libera/##covid-19/ Sunday, 2020-11-08

LjLi don't think that question will get an answer any time soon...00:04
BrainstormUpdates for US: +33284 cases (now 10.2 million), +341 deaths (now 243216) since 2 hours ago00:05
de-factoto be honest I would prefer if that question would become irrelevant soon00:12
LjLeh00:14
BrainstormUpdates for US: +33430 cases (now 10.2 million), +348 deaths (now 243223) since 3 hours ago00:20
BrainstormNew from "Cluster 5" on Wikipedia: Rich Farmbrough: /* Timeline */: Timeline ← Previous revision Revision as of 23:31, 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/74bzDF00:35
BrainstormUpdates for Canada: +1601 cases (now 260055) since 3 hours ago — US: +33685 cases (now 10.2 million), +351 deaths (now 243226) since 3 hours ago00:36
BrainstormUpdates for US: +33923 cases (now 10.2 million) since 3 hours ago00:50
BrainstormUpdates for US: +34520 cases (now 10.2 million), +353 deaths (now 243228) since 3 hours ago01:06
ryouma%cases bhutan01:16
Brainstormryouma: In Bhutan, there have been 358 confirmed cases (0.0% of the population) and 0 deaths (0.0% of cases) as of 3 days ago. 180939 tests were performed (0.2% positive). See https://offloop.net/covid19/?default=Bhutan for time series data.01:16
BrainstormUpdates for US: +38244 cases (now 10.2 million), +370 deaths (now 243245) since 4 hours ago — France: +21774 cases (now 1.7 million) since 17 hours ago — Netherlands: +2 cases (now 404403) since 9 hours ago01:20
LjLi think the updates are a little too frequent now but if i make them less frequent this thing won't work ugh01:35
LjLthe code really is crap01:35
BrainstormUpdates for France: +62981 cases (now 1.7 million) since 17 hours ago — US: +38425 cases (now 10.2 million), +372 deaths (now 243247) since 4 hours ago01:36
LjLi don't even know if that number for france is a sign of a bug in the new mechanism, or they really have such crazy numbers01:36
LjL%cases france01:37
BrainstormLjL: In France, there have been 1.7 million confirmed cases (2.6% of the population) and 40169 deaths (2.3% of cases) as of 3 minutes ago. 17.7 million tests were performed (9.9% positive). See https://offloop.net/covid19/?default=France for time series data.01:37
LjLit's probably real ;(01:38
LjLgood lord01:38
LjLat least belgium is slowing down a little bit01:39
LjLlook at that, de-facto https://offloop.net/covid19/?default=France;Italy;Belgium&byPopulation=yes01:39
LjLthe curves are fairly different01:39
LjLbut we're converging to the same doubling time01:39
de-factoyes i have seen that already, Belgium peaking at end of Oct and reversing incidence, hopefully thats a solid trend01:41
LjLbut aside from belgium, you were always puzzled at similarities across europe despite differences in weather and lockdowns etc01:42
de-factothey have been hit extremely hard, i really hope they can get ontop of it again01:42
LjLconverging doubling times looks like a possible other one01:43
LjLyeah01:43
de-factoyes indeed they are converging01:43
tinwhiskersI think I should remove doubling times. They don't work properly except for first peak.01:44
LjLoh01:44
tinwhiskersI mean it's done correctly. It's just a flawed method to look at data with multiple peaks.01:45
de-factohow about taking doubling times from incidence (daily new cases)?01:45
tinwhiskersI'm not sure. It took me a while to figure out it doesn't work right. I'd need to tinker with that and see what happens.01:46
CoronaBot04/r/covid19: Declines in SARS-CoV-2 Transmission, Hospitalizations, and Mortality After Implementation of Mitigation Measures— Delaware, March–June 2020 (82 votes) | https://www.cdc.gov/mmwr/volumes/69/wr/mm6945e1.htm | https://redd.it/jpusli01:47
de-factoafaik the doubling times for incidence in Germany were around only 7 days or such in the last few days (maybe they are on the raise, hopefully)01:47
de-factoso maybe just take the algo and use it on incidence (daily new cases) directly=01:48
tinwhiskersmaybe01:48
de-factoor maybe if you have a smoothed Reff = sum(past week) / sum(past week delayed by serial time 4 days)    one could use t_double = t_serial ln(2) / ln(Reff)01:49
BrainstormUpdates for US: +38628 cases (now 10.2 million) since 4 hours ago01:50
de-factothat last equation coming from solving for t in   Reff^(t / t_serial) = factor   hence t = t_serial * ln(factor) / ln(Reff)  with factor=2 hence t=t_double01:52
de-factook more like 9.2 days = 4 days ln(2) / ln(1.35)01:53
de-factopossibly first shy signs of success may be seen at http://metrics.covid19-analysis.org/01:55
de-factoR_Ireland = 0.72, R_Belgium = 0.74, R_Netherlands = 0.88, R_CzechRep = 0.98, R_Slovakia = 0.97, R_Slovenia = 0.9, R_Iceland = 0.6301:58
de-factoso hopefully this is not only a short term picture but maybe the shy start of the begin of a trend01:59
de-factohttps://offloop.net/covid19/?default=Belgium;Netherlands;Czechia;Slovakia;Ireland;Slovenia;Iceland&byPopulation=yes&cumulative=no&smooth=yes&miscType=Reff02:03
de-factoi mean for an edge effect it lasts too long, look at Reff it goes below 1 for all of them on the timeline02:06
BrainstormUpdates for US: +38766 cases (now 10.2 million), +373 deaths (now 243248) since 4 hours ago02:07
de-factothat would give hope that it can be controlled02:07
de-factotbh i am a bit worried when i see crowds gathering02:18
de-factohopefully they are careful and keep distance to each others02:20
BrainstormUpdates for US: +43512 cases (now 10.2 million), +382 deaths (now 243257) since 5 hours ago02:21
de-factobecause in US incidence is going up exponentially too with R=1.2 and on the raise02:25
BrainstormUpdates for Canada: +2160 cases (now 260614), +26 deaths (now 10507) since 5 hours ago02:35
BrainstormUpdates for New Zealand: +6 cases (now 1982) since a day ago02:51
tinwhiskers^ 5 news cases in quarantine and 1 community case. r'oh roh.02:54
tinwhiskersA Covid-infected quarantine worker in Auckland is thought to have infected another person who then travelled to Wellington, but the Health Ministry is currently advising no change to alert levels.02:55
tinwhiskersOfficials are now asking all people sitting within two rows of the worker to get tested and to isolate until November 19. All of their household contacts are also being asked to isolate until the contact on the flight tests negative.02:55
BrainstormNew from r/WorldNews: worldnews: Two New Zealand Defence Force Employees, one civilian, one in uniform test positive for Covid-19. Entire Defence Headquarters to be deep cleaned, all staff to work from home for 7 days. → https://is.gd/tkpw5v02:55
ryoumaso letting it sit for 7 days is not enough02:56
tinwhiskersBrainstorm has a curious habit of reading people's minds.03:02
LjLtinwhiskers, Brainstorm is one giant kludge - just like our brains03:13
tinwhiskersheh03:13
LjLsorry about your destination land, though. hopefully they'll squash it for the nth time03:13
LjL"Entire Defence Headquarters to be deep cleaned" ← how is it that countries that are mostly successful at squashing it do things that other countries, like mine, barely do... let our minds go back to the mysterious sprayings of disinfectant(?) in China, Korea and elsewhere03:17
LjLbut in the west we just say fomites are probably not important, nah, there's like no study confirming it, so not important03:17
LjLetc03:17
tinwhiskersyeah, an abundance of caution doesn't seem to hurt. 03:23
BrainstormNew from StatNews: Biden promises to roll out a Covid-19 task force on Monday: In a pandemic-heavy victory address, Biden promised to name a panel of Covid-19 advisors on Monday. → https://is.gd/bsog8u03:23
de-factowell it has many ways to be transmitted it always depends on the situation, if many people currently have it in high prevalence regions fomites probably are the biggest contributions, but if prevalence is very low other transmission paths also may play a role, such as surface contamination that may last long times, especially when people touch surfaces and then their face or such03:24
de-factoyeah Biden said "On Monday i will name a group of leading scientists and experts as transition advisors to help take the Biden Harris COVID plan and convert it into an action blueprint that will start on January the 20th 2021. That plan will be build on bedrock science, it will be constructed out of compassion, empathy and concern, I will spare no effort, none, or any commitment to turn around this pandemic."03:24
LjLde-facto, fomites *are* surfaces :P03:25
de-factooh yeah i meant aerosol transmission for high prevalence and surfaces becoming significant contributions on lower prevalence03:27
de-factoi am not a native English speaker :P03:28
de-factoi heard in a podcast that they stated in somewhat high prevalence regions being extremely pedantic about hand hygiene could safe 16% of incidence03:33
de-facto%title https://pubmed.ncbi.nlm.nih.gov/16553905/03:37
Brainstormde-facto: From pubmed.ncbi.nlm.nih.gov: Handwashing and risk of respiratory infections: a quantitative systematic review - PubMed03:37
de-facto"Results: All eight eligible studies reported that handwashing lowered risks of respiratory infection, with risk reductions ranging from 6% to 44% [pooled value 24% (95% CI 6-40%)]. Pooling the results of only the seven homogenous studies gave a relative risk of 1.19 (95% CI 1.12%-1.26%), implying that hand cleansing can cut the risk of respiratory infection by 16% (95% CI 11-21%)."03:37
de-factothat is where CDC refers to, but its from 2006 and they say studies could be improved03:38
BrainstormUpdates for Netherlands: +1669 cases (now 406070), +15 deaths (now 7975) since 12 hours ago03:51
BrainstormNew from The Indian Express: World: Joe Biden announces 12-member task force for coronavirus response → https://is.gd/jw2RCF04:01
BrainstormUpdates for Canada: +2161 cases (now 260615) since 8 hours ago04:50
LjLde-facto, they keep telling us to wash our hands, i don't know how more pedantic it could get05:04
LjLsome people are careless and will probably keep being careless no matter how many time TV says "wash your hands"05:04
BrainstormUpdates for Belgium: +6124 cases (now 494168), +199 deaths (now 12907) since 22 hours ago05:06
de-factoyeah hand hygiene is important but obviously the other 84% transmission for respiratory diseases should be targeted first 05:06
de-factoyet i have to admit i do sanitize door handles with ethanol on regular basis05:07
de-factoif they would hand out FFP2/3 masks to everyone it probably would have a much bigger impact05:09
tinwhiskersde-facto++05:10
tinwhiskersget manufacturing ffs05:10
tinwhiskersthis needs to be treated as a wartime effort, not all this pantsing about05:11
tinwhiskersspend what needs spending to knock it on the head05:11
LjLnooooooooooooo but the economy05:11
de-factoindeed its really about manufacturing, it can be scaled with machines and does not require humans (e.g. like medical personal for ICUs or such)05:11
de-factotinwhiskers, exactly 05:12
ryoumai read that the machines are a big deal.  possibly gov needs to guarantee that there will be enough purchased.  05:12
tinwhiskerswell, that's bullshit05:12
tinwhiskersnot to put too finer point on it.05:13
tinwhiskersbut I think you may be right in that that is their reasoning05:13
ryoumawell they were saying that they would not purchase machines becasue they take a year to set up and they are not sure th pandemic will still be around for long enough05:13
ryoumai am just reporting what i read05:13
tinwhiskersany developed country could be making masks and it doesn't matter one iota if they will not be used after the pandemic is over.05:13
tinwhiskersIf this was war you can be damn sure they would have masks in production by now.05:14
LjLnot sure it'll still be around, ah the naivety05:14
LjLit'll be around for fucking years, if not decades, especially if they don't do this stuff05:15
ryoumawe are conflating gov with industry05:15
tinwhiskersEngland produced millions of chemical weapon grade masks in no time flat05:15
ryoumain the us there were no such guarantees05:15
tinwhiskersthe only reason is that it is not being taken seriously enough05:15
de-factoi can not imagine it would take a year to setup industrial manufacturing of FFP2/3 masks, what would take so long? If enough money is investigated it why would it not be possible to have something up and running in weeks? 05:16
ryoumawell it was a decently thorough article with quotes and stuff i wish i had it to post05:16
tinwhiskerssufficient money and manpower would have production up in no time. they are not *that* complicated.05:16
de-factoanyhow it taking time would not be a reason to postpone it anyhow, quite the contrary actually05:17
tinwhiskersright05:17
ryoumaright.  which is where the guarantees come in.  they might be rent seeking OR they might be right.  but if they were rent seeking they'd eventually in places like the us just purchase the machines you would think if their argument is false.05:17
tinwhiskersyou don't need any guarantees. you spend the money to win the war.05:18
ryoumawe are conflating gov with industry05:18
ryoumauntil jan 20 in the us there will be no gov05:18
tinwhiskersit doesn't make any difference. 05:18
de-factoin the lucky case the pandemic would be over by then (i doubt it to be honest), they would have achieved local production of PPE, so that should be mandatory anyhow05:18
ryoumade-facto: right05:19
tinwhiskersif you approach it like a wartime effort the government oversees production using current industry to build whatever is needed and pays a reasonable amount to do that.05:20
de-factoon the other hand if they make production start in time and can scale the investment will safe a LOT of money, many orders of magnitude payback imho05:21
tinwhiskersyou don't ask nicely for people to make bids. You appropriate the necessary machinery from where it exists and you get to work.05:22
de-factothey would not even have to be perfect at first, just widely available as soon as possible05:22
de-factoyep05:22
ryoumawell i recommend reading about it in a little detail if possible if you are inteerested.  wish i could give you a link.05:25
tinwhiskersI think some people have no concept of what a government can do if they *really* want to win05:27
ryoumabut why are we talking about this now and not in february05:27
tinwhiskersexzactly05:27
tinwhiskerswhere are the masks? They could be in mass production by now had sufficient effort been made.05:27
ryoumathe article had specific numbers05:29
BrainstormNew from r/WorldNews: worldnews: COVID-19 drug and vaccine patents are putting profit before people → https://is.gd/vsiAgq05:34
tinwhiskersThe hardest part is the melt-blown fabric. China made a second melt-blown fabric factory in March. Where are ours?05:35
ryoumai was trying to tell you there are investigatios into that05:35
tinwhiskerseverything else is easily produced by using and retooling existing industry05:35
LjLi think there is also the fact that many governments seem to perceive "simple" surgical masks as sufficient05:38
tinwhiskerstrue. It's a damn shame we didn't step up.05:39
LjLwith the problem, at least in italy, that the definition of what counts as a surgical mask has really degenerated into any piece of fabric you can put on your face05:39
LjLbut if everyone wore surgical mask, it would probably suffice... IF this disease only spread via droplets, as was repeated ad nauseam05:39
LjLbut it doesn't, i'm pretty sure this disease is fully airborne, but try to tell governments that05:40
LjL"not being measles" doesn't automatically reduce it to just being big ball of nice spat out mucus05:40
gigasu_shidait seems like they think cotton cloth is good enough05:42
tinwhiskersthe way wartime governments rose to manufacturing challenges was frankly amazing and we could really learn a thing or two. You don't need a single company to make a new melt-blown fabric plant in 6 months. You break the job down into massively parallelised parts and get get industry as a whole to work on the job. It's a big logistics and management job and you get work done in weeks instead of months.05:43
ryoumasound slike you have your new position planned out05:44
ryoumadirector of logistics05:44
de-factoafaik China does things like that, and i heard several times that that is the main reason production in China cant easily be done elsewhere: the extremely fast supply chain, they just go ahead and make it happen, no long discussions or such05:48
tinwhiskersyes, if it takes a state of emergency to be able to mandate such things then that's what should have happened.05:48
tinwhiskersthe military are really good at that stuff05:49
de-factoi mean come on its not rocket science05:50
tinwhiskersright. You get the right logistics teams together and give them the authority to do what is required and stuff can happen fast.05:51
tinwhiskersit's a bit different where research is required but for manufacturing using known processes it's just breaking the work down and allocating out the right jobs to the right people.05:52
de-factoits all about making decisions about a proper aggressive strategy in advance, not reacting after the fact as most governments seem to do05:53
tinwhiskersmmm05:53
de-factoproducing the fabric can not possibly be that difficult, get some polypropylene make fibers out of it, make fabric out if that, charge it electrostatically and heat stamp a mask out of it. can that be that difficult?05:55
tinwhiskersit required specialised machinery to get it right05:55
tinwhiskersyou do need to make that machinery05:55
de-factoif patents are involved, seize them.05:55
tinwhiskerssure05:55
gigasu_shidatinwhiskers: can i ask you a medical question privately05:58
tinwhiskersumm. I guess, but I am not any sort of doctor05:59
gigasu_shidaoh ok nvm06:00
gigasu_shidai thought you were06:00
BrainstormNew from This Week In Virology: TWiV 679: Mink, mutation, and myocytes: Daniel Griffin provides a clinical report on COVID-19, Slovlakia’s plan to test all adults for SARS-CoV-2 infection, viral variants arising in Danish mink and their potential threat to humans, why it is unethical to carry out challenge trials, Nipah virus dynamics in bats and [... want %more?] → https://is.gd/jrwDCY06:11
de-factoi really hope the gathering and celebrating in US does not cause a spike06:57
Skunnyit will06:58
de-factoits outdoors but i have seen people saluting and drinking without masks, some seem to distance but others are densely packed crowds (e.g. in front of WH) and it probably is a nationwide phenomena, not only an isolated demonstration at one location or such07:01
de-factobtw probably very interesting "This week in Virology" above07:06
de-facto"Daniel Griffin provides a clinical report on COVID-19, Slovlakia’s plan to test all adults for SARS-CoV-2 infection, viral variants arising in Danish mink and their potential threat to humans, why it is unethical to carry out challenge trials, Nipah virus dynamics in bats and spillovers into humans, and direct cardiac damage by spike-mediated cardiomyocyte fusion."07:06
de-factoSo assuming an IFR~0.5% with daily ~960 fatalities, USA would have had 960/0.005 = 192k cases ~14 days ago, reported were around 70k cases at 25th Oct, so something like 2.7-fold?07:16
de-factomeaning current ~110k cases really would be more like 302k cases per day?07:17
de-factothats crazy07:17
de-factothat would be daily ~1/1010-th of the entire population or 0.099% daily07:20
tinwhiskersWhat will it be by the start of January?07:21
de-factowell that is hard to estimate, but assuming current R=1.2 one could extrapolate07:22
tinwhiskersI was just thinking you'd use the 2.7-fold figure every x days07:25
de-factoe.g. N(t) = N0 R^(t/t_serial) with N0=110k and t_serial=4 it would be 53 days till end of the year hence 53/4=13.25 serial times or a 1.2^13.25=11.2-fold of current 110k daily cases, that already would be daily 1.2M, quite unrealistic that this might be allowed07:25
de-factoso taking the 2.7 fold of that it would mean daily 3.3M cases at the end of the year07:26
de-factoi doubt that this would manifest itself like that, it would be completely insane, people would not allow for that07:27
tinwhiskersmaybe...07:27
tinwhiskersOh. 3.3 million per day??07:27
de-factoyeah07:27
tinwhiskersOh07:27
tinwhiskersWell that would make herd immunity feasible :-/07:28
de-facto11.2 fold of todays incidence with R=1.2 in 13.25 serial times (end of year)07:28
de-factothat would be 25.3M additionally accumulated cases until end of the year in USA07:30
de-factotaking the 2.7 fold of that would be real 68.31M additional until end of year07:32
de-factoso taking current 10.2M 2.7 = 27.5M and adding those 68.3M would give a total of 95,8M real cases until end of year07:35
de-factowith a population of 328.2M it would be like ~29% or such07:35
de-factoso not really heard immunity if that even is a thing07:36
de-factowith a portion p = 1 - 1/R0  immune at endemic it would mean R0 = 1 / (1 - p) = 1 / (1 - 0.3) = 1.4 thats unrealistic low07:38
de-factoreal R0 would be more like 2-507:38
de-factoso assuming a best case of R0=2.5 would give p=0.6 hence 29% would be around half the way to that07:40
BrainstormNew from r/WorldNews: worldnews: Coronavirus: Sweden keeps its laid-back COVID-19 strategy → https://is.gd/XkXvmL07:44
de-factoso for USA a portion of p=0.6 would have had the infection in 72 days from now at 19th of Jan 2021 when R=1.2 and t_serial=4 days with a 2.7-fold of currently reported incidence (e.g. meaning a CFR or 0.5%)07:47
de-factobut that makes one BIG and unrealistic assumption: that parameters are not changing at all, yet they will change07:48
de-factoso such longterm projections get exponentially inaccurate with time07:48
de-factomaybe they might be accurate for 1-2 weeks from now, but not months, e.g. end of year or even into Jan07:49
de-factoso it might be fun to play with numbers, but those are not real predictions, only some calculations about "what if...?"07:49
de-factobtw with a serial time of t_serial = 4d and R = 1.2 incidence in USA would double each t_double = t_serial * Log[2]/Log[R] =  4d  Log[2]/Log[1.2] = 15.2 days07:55
Skunnyfeeling good guys08:16
Skunnyhad some food and almsot tasted it08:16
BrainstormNew from Medical Xpress: Doctors fear more death as Dakotas experience virus 'sorrow': With coronavirus cases running rampant in the Dakotas and elected leaders refusing to forcefully intervene, the burden of pushing people to take the virus seriously has increasingly been put on the families of those who have died. → https://is.gd/CDedJ208:21
tinwhiskersde-facto: yeah. Interesting08:30
BrainstormNew from Medical Xpress: France virus death toll tops 40,000: official: The number of people in France who have died from coronavirus topped the 40,000 mark on Saturday after 306 new fatalities were reported in the past 24 hours, the health authorities said. → https://is.gd/M8ptyM08:31
de-factoSkunny, very glad to hear :)08:33
BrainstormNew from Medical Xpress: Biden vows immediate, science-based action on virus: President-elect Joe Biden vowed Saturday immediate action to contain the United States' coronavirus crisis, signalling science would dominate the national response once Donald Trump leaves the White House. → https://is.gd/YRcKWJ08:40
BrainstormNew from Medical Xpress: Delhi fears the worst amid smog cloud and coronavirus wave: A steady stream of patients is coming out of New Delhi's brownish atmosphere for treatment at the Breathe Better clinic, where lung specialist Davinder Kundra is confronting what he calls the "double whammy" of deadly smog and the coronavirus. → https://is.gd/vT0u1e08:49
BrainstormNew from "Cluster 5" on Wikipedia: Alexcalamaro: Adding short description: "Outbreak of a mutated variant of the SARS-CoV-2" (Shortdesc helper): Adding short description : "Outbreak of a mutated variant of the SARS-CoV-2" ( Shortdesc helper ) ← Previous revision Revision as of 10:34, 8 November 2020 Line 1: Line 1: + {{short description|Outbreak of a [... want %more?] → https://is.gd/74bzDF11:36
BrainstormNew from BBC Health: Coronavirus: Hauliers included in Denmark restrictions: Rules for travel from Denmark were tightened after a coronavirus strain spread from mink to humans. → https://is.gd/UHPmCi11:55
BrainstormNew from r/WorldNews: worldnews: UK Covid vaccine taskforce head 'charging taxpayer £670,000 for PR consultants' → https://is.gd/YuDUtk12:51
BrainstormNew from StatNews: Opinion: A national Covid-19 vaccine confidence project: job No. 1 for President-elect Biden: The country needs to address the greatest sources of vaccine hesitation: the speed of the development process, potential side effects from the vaccine, and politicization of the process. → https://is.gd/ACeD0X13:09
CoronaBot04/r/covid19: Emergence of zoonoses such as COVID-19 reveals the need for health sciences to embrace an explicit eco-social conceptual framework of health and disease (82 votes) | https://www.sciencedirect.com/science/article/pii/S1755436520300347 | https://redd.it/jq9rtu14:02
CoronaBot04/r/coronavirus: Texas Becomes First U.S. State to Exceed 1 Million Coronavirus Cases (10047 votes) | https://www.usnews.com/news/top-news/articles/2020-11-07/texas-becomes-first-us-state-to-exceed-1-million-coronavirus-cases | https://redd.it/jq2rpa14:08
BrainstormNew from r/Coronavirus: Coronavirus: Daily Discussion Post - November 08 | Questions, images, videos, comments, unconfirmed reports, theories, suggestions → https://is.gd/IlVFXZ15:02
BrainstormNew from BMJ Open: Patient and general practitioner views of tools to delay diagnostic imaging for low back pain: a qualitative study: Objective Delayed prescribing is a promising strategy to manage patient requests for unnecessary tests and treatments. The purpose of this study was to explore general practitioner (GP) and patient views of three [... want %more?] → https://is.gd/f6BD8k15:40
BrainstormNew from r/WorldNews: worldnews: Researchers found a new coronavirus mutation that’s capable of sparking another pandemic → https://is.gd/MeQKzj15:50
BrainstormNew from r/WorldNews: worldnews: Brits flying from Denmark with coronavirus 'to be moved to infectious diseases centre' → https://is.gd/BULC0o16:18
ParvatiWhy are you recording and tracking people?16:54
ParvatiThat's so weird.16:54
Specwhat17:06
Parvatioh17:06
SphericalCowpervert alert17:07
Parvatiwhat?17:08
Parvatihttps://www.princewilliamtimes.com/opinion/guest-opinion-i-can-t-be-polite-about-this-anymore-yes-it-s-about-race/article_fe8a6cea-a529-11ea-8669-47fcba8bc4fd.html17:11
ParvatiI am glad that Prince Harry and Meghan Markle seem happy17:18
ParvatiAnd that their son is safe.17:18
BrainstormNew from CNBC Health: (news): U.S. reports more than 126,000 coronavirus cases for second day, fourth straight record as virus surges nationwide → https://is.gd/IGSTlW17:24
LjLBrainstorm, i mean, it was just a realization18:51
tinwhiskersIt's weird how we are almost exactly opposite each other on the globe yet have much the same sleeping hours.18:52
DocScrutinizer05moin18:55
LjLtinwhiskers, weird is an understatement :(18:55
BrainstormUpdates for Lombardy, Italy: +11489 cases (now 254436), +108 deaths (now 18226) since a day ago — Italy: +32614 cases (now 935104), +331 deaths (now 41394) since a day ago — US: +67198 cases (now 10.2 million), +513 deaths (now 243388) since 21 hours ago — United Kingdom: +20572 cases (now 1.2 million), +156 deaths (now 49044) since a day ago18:57
CoronaBot04/r/coronavirus: U.S. reports 128,000 new coronavirus cases, setting world record for the 4th day in a row (10011 votes) | https://twitter.com/BNODesk/status/1325224087417982978?s=20 | https://redd.it/jq4bdw18:57
DocScrutinizer05I think we actually see a tendency in R_eff in germany to decline towards 118:59
DocScrutinizer05probably 14. Oktober https://www.express.de/news/politik-und-wirtschaft/neue-corona-regeln-im-ueberblick-merkel---es-reicht-nicht--was-wir-hier-machen--37485256  takes effect 19:07
yuriwhoNew TWIV discussing the Mink issue @~50 mins https://www.youtube.com/watch?v=zq4k8HoRbMA LjL 19:09
LjLoh yeah Brainstorm posted that but i would have missed it from the far backscroll19:11
BrainstormUpdates for US: +74382 cases (now 10.2 million), +545 deaths (now 243420) since 22 hours ago19:20
CoronaBot04/r/coronavirus: 'Very worst of the pandemic' ahead in US with no apparent strategy, experts say (10038 votes) | https://www.theguardian.com/world/2020/nov/08/coronavirus-pandemic-trump-biden-strategy-experts | https://redd.it/jqafnf19:34
BrainstormUpdates for US: +75714 cases (now 10.2 million) since 22 hours ago19:36
BrainstormUpdates for France: +80566 cases (now 1.8 million), +270 deaths (now 40439) since 21 hours ago19:51
LjLholy shit. i hope there's a bug there19:51
LjLwell great, it isn't a bug19:53
LjLyesterday i was hoping the +60000 was a bug, and it wasn't...19:53
tinwhiskersouch19:53
LjLand they've been locked down longer than we have, and it's not the UK kind of "lockdown"19:54
blkshpIt's a joke 19:54
LjLyuriwho, are you aware some of the mink sequences are on nextstrain now?19:55
LjLblkshp, where, france or the UK?19:55
blkshpthe UK19:55
LjLi know19:55
LjLi asked a friend whether they need any paperwork to go out, after realizing they're not actually allowed to go out except for work, school, etc19:55
LjLhe was in disbelief at the question19:56
LjLbut how the hell do you enforce a lockdown if everyone can just make up an excuse at any point if they're stopped while outside19:56
LjLin italy we can still make silly excuses but at least we have to fill a form19:56
LjL*before* leaving, explaining why we're leaving19:56
blkshpYou can still go for KFC or a costa, go to school or work, drive anywhere, walk anywhere, 19:57
LjLhe remarked "once fascist, always fascist"... well sorry about that but i don't want to be +8000019:57
LjLi know that France is like Italy in this, not like the US, though19:57
LjL%fdroid attestation19:57
BrainstormLjL, Attestation de déplacement 3.1.0 (com.poupa.attestationdeplacement) in https://f-droid.org/repo: Generates the PDF attestation file required by the French government to go out. - updated 2020-11-08, see https://github.com/AdrienPoupa/AttestationDeplacement 19:57
LjLde-facto, wrt using quick tests to detect people who are infectious, as opposed to PCR which detects anything... i think you were in favor of that, and the UK does that, but this bit https://youtu.be/zq4k8HoRbMA?t=3176 mentions that according to a preprint only about 1/3 of "moderately infectious" people get picked up by the antigen test20:02
BrainstormUpdates for US: +80255 cases (now 10.2 million), +556 deaths (now 243431) since 22 hours ago — Switzerland: +23 deaths (now 2772) since 20 hours ago20:05
BrainstormNew from r/WorldNews: worldnews: WHO says mutant mink coronavirus outbreak in Denmark is a 'concern' → https://is.gd/0D6QP920:16
lenawachs[m]Merkelregime controll https://youtu.be/e9gnEq0YNpM20:16
BrainstormUpdates for US: +82412 cases (now 10.2 million), +580 deaths (now 243455) since 23 hours ago20:20
DocScrutinizer05france 3 times as high as germany20:26
LjLlenawachs[m], you won't find much fertile ground here for anti-mask propaganda20:27
de-factoLjL, hmm interesting, do they say anything about how the samples are taken for those moderately infectious carriers tested with antigen-quicktests?20:28
LjLde-facto, it's only mentioned briefly, if they said something that would let us identify the preprint, i didn't catch it20:28
de-factohmm their pronunciation is so bad that i am unable to catch the names20:32
de-factonor did they link their sources :(20:33
BrainstormUpdates for US: +95747 cases (now 10.2 million), +660 deaths (now 243535) since 23 hours ago — Arizona, US: +1880 cases (now 259264), +17 deaths (now 6164) since 23 hours ago — Canada: +4704 cases (now 263158), +34 deaths (now 10515) since 23 hours ago20:36
LjLuh that ought to have included Germany too and instead it didn't...20:36
LjLoh20:37
LjLi actually haven't Germany listed as one of the things to be output for this channel -.-20:37
LjLhow could i miss that for so long20:37
LjLanyway fyi <Brainstorm> Updates for Germany: +14890 cases (now 668882), +66 deaths (now 11483) since 22 hours ago20:38
BrainstormUpdates for US: +100427 cases (now 10.2 million), +699 deaths (now 243574) since 23 hours ago20:51
BrainstormUpdates for US: +110174 cases (now 10.2 million), +714 deaths (now 243589) since 23 hours ago21:09
BrainstormUpdates for US: +111149 cases (now 10.3 million) since a day ago21:21
de-factoRKI: Germany got in last 24h new infections +16017 (total 658505) and +63 new fatalities (total 11289)21:25
de-factoso JHU data probably is ahead of those21:25
DocScrutinizer05>>...mentions that according to a preprint only about 1/3 of "moderately infectious" people get picked up by the antigen test<< well, at least in germany quicktests get evaluated and validated before they are getting adopted for official testing purposes, and I seem to recall thevalidation thresholds for false negatives were in the range of <10%, not 33%21:25
LjLDocScrutinizer05, but that's if you average it over all infectivity levels21:30
LjL33% for "moderately infectious" means maybe 5% for "highly infectious"21:31
LjLbut how many are those?21:31
DocScrutinizer05I don't think so21:31
LjLyou don't think what?21:31
DocScrutinizer05>>that's if you average it <<21:31
LjLwell yes it is21:32
LjLfalse negatives in the range of <10% means all false negatives21:32
LjLin the TWIV they were looking at a specific part of those21:32
LjLthose classed "moderately infectious". the other classes were "highly infectious" and "not infectious". this is not a matter of opinion, it's just what they said21:32
BrainstormNew from Medical Xpress: Nursing home COVID-19 cases rise four-fold in surge states: Despite Trump administration efforts to erect a protective shield around nursing homes, coronavirus cases are surging within facilities in states hard hit by the latest onslaught of COVID-19. → https://is.gd/xDwzso21:33
DocScrutinizer05the validation process is targeted at detecting infectious people, they will test it against a reasinably low virus concentration21:33
CoronaBot04/r/covid19: Wearing of Cloth or Disposable Surgical Face Masks has no Effect on Vigorous Exercise Performance in Healthy Individuals (80 votes) | https://www.mdpi.com/1660-4601/17/21/8110/htm | https://redd.it/jqg7wm21:34
DocScrutinizer05actually that's one of the main criteria of the validation21:35
BrainstormUpdates for New Hampshire, US: +247 cases (now 12488) since 23 hours ago — US: +120889 cases (now 10.3 million), +767 deaths (now 243642) since a day ago21:36
BrainstormUpdates for Germany: +18515 cases (now 672507), +88 deaths (now 11505) since 23 hours ago — US: +121885 cases (now 10.3 million), +770 deaths (now 243645) since a day ago21:50
gigasu_shidahi ljl how is lockdown going?21:52
BrainstormUpdates for US: +121906 cases (now 10.3 million) since a day ago22:05
de-facto%title https://antigentest.bfarm.de/ords/antigen/r/antigentests-auf-sars-cov-2/liste-der-antigentests22:18
Brainstormde-facto: From antigentest.bfarm.de: error parsing title ('NoneType' object has no attribute 'string')22:18
de-facto%tr <de Die Liste wird kontinuierlich aktualisiert und beinhaltet die entsprechenden Tests zur professionellen Anwendung, die sich nach aktueller Kenntnis des BfArM in Deutschland in Verkehr befinden und laut den Herstellerangaben die durch das Paul-Ehrlich-Institut (PEI) in Abstimmung mit der Robert Koch-Institut (RKI) festgelegten Mindestkriterien für Antigen-Tests erfüllen.22:19
Brainstormde-facto, German to English: The list is continuously updated and contains the corresponding tests for professional use, which, according to the current knowledge of the BfArM, are on the market in Germany and, according to the manufacturer's information, are carried out by the Paul Ehrlich Institute (PEI) in coordination with the Robert Koch Institute ( RKI) meet the minimum [... want %more?]22:19
de-facto%tr <de Bei dieser Liste ist zu beachten, dass sie nur solche Antigen-Tests umfasst, die dem BfArM vom jeweiligen Hersteller im Hinblick auf eine Aufnahme in die Liste gemeldet wurden. Da das BfArM nicht in Fragen des Marktzugangs und der Konformitätsbewertung von Medizinprodukten eingebunden ist, stellt die Liste keine umfassende Übersicht aller in Europa und damit auch in Deutschland auf dem Markt verfügbaren entsprechend22:19
de-factoen Antigen-Tests dar. Seitens des BfArM erfolgt zudem lediglich ein Abgleich der Herstellerangaben mit den durch das PEI in Abstimmung mit dem RKI festgelegten Mindestkriterien.22:19
Brainstormde-facto, German to English: It should be noted that this list only includes antigen tests that have been reported to the BfArM by the respective manufacturer for inclusion in the list. Since the BfArM is not involved in questions of market access and the conformity assessment of medical devices, the list does not provide a comprehensive overview of all available on the market [... want %more?]22:19
BrainstormUpdates for US: +105455 cases (now 10.3 million), +522 deaths (now 243650) since 23 hours ago22:21
de-factominimum criteria for performance22:21
de-factoSensitivity:22:22
de-facto%tr <de Untersuchung parallel in PCR- und Antigentest von Personen mit Covid-19-Symptomen innerhalb von sieben Tagen nach Symptombeginn.22:22
Brainstormde-facto, German to English: Examination in parallel in PCR and antigen tests of people with Covid-19 symptoms within seven days of the onset of symptoms. (MyMemory, Google) — Assay parallel in *PCR- and *Antigentest from persons with *Covid-19-symptoms within from seven days #to *Symptombeginn. (Apertium)22:22
de-facto%tr <de Kriterium: >70% von unselektierten PCR-positiven Proben, positiv im SARS-CoV-2 Antigenschnelltest22:22
Brainstormde-facto, German to English: Criterion:> 70% of unselected PCR-positive samples, positive in the SARS-CoV-2 antigen rapid test (MyMemory, Google) — Criterion: >70% from *unselektierten *PCR-positive trials, positively in the *SARS-*CoV-2 *Antigenschnelltest (Apertium)22:22
de-factoSpecificity 22:23
de-facto%tr <de Untersuchung von asymptomatischen Personen ohne konkretes Expositionsrisiko im SARS-CoV-2 Antigenschnelltest; Abklärung etwaiger reaktiver Proben mittels PCR.22:23
Brainstormde-facto, German to English: Examination of asymptomatic persons without a specific risk of exposure in the SARS-CoV-2 rapid antigen test; Clarification of any reactive samples using PCR. (MyMemory, Google) — Assay from *asymptomatischen persons #absent concrete *Expositionsrisiko in the *SARS-*CoV-2 *Antigenschnelltest; *Abklärung Possible *reaktiver trials by *PCR. (Apertium)22:23
de-facto%tr <de Kriterium: Spezifität >97%22:23
Brainstormde-facto, German to English: Criterion: specificity> 97% (MyMemory, Google) — Criterion: *Spezifität >97% (Apertium)22:23
de-factoCross reactivity22:24
de-facto%tr <de Untersuchung auch von Proben mit hoher Konzentration (>106 Viren/ml) an verwandten humanen Coronaviren (z.B. „human coronavirus 229E, human coronavirus OC43, human coronavirus NL63, MERS coronavirus”).22:24
Brainstormde-facto, German to English: Examination of samples with a high concentration (> 106 viruses / ml) of related human coronaviruses (e.g. “human coronavirus 229E, human coronavirus OC43, human coronavirus NL63, MERS coronavirus”). (MyMemory) [... want %more?]22:24
de-factoInterferenz22:24
de-facto%tr <de Untersuchung auch von Pathogen-positiven Proben, bei denen das Pathogen analoge Symptomatik hervorrufen kann (z. B. Influenza A, B; RSV), oder mit dem Testprinzip interferieren könnte (z. B. Protein A-positive Staphylococcus aureus bei Nasenabstrichen als Probenmatrix).22:24
Brainstormde-facto, German to English: Examination of pathogen-positive samples, in which the pathogen can cause analogous symptoms (e.g. influenza A, B; RSV) or could interfere with the test principle (e.g. protein A-positive Staphylococcus aureus in nasal swabs as sample matrix ). (MyMemory) [... want %more?]22:24
de-factosource: https://www.bfarm.de/DE/Medizinprodukte/Antigentests/_node.html22:25
de-facto%title https://www.pei.de/DE/newsroom/dossier/coronavirus/coronavirus-inhalt.html?cms_pos=6 <-- this is the institute responsible for validating vaccinations in Germany22:26
Brainstormde-facto: From www.pei.de: Paul-Ehrlich-Institut - Coronavirus und COVID-19Coronavirus und COVID-1922:26
de-facto%title https://www.who.int/publications/i/item/antigen-detection-in-the-diagnosis-of-sars-cov-2infection-using-rapid-immunoassays22:26
Brainstormde-facto: From www.who.int: Antigen-detection in the diagnosis of SARS-CoV-2 infection using rapid immunoassays22:26
DocScrutinizer05could we get a summary?22:32
DocScrutinizer05wall of text22:32
DocScrutinizer05maybe https://translate.google.com/translate?hl=&sl=de&tl=en&u=https%3A%2F%2Fwww.bfarm.de%2FDE%2FMedizinprodukte%2FAntigentests%2F_node.html22:33
de-factothat was already the summary, there are criteria from RKI and PEI for antigen quicktests and those on the list i linked above fulfill those criteria22:35
DocScrutinizer05>>A further evaluation should consider the detection rate of the antigen test in patients with a Ct value below a defined value ( e.g. Ct <30), which is associated with a relatively high virus concentration ( e.g. detection rate> 90% in various studies) . <<22:36
BrainstormUpdates for Canada: +4097 cases (now 263317), +18 deaths (now 10516) since 23 hours ago — US: +105458 cases (now 10.3 million) since a day ago22:36
DocScrutinizer05they claim they fulfill those, yes22:36
de-factothe criteria can be read in English at https://translate.google.com/translate?hl=en&sl=de&tl=en&u=https%3A%2F%2Fwww.pei.de%2FDE%2Fnewsroom%2Fdossier%2Fcoronavirus%2Fcoronavirus-inhalt.html%3Fcms_pos%3D622:36
generaand somehow Staphylococus can trigger the test too22:37
de-factointeresting, source?22:37
generawhat you just posted22:37
generaor maybe i misunderstood22:37
de-factoah well they try to test against pathogen that may cause similar symptoms22:39
de-facto"Examination of pathogen-positive samples, in which the pathogen can cause similar symptoms (e.g. influenza A, B; RSV ) or could interfere with the test principle (e.g. protein A-positive Staphylococcus aureus in nasal swabs as sample matrix )."22:39
de-factoso yeah they suspect there may be an interference possible, hence they test against that i would guess22:39
de-facto"Details of the identified interferences in the package insert."22:40
de-factoso yeah those testing details are mentioned in the link for each test in that list i posted22:41
de-factoso i guess each test package insert would have to be checked it that interference was excluded22:42
de-factogenera, good catch indeed you are correct22:42
de-factothe last column in https://antigentest.bfarm.de/ords/antigen/r/antigentests-auf-sars-cov-2/liste-der-antigentests contains the links for the package inserts22:43
de-factowritten in English22:43
DocScrutinizer05LjL: sorry, actually my fault. I didn't realize what they meant by "weakly infectious". It seems to me in real life that's usually considered "very unlikely to spread infection at all"22:48
LjLi said "moderately"22:48
LjLthat's not "weakly"22:48
DocScrutinizer05aaah then, yeah, for "moderately" the sensitivity should be better than 1 false negative on 10 tests22:49
BrainstormNew from StatNews: With Murthy and Kessler, Biden leans on experience to steer Covid-19 task force: President-elect Joe Biden has turned to two prominent physicians to lead his coronavirus task force who have signaled that they will approach the pandemic far differently than the Trump administration. → https://is.gd/3q2wTt22:49
de-factoit also depends on the symptoms itself combines with the virion load, e.g. someone coughing or sneezing spreads a LOT more aerosol than someone not doing that (well its not voluntary i guess)22:50
BrainstormUpdates for US: +105461 cases (now 10.3 million) since a day ago22:50
DocScrutinizer05so far I heard "moderately" associated to "ct < 30", while highly infectious is sth like ct<24 iirc22:50
DocScrutinizer05I might recall incorrectly though, please correct me when due22:52
de-factoyeah but the problem with those Cycle Threshold values is that they never were meant as such a metric, they differ from PCR method and apparatus (hence are calibrated and validated individually for a testing pipeline) and also are highly dependent on the sample taking22:52
de-factothats why i asked about sample taking, swab tests may differ by a LOT in virion concentration22:53
de-factohence maybe those "dont eat for two hours" and then "gargle with saline solution" samples may be better because they essentially take it from the whole surface22:53
de-factoof the mucus22:54
de-factoideally they would even use some marker molecule to determine the sample concentration to have something to normalize virion concentration against22:54
de-factoalthough it seems most of those antigen-quicktests describe the sampling with swab tests, e.g. probing with a giant q-tip in the nasal and pharyngeal mucosa 22:56
DocScrutinizer05well ct is power of 2 aiui. 22:57
de-factoof course then concentration may differ by a lot and probably also people could not take such samples themselves, e.g. medical personal required to take the sample22:57
de-factoDocScrutinizer05, theoretically yeah22:58
DocScrutinizer05Drosten planned to, or already did ship standard calibration samples to all labs so ct can get adjusted to a common standard22:59
de-factoi thought for PCR there are those constant ring tests going on to continuously validate labs and ensure high predictive quality23:01
DocScrutinizer05those are yet another thing23:05
de-factoah ok23:05
BrainstormUpdates for US: +106247 cases (now 10.3 million) since a day ago23:05
DocScrutinizer05sending out the official "1kg" reference weifgt of virus concentration is what I referred to23:05
DocScrutinizer05so labs could calibrate "their scales"23:06
de-factoyeah we need to agree on standardized values, yet afaik they already do calibrate against live samples, so adjusting their pipeline against samples from patients that have known results23:07
DocScrutinizer05since it's pretty difficult to count a 10^5 virus/ml "at home"23:07
DocScrutinizer0510^6 even23:07
de-factotbh i still dont get why we did not switch to gargling or spitting tests, that would make things much easier23:08
DocScrutinizer05:nod:23:08
de-factoafaik they do those in Austria23:08
de-factoand if i remember correctly they said in some podcasts that their reliability is similar, possibly even better23:09
de-factowell samples are not taken from the nose but from a broader surface of mucus in the pharyngeal mucus23:10
de-factoand i guess salvia from the nose anyhow would run down the pharyngeal mucus at some point (correct me if i am wrong)23:10
de-factoso if those antigen quicktests are not as sensitive as PCR they might potentially not catch very early replications on nasal mucus anyhow? not sure23:11
BrainstormUpdates for Missouri, US: +5571 cases (now 218257), +24 deaths (now 3326) since a day ago — US: +116996 cases (now 10.3 million), +585 deaths (now 243713) since a day ago23:20
mycrowmachinese[BOO GG KNIGHTS?23:30
BrainstormUpdates for US: +114067 cases (now 10.3 million) since a day ago23:36
mycrowmachinese[87DRSHILLZ23:38
tinwhiskersmycrowmachinese[: stop please23:40
DocScrutinizer05amazing patience :-)23:49
DocScrutinizer05sigyn would have k-lined already 23:50
BrainstormUpdates for US: +117021 cases (now 10.3 million), +572 deaths (now 243718) since a day ago23:51

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