libera/##covid-19/ Saturday, 2020-11-07

dTalWHO's afraid of the Big Bad Mink00:01
dTalthat's what I would write, if I were a tabloid editor00:02
LjLi'd highlight everyone about it00:03
LjLexcept it doesn't really say anything00:03
LjLexcept that sequences are coming, i guess00:03
LjLbut then i might just highlight when the sequences do come00:03
dTalhighlight?00:03
LjLall the people00:03
dTalin the channel?00:03
LjLno just a bunch00:03
dTalhuh00:04
LjLlike four people would probably want to know about any news on this00:04
LjLprobably many more than four but those are the ones who fulfill the conditions of being here, wanting to know, and me knowing they want to know00:04
BrainstormUpdates for US: +13924 cases (now 10.0 million), +167 deaths (now 242081) since 49 minutes ago — Canada: +19 cases (now 253809) since 45 minutes ago00:06
BrainstormNew from "Cluster 5" on Wikipedia: Biscuit-in-Chief: more information of the mutated virus from ref "ssi". Placed it in lead; might need to go somewhere else: more information of the mutated virus from ref "ssi". Placed it in lead; might need to go somewhere else ← Previous revision Revision as of 23:10, 6 November 2020 Line 1: Line 1: − ''' " [... want %more?] → https://is.gd/74bzDF00:11
de-facto"To date, six countries, namely Denmark, the Netherlands, Spain, Sweden, Italy and the United States of America have reported SARS-CoV-2 in farmed minks to the World Organisation for Animal Health (OIE)."00:15
de-factowhat about China and Poland?00:17
LjLgood luck with them00:18
BrainstormNew from "Cluster 5" on Wikipedia: Biscuit-in-Chief: link: link ← Previous revision Revision as of 23:13, 6 November 2020 Line 3: Line 3: The [[World Health Organisation]] has yet to release scientific details of this mutation. {{Cite news|last=Gorman|first=James|date=2020-11-04|title=Denmark Will Kill All Farmed Mink, Citing Coronavirus [... want %more?] → https://is.gd/74bzDF00:20
BrainstormUpdates for US: +6830 cases (now 10.0 million), +47 deaths (now 242128) since 18 minutes ago00:21
LjLokay, well, i don't know why it didn't post any edit before since it's been some hours, but as i cleverly suspected, that is not sustainable00:21
LjLalthough hey it did give us the news about the WHO statement just a bit after we got them anyway00:21
de-factoI wonder why it is called cluster 5, did cluster 1-4 fail to mutate in minks?00:26
LjLi don't know, but it sounds spooky00:26
LjLalso that wasn't actually the edit adding a WHO link00:27
LjLi added a WHO link instead, but now i bet it'll be removed due to it being considered a primary source (lol as if)00:27
LjL"The Government is aware that the actions now taken will entail a de facto shutdown of the Danish mink industry ­— at least for a number of years — but, according to the Danish health authorities, even a small number of breeding animals will pose a risk to public health."00:29
LjLhttps://www.oie.int/fileadmin/Home/MM/Update_6_Letter_to_the_OIE_on_Sars-CoV-2_in_Denmark_5_november2020.pdf00:29
BrainstormNew from "Cluster 5" on Wikipedia: LjL: WHO released a statement: WHO released a statement ← Previous revision Revision as of 23:23, 6 November 2020 Line 15: Line 15: On 6 November, the United Kingdom announced that all travellers returning from Denmark would be removed from a whitelist for its COVID-19 travel restrictions. Those entering the [... want %more?] → https://is.gd/74bzDF00:30
de-factoi am somewhat worried that the Danish government may be the only one acting responsibly on mink farms now (well maybe together with the Netherlands), but what about the other mink farming locations we dont hear anything about?00:34
de-factosurely China would censore such news it something similar occurred in their farms00:35
de-factoand what about the other countries00:36
de-factoi mean if farmers know they would have to cull all their animals and maybe end farming all together, would they think twice reporting about outbreaks?00:37
LjLWikipedia isn't what it used to be (and it used to be useful for realtime news, even though they didn't want to be)... neither the article about COVID-19 nor the one about the pandemic mention the mink incident. the COVID-19 article just mentions mink once as susceptible animals. "Cluster 5" doesn't appear to be linked from either of them, OR from their talk pages00:37
de-factoi am not saying they do hide anything, just that i am worried some might think about it00:37
LjLde-facto, i am taking for granted that at least Poland and China won't do what's required, especially China being a primary consumer, not just producer, of mink00:38
LjLmaybe some of the others too00:38
LjLi bet if you told most Italian we have mink factory-farms in Italy they'd be like "ew, really? stop them!"00:38
LjLso you don't tell them00:38
de-factoi bet they even might not be too sad about taking over the market share of Denmarks and Netherlands production00:43
de-factoit should be banned worldwide00:43
DocScrutinizer05cluster fuck :-/00:43
DocScrutinizer05cluster sputnik00:47
BrainstormNew from The Lancet: [Correspondence] SARS-CoV-2 seroprevalence in Spain – Authors' reply: We thank Christian Hoffmann and Eva Wolf for pointing out the contradiction of similar severe acute respiratory syndrome corona­virus 2 (SARS-CoV-2) seroprevalence figures between men and women in our nationwide study,1 compared with the distribution of [... want %more?] → https://is.gd/a8UFwR00:48
BrainstormUpdates for Canada: +2000 cases (now 255809), +8 deaths (now 10435) since 48 minutes ago — US: +3546 cases (now 10.0 million), +34 deaths (now 242162) since 32 minutes ago00:51
BrainstormNew from CNBC Health: (news): Dr. Scott Gottlieb says actual number of new daily U.S. Covid cases is 'at least half a million' → https://is.gd/dU8PSq01:15
CoronaBot04/r/covid19: Opinion: To stop the next pandemic, we need to unravel the origins of COVID-19 (81 votes) | https://www.pnas.org/content/early/2020/11/03/2021133117 | https://redd.it/jp7h1c01:19
BrainstormNew from BBC Health: 'I was refused a home Covid test after credit check': A BBC investigation finds people are being refused home Covid tests because of their credit histories. → https://is.gd/Utqh9A01:25
rpifanyea01:29
BrainstormNew from BBC Health: Covid: How to survive a winter lockdown, from those who've done it: Tips on lockdown life in cold weather - from sub-zero coffee meet-ups to watching films in the bath. → https://is.gd/grOYEx01:34
Skunnyhaving no smell or taste sucks01:36
Skunnyi been watching food network all day01:36
ryoumai have had anosmia and dysgeusia since late 1990s.  every once in a while zinc helped.01:36
ryoumaone of these days i will find out what the principles for cooking for those are.01:38
Skunnydamn, I have had it for 2 days now and it blows01:39
LjLSkunny, this may be a silly question given the place, but do you have COVID?01:41
Skunnyyeah01:43
LjLi think you're actually the first person in the channel who has it (and says it), interestingly enough01:46
LjL(or else i missed others)01:46
Skunnywierd01:47
SkunnyIf it doesn't recover I could always start my new career in a water treatment plant. Or a garbage man.01:47
LjLpositive thinking01:47
LjLhow many days since testing positive?01:48
Skunnywell I took my test tueday01:49
Skunnyand still waiting, can you beleive that01:49
Skunnybut I have had all the syptoms01:49
Skunnybut my breathing has been fine01:49
SkunnyI took another test today because I have no clue why the first one is taking so long01:50
LjLwell, it's sort of lucky that you are able to do that01:50
LjLthey aren't testing even first-degree contacts of positives here anymore01:50
Skunnymonday I started to notice I was getting sick01:51
Skunnyso I went tuesday01:51
LjLdo you have a pulse oximeter? if not, get a pulse oximeter01:52
LjLthey're cheap unless they stopped being cheap again01:52
LjLi won't mention a thermometer because that should be pretty obvious01:52
BrainstormNew from r/Coronavirus: Coronavirus: Join the official Coronavirus Community Discord with live data, discussion and curated news! :) → https://is.gd/hVuuxW02:02
SkunnyI have oximeter02:04
BrainstormNew from CNBC Health: Why Germany's coronavirus strategy doesn't appear to be working this time around: While Germany was lauded for its initial response to the pandemic, another lockdown raises questions over the effectiveness of its strategy second time around. → https://is.gd/olT27v02:11
de-factomake sure you drink enough and eat healthy of course, maybe even things that may have anti-coagulant effects02:28
BrainstormNew from CNBC Health: For doctors who think Trump fumbled the pandemic, the tight election is seen as an insult: Many front-line medical workers expected that the coronavirus would be a top priority for voters, and that Biden would win by a landslide. → https://is.gd/TZ6aF002:38
BrainstormUpdates for US: +8759 cases (now 10.1 million), +68 deaths (now 242230) since 2 hours ago — Canada: +443 cases (now 256252), +16 deaths (now 10451) since 2 hours ago — New Zealand: +2 cases (now 1976) since 19 hours ago02:51
LjL%title https://www1.cbn.com/cbnnews/world/2020/november/north-korea-reportedly-leaving-covid-19-victims-to-die-in-secret-quarantine-camps04:47
BrainstormLjL: From www1.cbn.com: North Korea Reportedly Leaving COVID-19 Victims to Die in Secret 'Quarantine Camps' | CBN News04:47
BrainstormNew from r/WorldNews: worldnews: North Korea Reportedly Leaving COVID-19 Victims to Die in Secret 'Quarantine Camps' → https://is.gd/zbdcHf04:57
LjLBrainstorm, jinx05:01
de-factolol05:01
de-factoyuck @ NK if thats true05:01
ryoumaso they did not have 0 cases?05:28
CoronaBot04/r/coronavirus: U.S. reports 125,000 new coronavirus cases, setting world record for the 3rd day in a row (10066 votes) | https://twitter.com/BNODesk/status/1324874679169986566?54 | https://redd.it/jph6tj05:39
tinwhiskersThey did indeed have 0 *confirmed* cases.05:41
tinwhiskers"... The same day, Daily NK reported that a defecting North Korean who was shot attempting to cross the Tumen River into China tested positive for the virus."05:42
BrainstormNew from The Indian Express: World: Trump’s chief of staff, Mark Meadows, infected by coronavirus → https://is.gd/t3FLvx05:42
gigasu_shidahow the heck did taiwan get rid of the virus so well?05:58
gigasu_shidai see so many videos on the internet of taiwanese folks eating in large dining areas without a mask05:59
tinwhiskersgigasu_shida: there's several countries who have done similarly; australia, vietname, cambodia, New Zealand, Thailand. All these places have fairly normal lives again.06:01
tinwhiskers*Vietnam (there goes my extra e muscle memory thing again)06:01
gigasu_shidai wonder when taiwanese people went back to eating in food courts / dining halls together without a mask06:01
tinwhiskersWe've been doing it for months in NZ. Australia more recently.06:02
gigasu_shidais their contact tracing for that?06:02
gigasu_shidathere*06:02
tinwhiskersyes, people do record where they go in NZ by scanning QR codes.06:03
gigasu_shidalike if someone tests positive is contact tracing done rapidly?06:03
gigasu_shidaoh wow that's cool06:03
tinwhiskersif there is an outbreak that aids contact tracing but contact tracing goes well beyond that. It's mostly done via phone calls.06:03
tinwhiskersthe main reason these places have been successful is due to clear communication and policies, and a recognition that the an investment in a hard lockdown has a fairly quick payback period.06:04
tinwhiskersOf course China deserves mention as well.06:05
tinwhiskersLocal tourism is up and going again in many of these countries too.06:05
tinwhiskersI know I've missed a bunch of countries in that list, but my brain isn't that good.06:06
tinwhiskerspeople trusting and following government advice is critical, and that takes a long time to build.06:07
ryoumathis was 100k a coiupld of days ago iirc --- 21:39 <CoronaBot> 04/r/coronavirus: U.S. reports 125,000 new coronavirus cases, setting world record for the 3rd day in a row (10066 votes) | https://twitter.com/BNODesk/status/1324874679169986566?54 | https://redd.it/jph6tj06:08
ryoumapacifgic islands06:09
tinwhiskerson target for > 1 m cases in the next ten days06:09
ryoumasingapore06:09
tinwhiskersmaybe just in the next week :-(06:09
BrainstormNew from The Indian Express: World: Denmark defends coronavirus measures amid mink mutation → https://is.gd/5BB0Ct06:10
tinwhiskersof course the contact tracing really only works well once/if your numbers are quite low. In NZ news coverage on TV and radio warns people where hotspots have occurred; like if you visted the petrol station at X on day Y please self-isolate. That sort of things is obviously not possible if you have a lot of hotspots.06:12
tinwhiskersKiwis have become quite proud of having beaten down three outbreaks now so they are really getting behind things (in general - there's still the obligatory maskholes).06:13
ryoumawill you fly or sail?06:15
tinwhiskersfly06:15
tinwhiskerswe may well be the only people on the plane06:16
ryoumawhy would it fly?06:16
tinwhiskersa plane comes here once a week to deliver mail and supplies but only kiwi expats can travel back on it and there's only a handful left here.06:16
ryoumagreat06:17
tinwhiskersThe chances of two lots of expats returning home in the same week is fairly low.06:17
tinwhiskersnot that it matters since they will be clear anyway06:17
ryoumabut quarantine is not separated and all at once?06:17
tinwhiskersit's when we reach the quarantine facility that the worry starts06:17
ryoumathat makes little sense to me you shoul dhave separate rooms with separate hvac06:18
ryoumawhy does your kayak or whatever it was point so high without a keel?  is it a sharp bottom?06:18
tinwhiskersyeah. Nobody seems to know if there are high-rsi and low-risk facilities but there are not any no-risk facilities anyway :-(06:18
tinwhiskersit has a keel06:18
tinwhiskerswell, a daggerboard06:18
ryoumaso it was designed for it or you built it?06:19
tinwhiskersI made it. The daggerboard is just a drop-in keel that slots into the frame.06:19
tinwhiskersyou pull it out when you get into the shallows.06:19
ryoumabut you have to make the frame leakproof06:20
tinwhiskersno, the frame doesn't matter. 06:20
ryoumabut hte slot for the daggerboard has to be above water06:20
tinwhiskersmy daggerboard is *beside* the kayak06:20
ryoumaoh06:20
tinwhiskersIt took me a long time to sew the sail by hand :-/06:22
BrainstormUpdates for Belgium: +8703 cases (now 488044), +188 deaths (now 12708) since a day ago — France: +8690 cases (now 1.7 million) since 11 hours ago — Netherlands: +1511 cases (now 399241), +4 deaths (now 7891) since 15 hours ago — Canada: +382 cases (now 256634), +3 deaths (now 10454) since 4 hours ago07:07
BrainstormNew from r/WorldNews: worldnews: Hong Kong protests: pair admit rioting and beating resident who complained of noise and being woken up during outbreak of unrest → https://is.gd/bUsPLK07:13
BrainstormNew from BBC Health: Covid travel ban for visitors to UK from Denmark: An immediate ban is imposed after a new coronavirus strain spreads to humans from mink. → https://is.gd/JzkjES07:22
BrainstormNew preprint: Characterising heterogeneity and sero-reversion in antibody responses to mild SARS-CoV-2 infection: a cohort study using time series analysis and mechanistic modelling by Charlotte Manisty et al, published on 2020-11-06 at https://medrxiv.org/cgi/content/short/2020.11.04.20225920 [... want %more?]07:22
BrainstormUpdates for Lombardy, Italy: +9934 cases (now 242947), +131 deaths (now 18118) since a day ago — France: +15181 cases (now 1.7 million), +26 deaths (now 39891) since 47 minutes ago — Netherlands: +1820 cases (now 401061), +30 deaths (now 7921) since 47 minutes ago — United Kingdom: +1653 cases (now 1.1 million), +45 deaths (now 48520) since 13 hours ago07:53
BrainstormNew from "Cluster 5" on Wikipedia: Ipigott: ce: ce ← Previous revision Revision as of 07:14, 7 November 2020 Line 3: Line 3: The [[World Health Organisation]] has yet to release scientific details of this mutation. {{Cite news|last=Gorman|first=James|date=2020-11-04|title=Denmark Will Kill All Farmed Mink, Citing Coronavirus [... want %more?] → https://is.gd/74bzDF08:16
BrainstormNew from The Indian Express: World: Amazon Fires Cause Brazil’s CO2 Emissions to Jump Amid Pandemic → https://is.gd/dufcZc08:34
BrainstormNew from "Cluster 5" on Wikipedia: Ipigott: /* Timeline */ ce: Timeline: ce ← Previous revision Revision as of 07:35, 7 November 2020 Line 15: Line 15: On 6 November, the United Kingdom announced that all travellers returning from Denmark would be removed from a whitelist for its COVID-19 travel restrictions. Those entering the country, including [... want %more?] → https://is.gd/74bzDF08:43
BrainstormNew from "Cluster 5" on Wikipedia: Ipigott: sp: sp ← Previous revision Revision as of 07:46, 7 November 2020 Line 3: Line 3: In Denmark there have been five clusters of mink variants of SARS-CoV-2; the Danish [[Statens Serum Institut|State Serum Institute]] (SSI) has designated these as clusters 1–5 (Danish: {{lang|da|cluster 1-5}}). Among these [... want %more?] → https://is.gd/74bzDF08:53
BrainstormNew from r/WorldNews: worldnews: Military forces drafted in as Europe risks being overwhelmed by Covid cases → https://is.gd/aVBzoU09:20
BrainstormUpdates for US: +682 cases (now 10.1 million), +17 deaths (now 242256) since an hour ago09:39
de-facto%title https://twitter.com/firefoxx6609:40
Brainstormde-facto: From twitter.com: error parsing title ('NoneType' object has no attribute 'string')09:41
de-factolol09:41
humpelstilzchen[sounds like something a snake would say09:41
de-factoDr Emma Hodcroft shows the mutations of the danish mink farms on nextstrain.org09:42
de-factoH69del/V70del, Y453F, I692V, and M1229I09:45
de-factoand also other mutations09:45
de-factoif one would want to be informed about the latest developments look at her tweets there09:45
de-factohttps://nextstrain.org/groups/neherlab/ncov/denmark?f_country=Denmark&p=grid&r=division09:49
de-facto%title https://www.biorxiv.org/content/10.1101/2020.11.04.355842v1 <-- another nasty mutation?10:15
Brainstormde-facto: From www.biorxiv.org: The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity | bioRxiv10:15
de-facto%title https://twitter.com/robertson_lab <-- published on their twitter10:17
Brainstormde-facto: From twitter.com: error parsing title ('NoneType' object has no attribute 'string')10:17
de-facto"Robertson lab" Computational biology research group exploring virus and molecular evolution, genomics & disease.10:18
BrainstormNew from Medical Xpress: Six countries reported coronavirus on mink farms, WHO says: Denmark and the United States are among six countries that have reported new coronavirus cases linked to mink farms, the World Health Organization said. → https://is.gd/bQqjeK11:02
BrainstormNew from Medical Xpress: US Covid-19 cases hit record for third day, topping 127,000: monitor: The United States has set a third straight daily record for new COVID-19 infections, notching more than 127,000 cases, John Hopkins University reported Friday. → https://is.gd/dexB1b11:11
BrainstormNew from Medical Xpress: UK bans entry from Denmark after COVID mink outbreak: Britain on Saturday banned entry to all non-resident foreigners coming from Denmark after a mutated version of the coronavirus linked to mink farms was found in humans. → https://is.gd/Fmea7w11:20
BrainstormUpdates for US: +1375 cases (now 10.1 million) since 2 hours ago11:39
BrainstormNew from r/WorldNews: worldnews: Coronavirus: France records more than 60,000 cases → https://is.gd/kk9YNE12:24
BrainstormUpdates for US: +1832 cases (now 10.1 million), +5 deaths (now 242261) since an hour ago12:39
BrainstormNew from PubMed: Shelter from the cytokine storm: pitfalls and prospects in the development of SARS-CoV-2 vaccines for an elderly population: The SARS-CoV-2 pandemic urgently calls for the development of effective preventive tools. COVID-19 hits greatly the elder and more fragile fraction of the population boosting the evergreen issue of the [... want %more?] → https://is.gd/Ugu98112:42
BrainstormNew from r/WorldNews: worldnews: Sexual violence consultations in Japan up 15% during pandemic. → https://is.gd/oqfpZm12:51
CoronaBot04/r/covid19: Persistence of SARS-CoV-2 specific B- and T-cell responses in convalescent COVID-19 patients 6-8 months after the infection (81 votes) | https://www.biorxiv.org/content/10.1101/2020.11.06.371617v1 | https://redd.it/jpnczo13:04
BrainstormNew from "Cluster 5" on Wikipedia: Ipigott: /* Timeline */ ce: Timeline: ce ← Previous revision Revision as of 12:12, 7 November 2020 Line 16: Line 16: On 6 November, the United Kingdom announced that all travellers returning from Denmark would be removed from a whitelist for its COVID-19 travel restrictions. Those entering the country, including [... want %more?] → https://is.gd/74bzDF13:18
BrainstormUpdates for US: +1013 cases (now 10.1 million) since an hour ago — Switzerland: +9 deaths (now 2721) since 5 hours ago13:35
BrainstormNew from r/WorldNews: worldnews: Covid-20 is a muted form of covid-19 found in mink. 214 people in Denmark are infected. All the mink farms will stop their businesses and eliminate the minks. → https://is.gd/UhXHyi13:45
BrainstormNew from "Cluster 5" on Wikipedia: Arjayay: Duplicate word removed: Duplicate word removed ← Previous revision Revision as of 13:32, 7 November 2020 Line 3: Line 3: In Denmark there have been five clusters of mink variants of SARS-CoV-2; the Danish [[Statens Serum Institut|State Serum Institute]] (SSI) has designated these as clusters 1–5 (Danish: [... want %more?] → https://is.gd/74bzDF14:41
BrainstormNew from r/Coronavirus: Coronavirus: Daily Discussion Post - November 07 | Questions, images, videos, comments, unconfirmed reports, theories, suggestions → https://is.gd/Nikbym14:59
BrainstormUpdates for US: +3871 cases (now 10.1 million), +55 deaths (now 242316) since 2 hours ago — Netherlands: +3340 cases (now 404401), +48 deaths (now 7960) since 8 hours ago15:50
BrainstormNew from CNBC Health: For doctors who think Trump fumbled the pandemic, the tight election is seen as an insult: Many front-line medical workers expected that the coronavirus would be a top priority for voters, and that Biden would win by a landslide. → https://is.gd/TZ6aF015:55
BrainstormUpdates for US: +1031 cases (now 10.1 million), +14 deaths (now 242330) since 19 minutes ago16:05
BrainstormNew from CNBC Health: (news): U.S. reports record 126,400 new coronavirus cases as medical experts warn worst days of pandemic are 'still ahead of us' → https://is.gd/IGSTlW16:31
BrainstormUpdates for US: +1509 cases (now 10.1 million), +9 deaths (now 242339) since 34 minutes ago — Switzerland: +10 deaths (now 2731) since 3 hours ago16:36
BrainstormUpdates for US: +573 cases (now 10.1 million), +1 deaths (now 242340) since 32 minutes ago — Canada: +378 cases (now 257012) since 9 hours ago17:06
BrainstormUpdates for Italy: +39809 cases (now 902490), +425 deaths (now 41063) since a day ago — United Kingdom: +23304 cases (now 1.2 million), +413 deaths (now 48888) since 9 hours ago — US: +655 cases (now 10.1 million), +15 deaths (now 242355) since 17 minutes ago17:21
BrainstormNew from StatNews: Biden’s ready to start his pandemic response immediately: Biden's top health advisers say he’s already preparing an unprecedented, mid-pandemic transition of power that aims to reboot the federal government’s Covid-19 response. → https://is.gd/aurqqG17:44
BrainstormUpdates for US: +6092 cases (now 10.1 million), +62 deaths (now 242417) since 35 minutes ago — Canada: +1170 cases (now 258182), +15 deaths (now 10474) since 46 minutes ago17:51
BrainstormUpdates for US: +1870 cases (now 10.1 million), +10 deaths (now 242427) since 32 minutes ago18:21
BrainstormNew from "Cluster 5" on Wikipedia: Dipsacus fullonum: /* Timeline */ fix template parameter: Timeline: fix template parameter ← Previous revision Revision as of 17:28, 7 November 2020 Line 18: Line 18: Also on 6 November, the [[World Health Organization]] (WHO) released a statement on the SARS-CoV-2 variants associated with farmed minks in Denmark [... want %more?] → https://is.gd/74bzDF18:33
BrainstormNew from r/WorldNews: worldnews: Denmark finds 214 people infected with mink-related coronavirus, experts fear impact on future Covid-19 vaccines → https://is.gd/CuyQF519:19
de-factoIf antibodies from the "normal" wild type would not properly fit for that mutated S-protein e.g. from Cluster 5 in the Danish Mink farms, would that potentially give raise to something nasty like ADE (Antibody Dependent Enhancement) meaning more severe progressions for reinfections by the new variant?19:20
LjLan investigative journalism programme on TV here just said that during a WHO review i think (also there was a WHO document that appeared for just a few hours and then was deleted), Italy, Spain and Belgium were the countries with a non-updated pandemic plan (in Italy's case 2006, not sure if 2006 for those other two as well, but i think they said so) out of i'm not sure what selection of countries19:23
LjLi guess they could cherrypick retrospectively to show that the countries that fared the worst were ones that were predicted to except it was subsequently hidden. but still.19:23
JigsyHuh.19:28
JigsyThe UK actually had 30,000 cases on the 2nd of November.19:28
de-factoYou mean hospital capacity?19:34
de-factoor what would "non updated pandemic plan" actually refer to?19:35
de-factoupdated to population density and demographics?19:35
de-factowere there such significant changes in last 14 years?19:35
Jigsyhttps://coronavirus.data.gov.uk/details/cases <--- Look at the graph.19:36
BrainstormUpdates for US: +8839 cases (now 10.1 million), +97 deaths (now 242524) since an hour ago19:37
JigsyWonder why it only got reported as around 20K, though...19:37
JigsyActually, it got reported as 18K...19:38
de-factoaverage vs spike or such?19:40
de-factobtw those plotly.js graphs are awesome :)19:41
de-factoAlso sometimes new reported cases distribute over the last few days due to reporting lag19:44
de-factoAt least that is the case in the German reporting system from RKI19:44
de-factobasically the last few days always will get "patched" with the newest data19:45
BrainstormUpdates for US: +14262 cases (now 10.1 million), +96 deaths (now 242620) since 32 minutes ago19:52
LjLi'm trying to implement a 24-hour window for Brainstorm's updates, and i don't really have a distinction between production and dev, so you may see some strange numbers for a while19:58
de-factoyay :))19:59
de-factothank you already for looking into that :)20:00
de-factoi wonder if ADE really could play a role for the mutations emerging right now e.g. from the Cluster 5 20:01
de-facto%title %title https://www.medrxiv.org/content/10.1101/2020.10.08.20209114v1 <-- was written before that incidence though20:01
Brainstormde-facto: From www.medrxiv.org: Antibody-dependent enhancement (ADE) of SARS-CoV-2 infection in recovered COVID-19 patients: studies based on cellular and structural biology analysis | medRxiv20:01
de-facto..."The enhancement of SARS-CoV-2 entry into cells was more commonly detected in plasma from severely-affected elderly patients with high titers of SARS-CoV-2 spike protein-specific antibodies. Cellular entry was mediated via the engagement of FcγRII receptor through virus-cell membrane fusion, but not by endocytosis. Peptide array scanning analyses showed that antibodies which promote SARS-CoV-2 infection targeted the variable regions20:02
de-facto of the RBD domain."...20:02
de-facto" Peptide array scanning analyses showed that antibodies which promote SARS-CoV-2 infection targeted the variable regions of the RBD domain."20:04
de-facto"To further characterize the association between the spike-specific antibody and ADE, an RBD-specific monoclonal antibody (7F3) was isolated from a recovered patient, which potently inhibited SARS-Cov-2 infection of ACE-2 expressing cells and also mediated ADE in Raji cells. Site-directed mutagenesis the spike RBD domain reduced the neutralization activity of 7F3, but did not abolish its binding to the RBD domain."20:05
de-facto" Structural analysis using cryo-electron microscopy (Cryo-EM) revealed that 7F3 binds to spike proteins at a shift-angled pattern with one “up” and two “down” RBDs, resulting in partial overlapping with the receptor binding motif (RBM), while a neutralizing monoclonal antibody that lacked ADE activity binds to spike proteins with three “up” RBDs, resulting in complete overlapping with RBM"20:05
de-facto"Our results revealed that ADE mediated by SARS-CoV-2 spike-specific antibodies could result from binding to the receptor in slightly different pattern from antibodies mediating neutralizations. Studies on ADE using antibodies from recovered patients via cell biology and structural biology technology could be of use for developing novel therapeutic and preventive measures for control of COVID-19 infection."20:05
LjLthis is really beyond my league20:06
de-factonote: "To study whether ADE is involved in COVID-19 infections, in vitro pseudotyped SARS-CoV-2 entry into Raji cells, K562 cells, and primary B cells mediated by plasma from recovered COVID-19 patients were employed as models."20:07
de-factoso in the lab, question remains if its also an effect in vivo (e.g. in patients)20:07
LjLi guess they'll be able to make a similar in vitro study with antibodies from the "mink" coronavirus20:07
de-factothey really should do that20:08
LjLwell not with the antibodies, with the new virus, and old antibodies20:08
de-factoexactly20:08
de-factothats why i said a few days ago that i hope they did isolate a live virus sample from those mink clusters20:09
LjLi would assume so20:11
LjLthey've been acting a bit stupid but they'd have to be *braindead* not to20:11
LjLyou know, general they, all of them20:11
LjLalso, there are still patients with the virus circulating20:12
LjLi don't think this mutated virus will be gone any time soon :( so you will have plenty of samples around20:12
de-factounfortunately they discover more of them, indeed20:12
tinwhiskersI think you're right LjL. 20:13
de-factoi wonder if they also could find reinfections among them, probably not so likely though20:13
de-factobecause of prevalence i mean20:13
LjLyou go and calculate the probability of that :P20:13
de-factobtw the samples are already on nextstrain20:13
LjLi think it's not so low, but that's just a guess20:14
LjLoh20:14
LjLi guess they put them there after the WHO announcement20:14
LjLalso i forgot i was going to see if nextstrain has any kind of RSS feed for anything20:14
de-facto"Dr Emma Hodcroft"  tweeted about them on her account https://twitter.com/firefoxx6620:14
LjLshe was the one who tweeted... what, about the mink virus, before?20:17
LjLno RSS anything from nextstrain. but on the other hand, i wasn't really sure what i'd be expecting to find one for20:19
LjLbut they have textual "situation reports", like this https://nextstrain.org/narratives/ncov/sit-rep/2020-08-14 which i guess could have an RSS feed. but this is actually the latest one20:19
de-facto%title https://www.gisaid.org/references/gisaid-in-the-news/mutations-in-spike-putatively-linked-to-outbreak-in-danish-mink-farm/20:22
Brainstormde-facto: From www.gisaid.org: GISAID - Mutations in spike putatively linked to outbreak in Danish mink farm20:22
dzho> i don't think this mutated virus will be gone any time soon :( so you will have plenty of samples around20:23
dzhowell, that's sort of the point of tracking things over time is that they *mutate* 20:24
dzhoso you only know how similar or different the thing you look at later is to the thing that happened earlier is if you sample earlier, or you sample broadly later and infer what the earlier thing might have looked like20:24
de-facto%title https://www.gisaid.org/references/gisaid-in-the-news/first-new-arrivals-of-hpai-h5-in-the-2020-2021-winter-in-the-eu/ <-- oh btw that website also may have other bad news?20:25
Brainstormde-facto: From www.gisaid.org: GISAID - First new arrivals of HPAI H5 in the 2020-2021 Winter in the EU20:25
dzhoLjL: ^^^ anyway sorry forgot to highlight you on that but since I quoted you I figure it's only fair to point it out20:27
LjLdzho, but we have the sequence, so if it mutates we're going to know that much20:28
LjLde-facto, does this happen every year?20:29
de-factoi am not sure, i have to admit i did not follow such news before this pandemic20:29
de-factobtw its a very informative website https://www.gisaid.org/20:30
de-factothey also state latest submissions "hCoV-19/Denmark/DCGC-6387/2020"20:31
de-factoso those are probably the 6k sequences Hodcroft was tweeting about20:32
LjL%title https://www.globaltimes.cn/content/1206008.shtml20:46
BrainstormLjL: From www.globaltimes.cn: No infections among 56,000 people who traveled abroad after receiving Sinopharm-developed COVID-19 vaccine: developer - Global Times20:46
LjLto parrot a redditor, it's not a phase 3 trial, but... i think it's also the first time we learn a vaccine is supposedly effective? like for real?20:47
CoronaBot04/r/coronavirus: Denmark is testing all 280.000 residents in the region where a mutated strain of Covid-19 from minks where found (Cluster-5) (10269 votes) | https://www.dr.dk/nyheder/indland/20000-nordjyder-skal-testes-i-weekenden-jeg-er-ikke-bange-men-svaert-ikke-blive-lidt | https://redd.it/jppsxc20:51
BrainstormUpdates for US: +1549 cases (now 10.1 million), +13 deaths (now 242774) since 18 minutes ago21:07
de-factoits the inactivated original SARS-CoV-2 pathogen: https://covidvax.org/covid19-vaccine/BeijingInstBio/Inactivated-Beijing-Institute-of-BioProducts-Sinopharm-Chinese-Center-for-Disease-Control-and-Preven21:16
LjLde-facto, those things generally tend to work, don't they? the problems being that they may fail to inactivate even if in rare cases, and then whoops?21:21
de-factowell the virus inactication is one of the "oldest" production techniques for vaccines, so i guess if it was that problematic it would not be done anymore21:22
de-factoof course the procedure would have to be done properly 21:23
BrainstormUpdates for US: +0 cases (now 10.1 million), +0 deaths (now 242875) since 5 minutes ago21:24
de-factoi would not thing that its too bad at all, especially because the production could also employ already existing facilities in third world countries that were established to produce other vaccines21:24
de-factoand also working with the "original" somewhat is a neat idea imho21:24
LjLde-facto, well, there is also issues of cost. for instance there are (at least) two types of polio vaccines, one is attenuated, the other is inactivated. the inactivated one mostly gets used in developed countries, the attenuated one gets used elsewhere in the world, and it works, but in rare cases, it can un-attenuate itself, and give you polio. currently (well, before COVID) polio vaccination was so widespread that, worldwide, there were more polio cases 21:25
LjLdue to the vaccine than "natural" ones21:25
de-factoim not sure, would those need adjuvants?21:25
LjLso why do they keep using the attenuated one in developing countries? because it's cheaper and specifically because the other one requires a cold chain.21:25
LjLi realize in this case i'm saying the "risky" one is the attenuated, not the inactivated one, but i'm just using it as an example to show that the criterion is not always just "the one that's safest and works best"21:26
de-factoidk if an attenuated vaccine from original pathogen could be made safe and stable and even applied to the original entry of infection e.g. in the case of SARS-CoV-2 to the nasal and pharyngeal mucus it might even be able to produce sterilizing immunity, e.g. prevent an infection completely (and also having infectious status thereby)21:27
de-factothat may be different for current first gen vaccines that are injected into the muscle, afaik its not really clear if they only prevent severe progressions or also are able to prevent infectious status 21:28
BrainstormNew from r/WorldNews: worldnews: Italy hits record 39,800 daily coronavirus cases → https://is.gd/MuBsCP21:28
LjLBrainstorm, thank you for the reminder21:28
de-factoafaik there are several viral vector (not with SARS-CoV-2 but some Adenovirus or such) in the pipeline that may be used via nasal stray21:29
de-factonasal spray21:29
de-factobut hey maybe some vaccines already can prevent infectious status, that would be great21:32
de-factoi mean they say "prevent infection" in that article you linked, but what exactly do they mean by that? 21:38
de-factohopefully that viral replication could be suppressed even in the upper respiratory tracts to such a degree that infectious status never was reached 21:39
de-factoif they just mean noone got sick it might be different from that though, and they admit there was disease among the not vaccinated employees there21:40
LjLde-facto, realistically i assume it's just going to mean they haven't reported symptoms. what else can you easily measure? you can't check if they have antibodies, obviously they do have antibodies. you can't run PCR because if they got it, it was a while ago and anyway who knows if PCR would detect virus that's also being suppressed by antibodies21:40
de-factoyes, thats why i think testing daily against the antigen (thei virus itself) in such studies should be done21:41
de-factojust to monitor if it ever is able to replicate in vaccinated hosts to a degree that they may reach infectious viral shedding threshold onto their environment21:42
LjLbut antigen tests aren't even as sensitive as PCR21:42
de-factobut they can detect concentrations of the virions that are considered infectious21:42
de-factoif it stays below that, great then vaccination and herd immunity may really work21:43
de-factoso antigen tests may be even better than PCR in this scenario, because the test should reveal if infectious status ever was reached for vaccinated21:44
de-factosomething that is as reproducible as possible, idk some standardized "dont eat, wait, gargle, spit onto the antigen test" procedure that also might employ some "tracer" (some molecule that always got a standardized concentration on mucus or such)  to calibrate for sample concentration21:46
de-factoi really think we need to attribute some part of our testing capacity to such screening efforts, this would be really valuable information21:47
de-factoat the end knowing such things may prevent far more infections (e.g. by choosing a vaccine that really can induce herd immunity) than that part of testing capacity could have prevented if used for normal testing21:49
de-factobut hey thats just my opinion, maybe the experts know better21:51
BrainstormNew from Medical Xpress: Iran daily virus infections exceed 9,000: Iran on Saturday announced a new record of more than 9,000 new cases of COVID-19 infections in the Middle East's worst hit country, as the government imposed new restrictions. → https://is.gd/TrUgHR22:04
de-factobtw what is the food of those mink farms in Denmark?22:22
BrainstormNew from CDC (old): Coronavirus [CoV]: Cases & Deaths by County → https://is.gd/yJtqEF22:23
de-factowhat did they feed their minks? was it excluded that this may have been the way the contagion was introduced into the mink population?22:23
de-factothey probably were fed with some sort of cheap meat, so from what source?22:25
de-factoasking because there are other animal populations also known to be able to reproduce SARS-CoV-2 pretty well, e.g. golden hamster (yeah well they wont feed the minks golden hamsters, but what instead?)22:27
LjLde-facto, Mink raised on farms primarily eat expired cheese, eggs, fish, meat and poultry slaughterhouse byproducts, dog food, and turkey livers, as well as prepared commercial foods.[14]22:31
LjLthat's quite a diversity22:31
de-factoi tried to google and it seems to be quite different depending on region22:32
de-factoprimarily i am curious because you said that they suspect transport of the pathogen between mink farms by unknown means, e.g. birds or such22:33
de-factoi would guess they excluded really obvious things like same workers on the affected farms22:33
de-factoso what else would they have in common? possibly their food supply chain22:33
de-factohmm were there any outbreaks in slaughterhouses recently in Denmark?22:35
de-factoor other farms or such?22:35
BrainstormUpdates for France: +21034 cases (now 1.7 million), +304 deaths (now 40169) since 14 hours ago — US: +17662 cases (now 10.2 million), +253 deaths (now 243128) since an hour ago22:35
de-factowould be interesting if samples exist for such potential sources to sequence them for comparison22:37
LjLde-facto, i'd say food is also a pretty obvious thing to exclude, but who knows22:37
LjLmaybe it's just not easy to exclude given the variety22:37
LjLde-facto, there were outbreaks in slaughterhouses elsewhere as you know and i don't think the cause of that has been sufficiently determined22:38
de-factoyeah they probably buy all cheap protein rich stuff and put them in cold storage or such22:38
LjLso i think your theory is not devoid of merit, but really i have no clue at this point22:38
LjLde-facto, what do you think of having a 25-hour window for Brainstorm's updates (apart from the fact that they aren't really working yet)? i think i'll run into problem with countries that provide daily updates (i.e. most) as opposed to many updates during the day if i make it strictly 2422:39
de-factohmm what are the usual patterns for the arrival of incidence chunks?22:40
LjLde-facto, in Italy it's always roughly at the same hour, but unless it's *always* a bit earlier than the previous day (which it clearly won't be), then a 24 hour window is bound to give bogus values22:41
LjLsome days it will just be zero22:41
de-factoafaik for the RKI data jitter may be more than one hour but they only would update once a day, so i just wait for fetching until i know they should be up to date22:41
LjLi don't know if there's a more elegant way to avoid this issue22:41
Skunnyhow do they test for covid? it's like a machine they put the sample in?22:42
LjLde-facto, i can't really do that, the bot has to work for all countries without adjustments for each of them22:42
BrainstormNew from CNBC Health: President-elect Joe Biden to announce Covid task force on Monday: Biden will not be sworn into office until Jan. 20, when epidemiologists and medical experts say the country could be in a dire situation with the pandemic. → https://is.gd/fXz8nS22:42
LjLSkunny, a sample and a bunch of reagents, but i'm really not sure on the details. i know that PCR involves "amplifying" the sample, which means that it's iterated many times until you are confident you will see a positive result if there is one22:43
de-factoLjL, hmm if you would know the update is only once a day you could "check" if the amount of plausible incidence came in roughtly 24h later22:43
LjLde-facto, i'm thinking i could also make it 24 hours but if the list becomes empty, then keep the last one, whatever it is. or i could just do that for every country: 24 hours + one sample from before22:44
LjLnah22:44
LjLbah, i don't know22:44
LjLit's not going to spit out results that actually match what's declared by the countries, because the window keeps changing22:44
LjLin a sense it doesn't have to. but it can be confusing22:44
de-factoSkunny, two pretty common methods are https://en.wikipedia.org/wiki/Reverse_transcription_polymerase_chain_reaction and https://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction 22:45
de-factoLjL, but offloop has incidence (e.g. daily new), is there any way to tell if the latest day is already "finalized"?22:47
LjLgod i have way too many RSS feeds for this channel, it takes more than 2 minutes to parse them all22:47
de-factofeedparser is slow22:48
LjLit really is22:48
LjLit has been a bane for years22:48
LjLthere is a new version of it for Python 322:48
LjL"one of these days" i will need to port the whole thing to Python 322:48
LjLideally before 2 stops being supported completely22:48
LjLde-facto, i don't think there is a clear way to know it's "finalized", which i think is pretty much why tinwhiskers removed the "live" data... also in my case i still definitely want to push out updates as soon as i have them (at least if they are significant by the criteria), so if Germany updates its data 10 times in a day, i will output a value 10 times in a day (only, before it would be "100 cases since 1 hour ago", now it will be "10000 cases since 24 22:50
LjLhours ago"), and i consider that a feature, because it's what differentiates the bot updates from just looking it up on any tracker once a day22:50
LjLanyway, for now i'm going "last 24h unless it's empty, in which case, whatever the previous one was"22:52
LjLwe'll see22:52
LjLit will still output "... since n hours ago" so one can differentiate22:52
de-factoyes but having the cases accumulated for same durations, e.g. one day they are much better comparable, e.g. 24h incidence22:52
dtruminteressanter Artikel zum Thema Metastudien zu Masken https://is.gd/PFEhEa22:53
de-factoits what i look upon every morning as soon as they are released by RKI22:53
LjLde-facto, when the country involved accumulates them and outputs them *once*, then no problem, the bot will just output that daily-accumulated total. but if it outputs partial totals many times a day, there's not much i can do (unless i handle it in a country-specific way) aside from taking all the updates that came within a certain window22:55
LjLwhich may or may not be the same as their accumulated total (pretty randomly depending on the time of day)22:55
de-factoLjL, could you know it yesterday is finalized? if so maybe you could remember the accumulated value for the point in time and report difference from that or such?22:55
tinwhiskersLjL: no, I removed the live data because the total from wordometers has significantly diverged from the JHU total that makes up the time series data, so it always looked like there was a HUGE spike in cases for the current day - like, REALLY huge.22:55
LjLtinwhiskers, but the CSV i get (not the covidly one obviously) has data from...?22:56
tinwhiskersyeah, worldometers22:56
tinwhiskersyou can enable the live data on offloop but it's pretty pointless due to this22:57
tinwhiskersi.e. I'm still collecting their data but only using it for you now.22:57
Skunnyde-facto thanks22:58
Skunnyyeah my test finally came back this morning22:58
Skunnypositive22:58
Skunnybut I knew that all ready22:58
Skunnyday 6 for me and I feel pretty good22:58
Skunnyjust the anosmia22:59
LjLtinwhiskers, i see. then de-facto i basically don't have any finalized data or any indication they are finalized... plus, the bot *mixes* the data from worldometers with the data from covidly (by using whichever is higher for any given place) and covidly already doesn't get daily data always in sync with how the countries output them22:59
LjLso really what i have is an inconsistently constant stream of "new totals" that has to be treated as a realtime sort of thing23:00
LjLit's not realtime, just there isn't a better way to treat it23:00
tinwhiskersthere's also a few other sources in the data you get for Italian, canadian, US regions. It's a bit of a cluster...23:01
LjLtinwhiskers, indeed, and for some regions (italian ones) i have my own table that translates names used by one csv into the ones used by the other csv, but in some cases they may still differ, so it's loads of fun23:02
de-factoSkunny, very glad to hear you are doing so well :)23:02
tinwhiskersthose regions tend to be daily, worldometers is several times a day and covidly is... *shrug*23:02
LjLtinwhiskers, i think what i'd actually want to do if i feel like doing something that isn't just patching the code i have, is to use Li, the local data scraper with a cleverly googleable name23:02
LjLthis guy https://github.com/covidatlas/li which is the offspring of daily-updated-but-deprecated https://coronadatascraper.com/23:03
tinwhiskersah23:03
tinwhiskersyeah, I'd do things quite differently if I revisited it now :-/23:04
tinwhiskersalthough I'd probably still download the entire dataset rather than do it ajax-style because I really like the snappy switching between countries, at the cost of loading time.23:05
de-factohow does the upstream get daily incidence in sub-daily chunks? just polling on the latest data?23:05
tinwhiskershowever, that becomes less tenable over time23:05
tinwhiskersde-facto: I poll every 15 minutes23:05
BrainstormUpdates for US: +21407 cases (now 10.2 million), +271 deaths (now 243146) since an hour ago23:06
de-factodo they have any indicators for having a day complete? e.g. even implicitly like not touching data if the associated date is more than 24h in the past?23:07
tinwhiskersno23:07
tinwhiskerswell, not that I noticed23:07
de-factoasking because if there is any point in the past where one could "timestamp" the state one could use that as reference point and subtract it from the current accumulated latest case numbers and divide by the duration since that point23:08
LjLde-facto, at the end of the... day... there is really nothing that determine what counts as a "finalized day" except what the government decides. the federal government gets data from the states at likely different times, and they just decide that they publish the daily tally at 18:00 or whatever23:08
tinwhiskersI guess you could look for changes in the data for "Yesterday" to tell when the day ends.23:08
LjLde-facto, we have timestamps that come with the data, but they are not always reliable23:09
de-factoyes like remember yesterday and look if its still the same, and if so assume it wont change anymore?23:09
tinwhiskersyeah23:09
LjLde-facto, plus yeah i could divide by the duration, but i'd still get very different results from the official ones, even if the timestamps were accurate23:09
LjLwhat is "yesterday"23:09
tinwhiskersworldometers has another table for data for "yesterday"23:10
LjLi deal with UTC, but countries may give their official data in their local time23:10
LjLand then yesterday is not the same yesterday23:10
CoronaBot04/r/coronavirus: Biden announcing COVID task force on Monday (11248 votes) | https://www.axios.com/biden-to-announce-covid-19-task-force-monday-23b353bd-863b-4e0f-bb64-c6da4a5758b2.html?utm_source=twitter&utm_medium=social&utm_campaign=organic&utm_content=1100 | https://redd.it/jpv8o723:10
rpifanok and23:10
rpifanwhat can he do23:10
rpifanhe must wait till january to do anyhting23:10
tinwhiskersright, but presumably they only update "yesterday" at the end of whatever day cut-off time they have.23:10
LjLtinwhiskers, in the case of covidly, i've verified the cutoff does *not* match the cutoff used by the individual countries23:11
tinwhiskersah. right. ok23:11
de-factobut countries always should use the same timestamping scheme i guess23:11
LjLwhat do you mean23:11
de-factolike they stick to their usual procedure with accounting case numbers to their local time or such23:11
LjLultimately i don't care if my "day" is not the same as the country's official "day" if not for the fact that people will ask "wait, why is the number different from the one i heard on TV?" - even though the number is different but equally valid23:12
LjLde-facto, yeah but there are 200 countries or so in the world, i can't look up what each of them does and tune the bot accordingly, and then do the same for all the separately-counted subregions23:12
de-factothe more important thing would be to get it somewhat jitter free, like if someone ask the bot every morning about the latest data remembering the incidence from yesterday for comparison23:13
LjLthat is what Jigsy does manually by knowing the times at which to ask for the UK :P23:13
de-factono i dont meant to tune accordingly, i just meant their upstream behaviour somehow should be constant23:14
de-factohehe indeed23:14
LjLi also eyeball the data for Italy. i know that Italy outputs once a day, so it's easy23:14
de-factoi always look at https://corona.rki.de/ and they display a warning if data is not "finalized" but to be honest sometimes they did not display the warning and still did change the number slightly23:15
de-factoso its not easy it seems23:15
LjLGermany is hard, i get data scattered out all over the day. which is good in a sense, because it means there is a constant stream of data from the states, which is... good?23:16
LjLhard to handle, but good in terms of having a stream of data that's updated often with fresh cases23:16
de-factoso how about choosing a point in time and "timestamping" it there, then accumulate for next 24h and timestamp again? if it comes in small chunks it should be somewhat accurate (hopefully), if it comes one a day one might need a "checklist" around the expected update time for timestamping it into "finalized"23:19
LjLde-facto, i think it makes sense to do the "divide by timestamps to get the closest possible to 24h" in the manual %cases command. right now, it only gives totals, but with this history i am now keeping of the past 24 hours, it should be able to do that. so if you call the command manually you would get a daily tally that's sort of artificial, but freer of jitter23:19
BrainstormNew from "Cluster 5" on Wikipedia: ViperSnake151: /* Timeline */: Timeline ← Previous revision Revision as of 22:11, 7 November 2020 Line 12: Line 12: As a preventative measure, Frederiksen announced that the country was already in the process of [[Animal slaughter|slaughtering]] all mink in Denmark—as many as 17 million. {{Cite [... want %more?] → https://is.gd/74bzDF23:19
BrainstormUpdates for US: +24162 cases (now 10.2 million), +294 deaths (now 243169) since 2 hours ago — Canada: +766 cases (now 259220), +17 deaths (now 10498) since 2 hours ago23:20
de-factoprobably would have to try and look at the amount of jitter? its kinda hard to tell how bit it may be23:20
de-factohow big the jitter might be23:21
de-factoproblem is if it comes in middle-sized chunks that have big temporal fluctuations in reporting, then jitter may be quite large23:22
de-factoproblem with current implementation is, 24k for US since 2h ago, how to know what that means? did it increase or decrease? by how much?23:24
LjLyes, i know23:25
de-factohaving the most current data and having it comparable to the previous days is really hard as can be seen by all the portals23:25
LjLbut it has the advantage that if you're following the US like a hawk, you'll get the latest update and you'll remember the previous one and you'll get a sense of it23:25
LjLif you're just sometimes looking casually, then you won't23:25
LjLbut the more i elaborate the data (like by dividing and making it proportional to exactly 24h), but more i get away from the "raw" data23:26
de-factoi could not remember the accumulated number for yesterday, but i would somewhat remember: ah yeah it was about +20k cases yesterday23:26
LjLwhich means the human can pay less attention but the bot really must do it correctly for it to make any sense23:26
LjLde-facto, as you say, if the day is not finalized, you pretty much can't compare it to previous days. you can divide and get a proportion but the jitter *is* large because no country outputs data every two minutes23:27
LjLi think the only way to get around that would be to make a smoother average... but ugh, within a single day? that's ugly and potentially misleading23:27
LjLon offloop when i select a smoother average (and it's over several days, not one) i do it because i want to, it doesn't do it for my by default23:27
LjLtinnitus galore23:29
Skunnytinnitus!23:30
de-factowell average for the edge is the value itself afaik23:30
de-factobecause future is unknown, so without extrapolation there is no average for most current data point23:31
LjLSkunny, yes, an obnoxious little beast23:31
LjLde-facto, no but you can do (most_current-previously_current)/(t_most_current-t_previously_current) * 3600*24 and if i'm not mistaken that should sort of make sense, but it's still jittery depending on the data23:32
SkunnyI have that for long time from playing in bands and going to shows23:33
de-factohow about just to use the date timestamps? accumulate for latest timestamp, accumulate for timestamp a day ago always with the latest updates, then call those today and yesterday23:33
Skunnyit sucks23:33
LjLSkunny, i've had it for about 3 years, i really can't just resign myself to having it. i wear a white noise machine around with me when i'm indoors all the time, but sometimes it's not enough to beat it, like now23:34
de-factoLjL, yeah or that linear extrapolation, would become more accurate with each update for that timegap then23:34
LjLi *hate* it when the white noise machine turns itself off (due to batteries or something) and i get to hear the full force of the thing. i just don't want to hear that, it ruins my mood every time to realize how obnoxious it is23:34
LjLde-facto, just using the date will mean using 0:00 UTC as a threshold. it will match official data for the UK and Portugal, but beyond that... :P23:35
BrainstormUpdates for US: +26320 cases (now 10.2 million), +311 deaths (now 243186) since 2 hours ago23:36
de-factoLjL, i mean what date will end up as daily incidence in the far past?23:36
de-factothe date inside the dataset i meant23:36
LjLfar past? i'm definitely not looking at the far past in the bot23:36
LjLi'm a bit confused23:37
de-factono i meant the dataset contains dates and at some point in the past the daily numbers will not change anymore, like patches to daily new infections a week ago probably wont happen anymore, but for today's date numbers will change every few minutes or such23:38
LjLi don't have changes to past data23:38
LjLmany countries don't do that23:38
LjLbut even for countries that do do that, i don't have that23:38
LjLthe data i get are always for "closest to the current time"23:39
de-factoyeah hence how about just using the date in the dataset itself and see if jitter is a problem 23:39
LjLthat could change if i started using data from Li, or elsewhere, i guess, but that's what it is now23:39
LjLbut i do that23:39
LjLthe dataset comes with a timestamp for the data point, and i use that timestamp23:40
LjLthat timestamp is the date, i have no other date23:40
LjLalso thanks to this history i'm keeping, and the way i'm keeping it, i now have circular references in my python and i'm not sure that's a good thing ;(23:41
de-factoah i see its unixtime, i hoped for a date like 2020-11-0723:41
de-facto"LastUpdated" and not "ReportedOn"23:42
LjLyou see there is no delta, it's just the total accumulated number of cases by the time of LastUpdated23:43
de-factoyeah my mistake, i did not look at the dateset before23:43
LjLany delta is only inside my code23:43
de-factoyeah23:43
de-factobut where does the incidence data for offloop come from then23:43
LjL(and that's really ugly because at first i had no delta at all, i only considered the %cases snapshot use case)23:43
de-factothey clearly have daily granularity for that data23:44
LjLde-facto, jhu, or covidly if you select alternate23:44
LjLand jhu and covidly's daily granularity doesn't even work the same, so you may end up with different but equally valid daily numbers in each of them :P23:44
JigsyHm?23:45
LjLJigsy, discussing how to change Brainstorm's output for more usable results23:49
de-factowhat i mean is that offloop.net is able to display the daily cases for yesterday (incidence or accumulated), so assuming that will remain constant once could take it as a reference point: take the difference from it to latest updated numbers (both cases and lastUpdated time) and either report that directly (since x hours ago with x<24) or even do your linear extrapolation (should be somewhat accurate)23:50
de-factoi am not sure that yesterday incidence is included in the endpoint you are using though, maybe its only in the HTML?23:51
BrainstormUpdates for US: +26921 cases (now 10.2 million) since 2 hours ago — Switzerland: +18 deaths (now 2749) since 7 hours ago23:51
LjLoh some output at last23:51
LjLde-facto, yeah only in the HTML23:51
LjLthe output it gave now looks much like the output it always gives, but that's (hopefully) just because it hasn't accumulated much history yet23:53
de-factobut where does that granularity originate from? upstream or offloop?23:53
LjLupstream for jhu, for covidly i'm not sure23:54
LjLanyway i am really tempted to play with https://github.com/covidatlas/li23:54
LjLit has subregions for a number of countries *and* i can fetch as often as i want until i get banned23:55
de-factobecause somehow you would have to get your grip at that granularity to be able to use latest granular datapoint as reference for latest update extrapolation 23:55
CoronaBot04/r/covid19: Humanized COVID‐19 decoy antibody effectively blocks viral entry and prevents SARS‐CoV‐2 infection (83 votes) | https://www.embopress.org/doi/abs/10.15252/emmm.202012828 | https://redd.it/jprhnd23:58
de-factonice also for cluster 5?23:59

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