exact figures but “hundreds” more people than usual had been taken to hospital in the last three months of 2019 in those areas - 20:22
nixonixtwo of Lombardy’s worst hit cities - with pneumonia and flu-like symptoms, and some of those had died."20:22
Arsaneritwhat I don't understand, if the virus was around much earlier and it's so contagious, why did we only see massive community spread in Europe in March?20:24
LjLnixonix, it's a bit handwavy, we really should have more specific who's and when's at this point :\20:27
LjLArsanerit, we "see" it because it is advertised as COVID, and because at some point it saturated Lombard hospitals completely. if it was taking place before January, doctors may have noticed there were "too many pneumonias" but evidently it wasn't investigated, or they found no clear answer, and so the media didn't get to know about it...20:28
nixonixit takes a while to spread. unless theres some super spreader or event early on. but it shows up, that trying to find the patient zero in italy was wasted effort, it was already in many places then20:29
nixonix-"up"20:29
LjLsometimes bureaucracy just stops things from happening in Italy. i can easily imagine doctors having duly filed "strange case" reports, and those subsequently having been thoroughly ignored or just sat in an inbox somewhere.20:29
LjLnixonix, well we already did know that the search for patient zero was wasted effort, it was already clear that there were multiple unrelated clusters20:30
Arsaneritbut early on they were reporting doubling times of 3 or 4 days20:30
LjLthe patient zero search didn't last *that* long20:30
Arsaneritthat means that in a month it would increase by a factor 100020:30
Arsaneritwhere those doubling times not true to actual case doublings?20:31
LjLwell the doubling time may have been lower. we are now often presuming that viral load has been going down... maybe back then it was lower too, then it surged due to weather or some other reason20:31
LjLbut i'm just guessing, i don't know that we can do more than that right now20:31
generamight have been the flu?20:32
nixonixthose pneumonia cases? maybe. or maybe sars-220:33
generathe ground glass inclusions should have been a warning sign20:34
Arsaneritor maybe it was a less contagious strain that was around earlier?20:34
nixonixor both. and other coronas etc. but i dont think hundreds pneumonia cases caused by sars-2 infection in december, otherwise the infection numbers would have been thousands in dec, tens of thousands in jan, or something like that. but some of them maybe was sars-220:35
generabut they have the RNA20:35
generaok first time i hear a commercial advertizing the corona WARN app20:37
generabut then again i didnt have the radio on before20:37
LjLi don't know, there are still a LOT of uncertain and strange things about this virus20:41
LjLwhat annoys me is that whenever something is uncertain, many people will insist to take the "it's probably fine" view instead of a precautionary view20:41
LjLit's happened from the start, and it's been quite a disaster20:41
BrainstormUpdates for Egypt: +1774 cases (now 52211), +79 deaths (now 2017) since 22 hours ago — Mauritania: +197 cases (now 2621), +5 deaths (now 102) since 22 hours ago — Louisiana, US: +506 cases (now 49140), +6 deaths (now 3090) since an hour ago — Ohio, US: +562 cases (now 43814), +34 deaths (now 2672) since 49 minutes ago20:51
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Urchin[emacs]%data croatia22:02
BrainstormUrchin[emacs]: In Croatia, there have been 2280 confirmed cases (0.1% of the population) and 107 deaths (4.7% of cases) as of 7 hours ago. 71814 tests were performed (3.2% positive). Fatality can be broadly expected to lie between 1.6% (assuming deaths/cases with ⅔ undetected), and less than 4.8% (considering only deaths and recoveries). See https://offloop.net/covid19/?default=Croatia for time series data.22:02
BrainstormUpdates for South Carolina, US: +1083 cases (now 22631), +18 deaths (now 639) since 23 hours ago — Massachusetts, US: +228 cases (now 106650), +30 deaths (now 7800) since 23 hours ago — US: +1330 cases (now 2.3 million), +49 deaths (now 121221) since 18 minutes ago — World: +1359 cases (now 8.7 million), +49 deaths (now 459633) since 18 minutes ago22:07
tinwhiskersnixonix, LJL, anyone: do you know if we have someone here from Sweden?22:10
tinwhiskersI've been into a bit of a Swedish population rabbit hole. I updated my system to account for double-ups on place names only to find covidly doesn't actually have populations info for Swedish regions so that was all for nothing :-)22:11
tinwhiskersSo I decided to plug them in manually but now I see covidly has doubled-up some of the places using different spellings and assigned some cases to each spelling. e.g. Vaesterbotten, Vasterbotten; Vaestmanland, Vasternorrland.22:13
tinwhiskersbut anyway, I thought I'd get the population data in anyway, putting the same population down for the duplicates. However, I'm uncertain about "Jaemtland" and "Jaemtland Harjedalen". Are these really different places or just another duplication?22:14
tinwhiskersAlso, is Sormland maybe another name for Soedermanland or Stockholm? I don't see a population for it.22:15
tinwhiskersSo hoping a local might clarify22:15
tinwhiskerserm, the other duplicate was meant to be Vaesternorrland, Vasternorrland - these names all look like swedish to me :-)22:17
LjLtinwhiskers, ugh, sounds like Covidly wants to be JHU 2.022:18
tinwhiskersheh22:18
tinwhiskersyeah22:19
LjLtinwhiskers, "Södermanland locally Sörmland, sometimes referred to under its Latin form Sudermannia..."22:19
tinwhiskersah. thank22:19
tinwhiskerss22:19
BrainstormUpdates for Guinea-Bissau: +49 cases (now 1541), +2 deaths (now 17) since 3 days ago — Kentucky, US: +257 cases (now 13454), +2 deaths (now 522) since a day ago — Connecticut, US: +47 cases (now 45557), +12 deaths (now 4238) since 21 hours ago — Germany: +210 cases (now 190660), +8 deaths (now 8960) since an hour ago22:37
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LjLtinwhiskers, wow, nice double standards r/covid19 seems to have (unless they delete the other message soon too): https://www.reddit.com/r/COVID19/comments/hbihs5/formal_request_for_the_retraction_of_zhang_et_al/fvd1ntn/22:58
LjLyou see my message, then you see someone's response, but you don't see my response to their response, which was22:58
LjLIndeed, it has been rather unfair of them not to provide that reasoning to us, and instead, use blatant lies. I will note that masks have been hoarded anyway, and there is no evidence, let alone scientific evidence, that avoiding lies would have made it worse.22:58
LjLEven from a simple practical perspective, it undermines any credibility they had among people, now that the lie has become apparent. Good luck getting me (or many others) to have any trust in anything the WHO says from now on. A pretty short-sighted strategy.22:58
LjLapparently, mine was "off-topic or political", but somehow theirs wasn't22:58
tinwhiskersyeah, lying is never going to work out well in the long run22:59
LjLtinwhiskers, what about selectively delete posts that denounce lying23:00
LjLdeleting*23:00
tinwhiskerswell, yeah23:00
tinwhiskersthat's not ideal :-)23:00
CoronaBot04/r/covid19: Airborne SARS-CoV-2 is Rapidly Inactivated by Simulated Sunlight (82 votes) | https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaa334/5856149 | https://redd.it/hc789d23:05
CoronaBot04/r/covid19: SARS-CoV-2 Viral Load Predicts COVID-19 Mortality (84 votes) | https://www.medrxiv.org/content/10.1101/2020.06.11.20128934v1 | https://redd.it/hc44ug23:05
LjL↑ looks important23:06
nixonixwe could really use good analysis between us states, with other factors filtered, than the climate23:08
nixonixand sun exposure23:08
LjLi was pointing at the viral load one23:09
LjLalthough it says "By the end of the study period, 807 werealive (70.5%; mean log10viral load 5.19+/-2.99 viral copies/mL) and338 had died (29.5%; mean log10viral load was 6.44 +/-2.66viral copies/mL)."23:09
LjLthe two intervals overlap23:09
nixonixyeah i guessed you were23:10
LjLevidence that viral load matters is important because more and more rumors are accumulating in italy that current cases, aside from being fewer, are *milder*23:13
LjLit's not easy to ensure those rumors don't stem from bias, because, well, doctors are seeing milder cases now, but before, they simply wouldn't see the milder cases as they would have never been brought to hospital23:14
LjLso it's not easy to determine whether this general sensation that "cases are milder" is true or an illusion23:14
LjLbut if viral load does matter, then it's likely that lowering viral load is causing this (masks, sunlight, the reason is also important to find of course)23:14
nixonixmild cases are more likely to just stay home, if the situation is bad in hospitals. also if they are not sure if its another ili or something, or sars-2, mild cases are not necessary willing to even go to test - if the risk of getting the actual sars-2 infection is high (in case they might have another ili)23:17
nixonixbut viral load thing, naturally if immune response is more succesful in killing the virus, the viral load will be lower, and the outcome likely better. maybe that observation still has some value, i dont know..23:18
LjLnixonix, if viral load is lower it's also plausible that viral shedding will be in lower amounts, which may both cause you to be less infectious, and if you do infect someone, they may *start* with a lower viral load, even before their immune system comes into play23:20
LjLtinwhiskers, oh good god, a mod of the subreddit "invited me to chat" (after i reported that post saying it's at least as political as mine)23:21
LjLwho thought realtime chat on reddit was a good idea?23:21
LjLthis is why i'm on IRC, because *that* is where i want to chat23:21
LjLon reddit i want to do a different thing, sheesh23:21
tinwhiskerspopcorn23:22
LjLtinwhiskers, hm that went well, she told me that the second line of my post was the one that crossed the line, and if i edited it out she'd reinstate it23:27
tinwhiskersoh. boring :-p23:27
LjLi guess no matter how i phrase it, the remark that lying has long-term consequences on trust is political, not scientific (unless it's r/sociology)23:27
tinwhiskersyeah23:29
tinwhiskerssorry, bit distracted23:29
LjLtinwhiskers, no problem, i just pointed this incident out to you because i know you uphold wearing masks with a bit of a passion :P23:30
tinwhiskersheh :-)23:30
LjLand have done so since well before the WHO conceded they were good23:30
tinwhiskersI understand the reasons they lied but never thought it was anything but a lie.23:31
tinwhiskersbasically they thought people weren't capable of understanding the complexity of the truth so simplified it but in doing so lied.23:31
ryoumait took authorities months to say wear masks that are not medical grade23:32
tinwhiskersand they weren't wrong either23:32
LjLtinwhiskers, "we don't have enough masks for everybody, and medical workers need them the most, also to protect all their patients, maybe one day you too" doesn't seem more complex than some of the public messages i've heard23:33
tinwhiskersI don't think in hindsight they made a good call but I'm not all anti-WHO about it either.23:33
tinwhiskersLjL: yeah23:34
tinwhiskersfair23:34
LjLgranted, at the "maybe one day you too", any Italian would likely do a very specific hand gesture23:35
LjLactually, either one or the other23:35
ryoumastockpiles of masks would have been useful23:36
tinwhiskersheh23:36
LjLwell the WHO didn't even have the burden of thinking "whoops, but if we tell them that we have no masks, they'll think it's our fault"23:37
LjLsince the WHO doesn't keep stocks of masks23:37
LjL... and neither do governments, apparently, but people may think they should23:37
BrainstormUpdates for Wyoming, US: +29 cases (now 1173), +2 deaths (now 20) since a day ago — Brazil: +23214 cases (now 1.0 million), +527 deaths (now 48954) since 4 hours ago — Peru: +3537 cases (now 247925), +199 deaths (now 7660) since 23 hours ago — Texas, US: +2028 cases (now 105641), +14 deaths (now 2161) since an hour ago23:37
ryoumathe us did but gave up keeping it up to date and large enough23:38
ryoumataiwan did23:38
LjLit's almost too easy to posit a correlation between that, and the fact Taiwan is faring well with the epidemic23:38
Arsaneritand maybe having domestic production for such things makes sense too, rather than having everything made in china or even cheaper countries23:41
LjLit's not even a matter of cheap... it's a matter of... everything gets confiscated and it's every man^W country for its own23:42
ArsaneritI mean that the reason production was in China is because of cheap23:45
tinwhiskersI think it's fine to have them produced in China (aside from general ethical issues of supporting producing *anything* in China) provided they are stockpiled in sufficient quantities in each country.23:48
Arsaneritwhen bringing ethics in it becomes hard where to draw the line23:49
tinwhiskersyes, aside from that23:49
Arsaneritbut you're right about stockpiles23:49
tinwhiskersthe stockpiles need to be sufficient to carry you through until local production can be mobilised OR sufficient to cover an entire pandemic (which is probably too vast to be practical)23:50
tinwhiskersthe former requires you maintain some degree of readiness for production but don't need to bear the full financial burden of keeping it running - e.g. planning to have retooling available in other industries or some such.23:53

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