dTal | WHO's afraid of the Big Bad Mink | 00:01 |
---|---|---|
dTal | that's what I would write, if I were a tabloid editor | 00:02 |
LjL | i'd highlight everyone about it | 00:03 |
LjL | except it doesn't really say anything | 00:03 |
LjL | except that sequences are coming, i guess | 00:03 |
LjL | but then i might just highlight when the sequences do come | 00:03 |
dTal | highlight? | 00:03 |
LjL | all the people | 00:03 |
dTal | in the channel? | 00:03 |
LjL | no just a bunch | 00:03 |
dTal | huh | 00:04 |
LjL | like four people would probably want to know about any news on this | 00:04 |
LjL | probably 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 know | 00:04 |
Brainstorm | Updates for US: +13924 cases (now 10.0 million), +167 deaths (now 242081) since 49 minutes ago — Canada: +19 cases (now 253809) since 45 minutes ago | 00:06 |
Brainstorm | New 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/74bzDF | 00:11 |
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-facto | what about China and Poland? | 00:17 |
LjL | good luck with them | 00:18 |
Brainstorm | New 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/74bzDF | 00:20 |
Brainstorm | Updates for US: +6830 cases (now 10.0 million), +47 deaths (now 242128) since 18 minutes ago | 00:21 |
LjL | okay, 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 sustainable | 00:21 |
LjL | although hey it did give us the news about the WHO statement just a bit after we got them anyway | 00:21 |
de-facto | I wonder why it is called cluster 5, did cluster 1-4 fail to mutate in minks? | 00:26 |
LjL | i don't know, but it sounds spooky | 00:26 |
LjL | also that wasn't actually the edit adding a WHO link | 00:27 |
LjL | i 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 |
LjL | https://www.oie.int/fileadmin/Home/MM/Update_6_Letter_to_the_OIE_on_Sars-CoV-2_in_Denmark_5_november2020.pdf | 00:29 |
Brainstorm | New 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/74bzDF | 00:30 |
de-facto | i 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-facto | surely China would censore such news it something similar occurred in their farms | 00:35 |
de-facto | and what about the other countries | 00:36 |
de-facto | i 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 |
LjL | Wikipedia 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 pages | 00:37 |
de-facto | i am not saying they do hide anything, just that i am worried some might think about it | 00:37 |
LjL | de-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 mink | 00:38 |
LjL | maybe some of the others too | 00:38 |
LjL | i bet if you told most Italian we have mink factory-farms in Italy they'd be like "ew, really? stop them!" | 00:38 |
LjL | so you don't tell them | 00:38 |
de-facto | i bet they even might not be too sad about taking over the market share of Denmarks and Netherlands production | 00:43 |
de-facto | it should be banned worldwide | 00:43 |
DocScrutinizer05 | cluster fuck :-/ | 00:43 |
DocScrutinizer05 | cluster sputnik | 00:47 |
Brainstorm | New 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/a8UFwR | 00:48 |
Brainstorm | Updates 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 ago | 00:51 |
Brainstorm | New 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/dU8PSq | 01:15 |
CoronaBot | 04/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/jp7h1c | 01:19 |
Brainstorm | New 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/Utqh9A | 01:25 |
rpifan | yea | 01:29 |
Brainstorm | New 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/grOYEx | 01:34 |
Skunny | having no smell or taste sucks | 01:36 |
Skunny | i been watching food network all day | 01:36 |
ryouma | i have had anosmia and dysgeusia since late 1990s. every once in a while zinc helped. | 01:36 |
ryouma | one of these days i will find out what the principles for cooking for those are. | 01:38 |
Skunny | damn, I have had it for 2 days now and it blows | 01:39 |
LjL | Skunny, this may be a silly question given the place, but do you have COVID? | 01:41 |
Skunny | yeah | 01:43 |
LjL | i think you're actually the first person in the channel who has it (and says it), interestingly enough | 01:46 |
LjL | (or else i missed others) | 01:46 |
Skunny | wierd | 01:47 |
Skunny | If it doesn't recover I could always start my new career in a water treatment plant. Or a garbage man. | 01:47 |
LjL | positive thinking | 01:47 |
LjL | how many days since testing positive? | 01:48 |
Skunny | well I took my test tueday | 01:49 |
Skunny | and still waiting, can you beleive that | 01:49 |
Skunny | but I have had all the syptoms | 01:49 |
Skunny | but my breathing has been fine | 01:49 |
Skunny | I took another test today because I have no clue why the first one is taking so long | 01:50 |
LjL | well, it's sort of lucky that you are able to do that | 01:50 |
LjL | they aren't testing even first-degree contacts of positives here anymore | 01:50 |
Skunny | monday I started to notice I was getting sick | 01:51 |
Skunny | so I went tuesday | 01:51 |
LjL | do you have a pulse oximeter? if not, get a pulse oximeter | 01:52 |
LjL | they're cheap unless they stopped being cheap again | 01:52 |
LjL | i won't mention a thermometer because that should be pretty obvious | 01:52 |
Brainstorm | New from r/Coronavirus: Coronavirus: Join the official Coronavirus Community Discord with live data, discussion and curated news! :) → https://is.gd/hVuuxW | 02:02 |
Skunny | I have oximeter | 02:04 |
Brainstorm | New 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/olT27v | 02:11 |
de-facto | make sure you drink enough and eat healthy of course, maybe even things that may have anti-coagulant effects | 02:28 |
Brainstorm | New 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/TZ6aF0 | 02:38 |
Brainstorm | Updates 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 ago | 02:51 |
LjL | %title https://www1.cbn.com/cbnnews/world/2020/november/north-korea-reportedly-leaving-covid-19-victims-to-die-in-secret-quarantine-camps | 04:47 |
Brainstorm | LjL: From www1.cbn.com: North Korea Reportedly Leaving COVID-19 Victims to Die in Secret 'Quarantine Camps' | CBN News | 04:47 |
Brainstorm | New from r/WorldNews: worldnews: North Korea Reportedly Leaving COVID-19 Victims to Die in Secret 'Quarantine Camps' → https://is.gd/zbdcHf | 04:57 |
LjL | Brainstorm, jinx | 05:01 |
de-facto | lol | 05:01 |
de-facto | yuck @ NK if thats true | 05:01 |
ryouma | so they did not have 0 cases? | 05:28 |
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/jph6tj | 05:39 |
tinwhiskers | They 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 |
Brainstorm | New from The Indian Express: World: Trump’s chief of staff, Mark Meadows, infected by coronavirus → https://is.gd/t3FLvx | 05:42 |
gigasu_shida | how the heck did taiwan get rid of the virus so well? | 05:58 |
gigasu_shida | i see so many videos on the internet of taiwanese folks eating in large dining areas without a mask | 05:59 |
tinwhiskers | gigasu_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_shida | i wonder when taiwanese people went back to eating in food courts / dining halls together without a mask | 06:01 |
tinwhiskers | We've been doing it for months in NZ. Australia more recently. | 06:02 |
gigasu_shida | is their contact tracing for that? | 06:02 |
gigasu_shida | there* | 06:02 |
tinwhiskers | yes, people do record where they go in NZ by scanning QR codes. | 06:03 |
gigasu_shida | like if someone tests positive is contact tracing done rapidly? | 06:03 |
gigasu_shida | oh wow that's cool | 06:03 |
tinwhiskers | if there is an outbreak that aids contact tracing but contact tracing goes well beyond that. It's mostly done via phone calls. | 06:03 |
tinwhiskers | the 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 |
tinwhiskers | Of course China deserves mention as well. | 06:05 |
tinwhiskers | Local tourism is up and going again in many of these countries too. | 06:05 |
tinwhiskers | I know I've missed a bunch of countries in that list, but my brain isn't that good. | 06:06 |
tinwhiskers | people trusting and following government advice is critical, and that takes a long time to build. | 06:07 |
ryouma | this 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/jph6tj | 06:08 |
ryouma | pacifgic islands | 06:09 |
tinwhiskers | on target for > 1 m cases in the next ten days | 06:09 |
ryouma | singapore | 06:09 |
tinwhiskers | maybe just in the next week :-( | 06:09 |
Brainstorm | New from The Indian Express: World: Denmark defends coronavirus measures amid mink mutation → https://is.gd/5BB0Ct | 06:10 |
tinwhiskers | of 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 |
tinwhiskers | Kiwis 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 |
ryouma | will you fly or sail? | 06:15 |
tinwhiskers | fly | 06:15 |
tinwhiskers | we may well be the only people on the plane | 06:16 |
ryouma | why would it fly? | 06:16 |
tinwhiskers | a 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 |
ryouma | great | 06:17 |
tinwhiskers | The chances of two lots of expats returning home in the same week is fairly low. | 06:17 |
tinwhiskers | not that it matters since they will be clear anyway | 06:17 |
ryouma | but quarantine is not separated and all at once? | 06:17 |
tinwhiskers | it's when we reach the quarantine facility that the worry starts | 06:17 |
ryouma | that makes little sense to me you shoul dhave separate rooms with separate hvac | 06:18 |
ryouma | why does your kayak or whatever it was point so high without a keel? is it a sharp bottom? | 06:18 |
tinwhiskers | yeah. Nobody seems to know if there are high-rsi and low-risk facilities but there are not any no-risk facilities anyway :-( | 06:18 |
tinwhiskers | it has a keel | 06:18 |
tinwhiskers | well, a daggerboard | 06:18 |
ryouma | so it was designed for it or you built it? | 06:19 |
tinwhiskers | I made it. The daggerboard is just a drop-in keel that slots into the frame. | 06:19 |
tinwhiskers | you pull it out when you get into the shallows. | 06:19 |
ryouma | but you have to make the frame leakproof | 06:20 |
tinwhiskers | no, the frame doesn't matter. | 06:20 |
ryouma | but hte slot for the daggerboard has to be above water | 06:20 |
tinwhiskers | my daggerboard is *beside* the kayak | 06:20 |
ryouma | oh | 06:20 |
tinwhiskers | It took me a long time to sew the sail by hand :-/ | 06:22 |
Brainstorm | Updates 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 ago | 07:07 |
Brainstorm | New 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/bUsPLK | 07:13 |
Brainstorm | New 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/JzkjES | 07:22 |
Brainstorm | New 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 |
Brainstorm | Updates 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 ago | 07:53 |
Brainstorm | New 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/74bzDF | 08:16 |
Brainstorm | New from The Indian Express: World: Amazon Fires Cause Brazil’s CO2 Emissions to Jump Amid Pandemic → https://is.gd/dufcZc | 08:34 |
Brainstorm | New 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/74bzDF | 08:43 |
Brainstorm | New 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/74bzDF | 08:53 |
Brainstorm | New from r/WorldNews: worldnews: Military forces drafted in as Europe risks being overwhelmed by Covid cases → https://is.gd/aVBzoU | 09:20 |
Brainstorm | Updates for US: +682 cases (now 10.1 million), +17 deaths (now 242256) since an hour ago | 09:39 |
de-facto | %title https://twitter.com/firefoxx66 | 09:40 |
Brainstorm | de-facto: From twitter.com: error parsing title ('NoneType' object has no attribute 'string') | 09:41 |
de-facto | lol | 09:41 |
humpelstilzchen[ | sounds like something a snake would say | 09:41 |
de-facto | Dr Emma Hodcroft shows the mutations of the danish mink farms on nextstrain.org | 09:42 |
de-facto | H69del/V70del, Y453F, I692V, and M1229I | 09:45 |
de-facto | and also other mutations | 09:45 |
de-facto | if one would want to be informed about the latest developments look at her tweets there | 09:45 |
de-facto | https://nextstrain.org/groups/neherlab/ncov/denmark?f_country=Denmark&p=grid&r=division | 09:49 |
de-facto | %title https://www.biorxiv.org/content/10.1101/2020.11.04.355842v1 <-- another nasty mutation? | 10:15 |
Brainstorm | de-facto: From www.biorxiv.org: The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity | bioRxiv | 10:15 |
de-facto | %title https://twitter.com/robertson_lab <-- published on their twitter | 10:17 |
Brainstorm | de-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 |
Brainstorm | New 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/bQqjeK | 11:02 |
Brainstorm | New 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/dexB1b | 11:11 |
Brainstorm | New 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/Fmea7w | 11:20 |
Brainstorm | Updates for US: +1375 cases (now 10.1 million) since 2 hours ago | 11:39 |
Brainstorm | New from r/WorldNews: worldnews: Coronavirus: France records more than 60,000 cases → https://is.gd/kk9YNE | 12:24 |
Brainstorm | Updates for US: +1832 cases (now 10.1 million), +5 deaths (now 242261) since an hour ago | 12:39 |
Brainstorm | New 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/Ugu981 | 12:42 |
Brainstorm | New from r/WorldNews: worldnews: Sexual violence consultations in Japan up 15% during pandemic. → https://is.gd/oqfpZm | 12:51 |
CoronaBot | 04/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/jpnczo | 13:04 |
Brainstorm | New 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/74bzDF | 13:18 |
Brainstorm | Updates for US: +1013 cases (now 10.1 million) since an hour ago — Switzerland: +9 deaths (now 2721) since 5 hours ago | 13:35 |
Brainstorm | New 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/UhXHyi | 13:45 |
Brainstorm | New 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/74bzDF | 14:41 |
Brainstorm | New from r/Coronavirus: Coronavirus: Daily Discussion Post - November 07 | Questions, images, videos, comments, unconfirmed reports, theories, suggestions → https://is.gd/Nikbym | 14:59 |
Brainstorm | Updates 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 ago | 15:50 |
Brainstorm | New 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/TZ6aF0 | 15:55 |
Brainstorm | Updates for US: +1031 cases (now 10.1 million), +14 deaths (now 242330) since 19 minutes ago | 16:05 |
Brainstorm | New 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/IGSTlW | 16:31 |
Brainstorm | Updates for US: +1509 cases (now 10.1 million), +9 deaths (now 242339) since 34 minutes ago — Switzerland: +10 deaths (now 2731) since 3 hours ago | 16:36 |
Brainstorm | Updates for US: +573 cases (now 10.1 million), +1 deaths (now 242340) since 32 minutes ago — Canada: +378 cases (now 257012) since 9 hours ago | 17:06 |
Brainstorm | Updates 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 ago | 17:21 |
Brainstorm | New 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/aurqqG | 17:44 |
Brainstorm | Updates 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 ago | 17:51 |
Brainstorm | Updates for US: +1870 cases (now 10.1 million), +10 deaths (now 242427) since 32 minutes ago | 18:21 |
Brainstorm | New 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/74bzDF | 18:33 |
Brainstorm | New from r/WorldNews: worldnews: Denmark finds 214 people infected with mink-related coronavirus, experts fear impact on future Covid-19 vaccines → https://is.gd/CuyQF5 | 19:19 |
de-facto | If 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 |
LjL | an 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 countries | 19:23 |
LjL | i 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 |
Jigsy | Huh. | 19:28 |
Jigsy | The UK actually had 30,000 cases on the 2nd of November. | 19:28 |
de-facto | You mean hospital capacity? | 19:34 |
de-facto | or what would "non updated pandemic plan" actually refer to? | 19:35 |
de-facto | updated to population density and demographics? | 19:35 |
de-facto | were there such significant changes in last 14 years? | 19:35 |
Jigsy | https://coronavirus.data.gov.uk/details/cases <--- Look at the graph. | 19:36 |
Brainstorm | Updates for US: +8839 cases (now 10.1 million), +97 deaths (now 242524) since an hour ago | 19:37 |
Jigsy | Wonder why it only got reported as around 20K, though... | 19:37 |
Jigsy | Actually, it got reported as 18K... | 19:38 |
de-facto | average vs spike or such? | 19:40 |
de-facto | btw those plotly.js graphs are awesome :) | 19:41 |
de-facto | Also sometimes new reported cases distribute over the last few days due to reporting lag | 19:44 |
de-facto | At least that is the case in the German reporting system from RKI | 19:44 |
de-facto | basically the last few days always will get "patched" with the newest data | 19:45 |
Brainstorm | Updates for US: +14262 cases (now 10.1 million), +96 deaths (now 242620) since 32 minutes ago | 19:52 |
LjL | i'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 while | 19:58 |
de-facto | yay :)) | 19:59 |
de-facto | thank you already for looking into that :) | 20:00 |
de-facto | i 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 though | 20:01 |
Brainstorm | de-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 | medRxiv | 20:01 |
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 regions | 20:02 |
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 |
LjL | this is really beyond my league | 20:06 |
de-facto | note: "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-facto | so in the lab, question remains if its also an effect in vivo (e.g. in patients) | 20:07 |
LjL | i guess they'll be able to make a similar in vitro study with antibodies from the "mink" coronavirus | 20:07 |
de-facto | they really should do that | 20:08 |
LjL | well not with the antibodies, with the new virus, and old antibodies | 20:08 |
de-facto | exactly | 20:08 |
de-facto | thats why i said a few days ago that i hope they did isolate a live virus sample from those mink clusters | 20:09 |
LjL | i would assume so | 20:11 |
LjL | they've been acting a bit stupid but they'd have to be *braindead* not to | 20:11 |
LjL | you know, general they, all of them | 20:11 |
LjL | also, there are still patients with the virus circulating | 20:12 |
LjL | i don't think this mutated virus will be gone any time soon :( so you will have plenty of samples around | 20:12 |
de-facto | unfortunately they discover more of them, indeed | 20:12 |
tinwhiskers | I think you're right LjL. | 20:13 |
de-facto | i wonder if they also could find reinfections among them, probably not so likely though | 20:13 |
de-facto | because of prevalence i mean | 20:13 |
LjL | you go and calculate the probability of that :P | 20:13 |
de-facto | btw the samples are already on nextstrain | 20:13 |
LjL | i think it's not so low, but that's just a guess | 20:14 |
LjL | oh | 20:14 |
LjL | i guess they put them there after the WHO announcement | 20:14 |
LjL | also i forgot i was going to see if nextstrain has any kind of RSS feed for anything | 20:14 |
de-facto | "Dr Emma Hodcroft" tweeted about them on her account https://twitter.com/firefoxx66 | 20:14 |
LjL | she was the one who tweeted... what, about the mink virus, before? | 20:17 |
LjL | no RSS anything from nextstrain. but on the other hand, i wasn't really sure what i'd be expecting to find one for | 20:19 |
LjL | but 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 one | 20:19 |
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 |
Brainstorm | de-facto: From www.gisaid.org: GISAID - Mutations in spike putatively linked to outbreak in Danish mink farm | 20:22 |
dzho | > i don't think this mutated virus will be gone any time soon :( so you will have plenty of samples around | 20:23 |
dzho | well, that's sort of the point of tracking things over time is that they *mutate* | 20:24 |
dzho | so 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 like | 20:24 |
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 |
Brainstorm | de-facto: From www.gisaid.org: GISAID - First new arrivals of HPAI H5 in the 2020-2021 Winter in the EU | 20:25 |
dzho | LjL: ^^^ anyway sorry forgot to highlight you on that but since I quoted you I figure it's only fair to point it out | 20:27 |
LjL | dzho, but we have the sequence, so if it mutates we're going to know that much | 20:28 |
LjL | de-facto, does this happen every year? | 20:29 |
de-facto | i am not sure, i have to admit i did not follow such news before this pandemic | 20:29 |
de-facto | btw its a very informative website https://www.gisaid.org/ | 20:30 |
de-facto | they also state latest submissions "hCoV-19/Denmark/DCGC-6387/2020" | 20:31 |
de-facto | so those are probably the 6k sequences Hodcroft was tweeting about | 20:32 |
LjL | %title https://www.globaltimes.cn/content/1206008.shtml | 20:46 |
Brainstorm | LjL: From www.globaltimes.cn: No infections among 56,000 people who traveled abroad after receiving Sinopharm-developed COVID-19 vaccine: developer - Global Times | 20:46 |
LjL | to 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 |
CoronaBot | 04/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/jppsxc | 20:51 |
Brainstorm | Updates for US: +1549 cases (now 10.1 million), +13 deaths (now 242774) since 18 minutes ago | 21:07 |
de-facto | its 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-Preven | 21:16 |
LjL | de-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-facto | well 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 anymore | 21:22 |
de-facto | of course the procedure would have to be done properly | 21:23 |
Brainstorm | Updates for US: +0 cases (now 10.1 million), +0 deaths (now 242875) since 5 minutes ago | 21:24 |
de-facto | i 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 vaccines | 21:24 |
de-facto | and also working with the "original" somewhat is a neat idea imho | 21:24 |
LjL | de-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 |
LjL | due to the vaccine than "natural" ones | 21:25 |
de-facto | im not sure, would those need adjuvants? | 21:25 |
LjL | so 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 |
LjL | i 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-facto | idk 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-facto | that 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 |
Brainstorm | New from r/WorldNews: worldnews: Italy hits record 39,800 daily coronavirus cases → https://is.gd/MuBsCP | 21:28 |
LjL | Brainstorm, thank you for the reminder | 21:28 |
de-facto | afaik there are several viral vector (not with SARS-CoV-2 but some Adenovirus or such) in the pipeline that may be used via nasal stray | 21:29 |
de-facto | nasal spray | 21:29 |
de-facto | but hey maybe some vaccines already can prevent infectious status, that would be great | 21:32 |
de-facto | i mean they say "prevent infection" in that article you linked, but what exactly do they mean by that? | 21:38 |
de-facto | hopefully 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-facto | if they just mean noone got sick it might be different from that though, and they admit there was disease among the not vaccinated employees there | 21:40 |
LjL | de-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 antibodies | 21:40 |
de-facto | yes, thats why i think testing daily against the antigen (thei virus itself) in such studies should be done | 21:41 |
de-facto | just 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 environment | 21:42 |
LjL | but antigen tests aren't even as sensitive as PCR | 21:42 |
de-facto | but they can detect concentrations of the virions that are considered infectious | 21:42 |
de-facto | if it stays below that, great then vaccination and herd immunity may really work | 21:43 |
de-facto | so antigen tests may be even better than PCR in this scenario, because the test should reveal if infectious status ever was reached for vaccinated | 21:44 |
de-facto | something 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 concentration | 21:46 |
de-facto | i really think we need to attribute some part of our testing capacity to such screening efforts, this would be really valuable information | 21:47 |
de-facto | at 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 testing | 21:49 |
de-facto | but hey thats just my opinion, maybe the experts know better | 21:51 |
Brainstorm | New 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/TrUgHR | 22:04 |
de-facto | btw what is the food of those mink farms in Denmark? | 22:22 |
Brainstorm | New from CDC (old): Coronavirus [CoV]: Cases & Deaths by County → https://is.gd/yJtqEF | 22:23 |
de-facto | what 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-facto | they probably were fed with some sort of cheap meat, so from what source? | 22:25 |
de-facto | asking 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 |
LjL | de-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 |
LjL | that's quite a diversity | 22:31 |
de-facto | i tried to google and it seems to be quite different depending on region | 22:32 |
de-facto | primarily i am curious because you said that they suspect transport of the pathogen between mink farms by unknown means, e.g. birds or such | 22:33 |
de-facto | i would guess they excluded really obvious things like same workers on the affected farms | 22:33 |
de-facto | so what else would they have in common? possibly their food supply chain | 22:33 |
de-facto | hmm were there any outbreaks in slaughterhouses recently in Denmark? | 22:35 |
de-facto | or other farms or such? | 22:35 |
Brainstorm | Updates 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 ago | 22:35 |
de-facto | would be interesting if samples exist for such potential sources to sequence them for comparison | 22:37 |
LjL | de-facto, i'd say food is also a pretty obvious thing to exclude, but who knows | 22:37 |
LjL | maybe it's just not easy to exclude given the variety | 22:37 |
LjL | de-facto, there were outbreaks in slaughterhouses elsewhere as you know and i don't think the cause of that has been sufficiently determined | 22:38 |
de-facto | yeah they probably buy all cheap protein rich stuff and put them in cold storage or such | 22:38 |
LjL | so i think your theory is not devoid of merit, but really i have no clue at this point | 22:38 |
LjL | de-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 24 | 22:39 |
de-facto | hmm what are the usual patterns for the arrival of incidence chunks? | 22:40 |
LjL | de-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 values | 22:41 |
LjL | some days it will just be zero | 22:41 |
de-facto | afaik 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 date | 22:41 |
LjL | i don't know if there's a more elegant way to avoid this issue | 22:41 |
Skunny | how do they test for covid? it's like a machine they put the sample in? | 22:42 |
LjL | de-facto, i can't really do that, the bot has to work for all countries without adjustments for each of them | 22:42 |
Brainstorm | New 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/fXz8nS | 22:42 |
LjL | Skunny, 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 one | 22:43 |
de-facto | LjL, 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 later | 22:43 |
LjL | de-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 before | 22:44 |
LjL | nah | 22:44 |
LjL | bah, i don't know | 22:44 |
LjL | it's not going to spit out results that actually match what's declared by the countries, because the window keeps changing | 22:44 |
LjL | in a sense it doesn't have to. but it can be confusing | 22:44 |
de-facto | Skunny, 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-facto | LjL, but offloop has incidence (e.g. daily new), is there any way to tell if the latest day is already "finalized"? | 22:47 |
LjL | god i have way too many RSS feeds for this channel, it takes more than 2 minutes to parse them all | 22:47 |
de-facto | feedparser is slow | 22:48 |
LjL | it really is | 22:48 |
LjL | it has been a bane for years | 22:48 |
LjL | there is a new version of it for Python 3 | 22:48 |
LjL | "one of these days" i will need to port the whole thing to Python 3 | 22:48 |
LjL | ideally before 2 stops being supported completely | 22:48 |
LjL | de-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 |
LjL | hours 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 day | 22:50 |
LjL | anyway, for now i'm going "last 24h unless it's empty, in which case, whatever the previous one was" | 22:52 |
LjL | we'll see | 22:52 |
LjL | it will still output "... since n hours ago" so one can differentiate | 22:52 |
de-facto | yes but having the cases accumulated for same durations, e.g. one day they are much better comparable, e.g. 24h incidence | 22:52 |
dtrum | interessanter Artikel zum Thema Metastudien zu Masken https://is.gd/PFEhEa | 22:53 |
de-facto | its what i look upon every morning as soon as they are released by RKI | 22:53 |
LjL | de-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 window | 22:55 |
LjL | which may or may not be the same as their accumulated total (pretty randomly depending on the time of day) | 22:55 |
de-facto | LjL, 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 |
tinwhiskers | LjL: 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 |
LjL | tinwhiskers, but the CSV i get (not the covidly one obviously) has data from...? | 22:56 |
tinwhiskers | yeah, worldometers | 22:56 |
tinwhiskers | you can enable the live data on offloop but it's pretty pointless due to this | 22:57 |
tinwhiskers | i.e. I'm still collecting their data but only using it for you now. | 22:57 |
Skunny | de-facto thanks | 22:58 |
Skunny | yeah my test finally came back this morning | 22:58 |
Skunny | positive | 22:58 |
Skunny | but I knew that all ready | 22:58 |
Skunny | day 6 for me and I feel pretty good | 22:58 |
Skunny | just the anosmia | 22:59 |
LjL | tinwhiskers, 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 them | 22:59 |
LjL | so really what i have is an inconsistently constant stream of "new totals" that has to be treated as a realtime sort of thing | 23:00 |
LjL | it's not realtime, just there isn't a better way to treat it | 23:00 |
tinwhiskers | there'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 |
LjL | tinwhiskers, 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 fun | 23:02 |
de-facto | Skunny, very glad to hear you are doing so well :) | 23:02 |
tinwhiskers | those regions tend to be daily, worldometers is several times a day and covidly is... *shrug* | 23:02 |
LjL | tinwhiskers, 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 name | 23:02 |
LjL | this guy https://github.com/covidatlas/li which is the offspring of daily-updated-but-deprecated https://coronadatascraper.com/ | 23:03 |
tinwhiskers | ah | 23:03 |
tinwhiskers | yeah, I'd do things quite differently if I revisited it now :-/ | 23:04 |
tinwhiskers | although 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-facto | how does the upstream get daily incidence in sub-daily chunks? just polling on the latest data? | 23:05 |
tinwhiskers | however, that becomes less tenable over time | 23:05 |
tinwhiskers | de-facto: I poll every 15 minutes | 23:05 |
Brainstorm | Updates for US: +21407 cases (now 10.2 million), +271 deaths (now 243146) since an hour ago | 23:06 |
de-facto | do 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 |
tinwhiskers | no | 23:07 |
tinwhiskers | well, not that I noticed | 23:07 |
de-facto | asking 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 point | 23:08 |
LjL | de-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 whatever | 23:08 |
tinwhiskers | I guess you could look for changes in the data for "Yesterday" to tell when the day ends. | 23:08 |
LjL | de-facto, we have timestamps that come with the data, but they are not always reliable | 23:09 |
de-facto | yes like remember yesterday and look if its still the same, and if so assume it wont change anymore? | 23:09 |
tinwhiskers | yeah | 23:09 |
LjL | de-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 accurate | 23:09 |
LjL | what is "yesterday" | 23:09 |
tinwhiskers | worldometers has another table for data for "yesterday" | 23:10 |
LjL | i deal with UTC, but countries may give their official data in their local time | 23:10 |
LjL | and then yesterday is not the same yesterday | 23:10 |
CoronaBot | 04/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/jpv8o7 | 23:10 |
rpifan | ok and | 23:10 |
rpifan | what can he do | 23:10 |
rpifan | he must wait till january to do anyhting | 23:10 |
tinwhiskers | right, but presumably they only update "yesterday" at the end of whatever day cut-off time they have. | 23:10 |
LjL | tinwhiskers, in the case of covidly, i've verified the cutoff does *not* match the cutoff used by the individual countries | 23:11 |
tinwhiskers | ah. right. ok | 23:11 |
de-facto | but countries always should use the same timestamping scheme i guess | 23:11 |
LjL | what do you mean | 23:11 |
de-facto | like they stick to their usual procedure with accounting case numbers to their local time or such | 23:11 |
LjL | ultimately 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 valid | 23:12 |
LjL | de-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 subregions | 23:12 |
de-facto | the 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 comparison | 23:13 |
LjL | that is what Jigsy does manually by knowing the times at which to ask for the UK :P | 23:13 |
de-facto | no i dont meant to tune accordingly, i just meant their upstream behaviour somehow should be constant | 23:14 |
de-facto | hehe indeed | 23:14 |
LjL | i also eyeball the data for Italy. i know that Italy outputs once a day, so it's easy | 23:14 |
de-facto | i 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 slightly | 23:15 |
de-facto | so its not easy it seems | 23:15 |
LjL | Germany 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 |
LjL | hard to handle, but good in terms of having a stream of data that's updated often with fresh cases | 23:16 |
de-facto | so 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 |
LjL | de-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 jitter | 23:19 |
Brainstorm | New 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/74bzDF | 23:19 |
Brainstorm | Updates 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 ago | 23:20 |
de-facto | probably would have to try and look at the amount of jitter? its kinda hard to tell how bit it may be | 23:20 |
de-facto | how big the jitter might be | 23:21 |
de-facto | problem is if it comes in middle-sized chunks that have big temporal fluctuations in reporting, then jitter may be quite large | 23:22 |
de-facto | problem 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 |
LjL | yes, i know | 23:25 |
de-facto | having the most current data and having it comparable to the previous days is really hard as can be seen by all the portals | 23:25 |
LjL | but 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 it | 23:25 |
LjL | if you're just sometimes looking casually, then you won't | 23:25 |
LjL | but the more i elaborate the data (like by dividing and making it proportional to exactly 24h), but more i get away from the "raw" data | 23:26 |
de-facto | i could not remember the accumulated number for yesterday, but i would somewhat remember: ah yeah it was about +20k cases yesterday | 23:26 |
LjL | which means the human can pay less attention but the bot really must do it correctly for it to make any sense | 23:26 |
LjL | de-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 minutes | 23:27 |
LjL | i 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 misleading | 23:27 |
LjL | on 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 default | 23:27 |
LjL | tinnitus galore | 23:29 |
Skunny | tinnitus! | 23:30 |
de-facto | well average for the edge is the value itself afaik | 23:30 |
de-facto | because future is unknown, so without extrapolation there is no average for most current data point | 23:31 |
LjL | Skunny, yes, an obnoxious little beast | 23:31 |
LjL | de-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 data | 23:32 |
Skunny | I have that for long time from playing in bands and going to shows | 23:33 |
de-facto | how 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 yesterday | 23:33 |
Skunny | it sucks | 23:33 |
LjL | Skunny, 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 now | 23:34 |
de-facto | LjL, yeah or that linear extrapolation, would become more accurate with each update for that timegap then | 23:34 |
LjL | i *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 is | 23:34 |
LjL | de-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... :P | 23:35 |
Brainstorm | Updates for US: +26320 cases (now 10.2 million), +311 deaths (now 243186) since 2 hours ago | 23:36 |
de-facto | LjL, i mean what date will end up as daily incidence in the far past? | 23:36 |
de-facto | the date inside the dataset i meant | 23:36 |
LjL | far past? i'm definitely not looking at the far past in the bot | 23:36 |
LjL | i'm a bit confused | 23:37 |
de-facto | no 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 such | 23:38 |
LjL | i don't have changes to past data | 23:38 |
LjL | many countries don't do that | 23:38 |
LjL | but even for countries that do do that, i don't have that | 23:38 |
LjL | the data i get are always for "closest to the current time" | 23:39 |
de-facto | yeah hence how about just using the date in the dataset itself and see if jitter is a problem | 23:39 |
LjL | that could change if i started using data from Li, or elsewhere, i guess, but that's what it is now | 23:39 |
LjL | but i do that | 23:39 |
LjL | the dataset comes with a timestamp for the data point, and i use that timestamp | 23:40 |
LjL | that timestamp is the date, i have no other date | 23:40 |
LjL | also 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-facto | ah i see its unixtime, i hoped for a date like 2020-11-07 | 23:41 |
de-facto | "LastUpdated" and not "ReportedOn" | 23:42 |
LjL | you see there is no delta, it's just the total accumulated number of cases by the time of LastUpdated | 23:43 |
de-facto | yeah my mistake, i did not look at the dateset before | 23:43 |
LjL | any delta is only inside my code | 23:43 |
de-facto | yeah | 23:43 |
de-facto | but where does the incidence data for offloop come from then | 23:43 |
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-facto | they clearly have daily granularity for that data | 23:44 |
LjL | de-facto, jhu, or covidly if you select alternate | 23:44 |
LjL | and 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 :P | 23:44 |
Jigsy | Hm? | 23:45 |
LjL | Jigsy, discussing how to change Brainstorm's output for more usable results | 23:49 |
de-facto | what 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-facto | i am not sure that yesterday incidence is included in the endpoint you are using though, maybe its only in the HTML? | 23:51 |
Brainstorm | Updates for US: +26921 cases (now 10.2 million) since 2 hours ago — Switzerland: +18 deaths (now 2749) since 7 hours ago | 23:51 |
LjL | oh some output at last | 23:51 |
LjL | de-facto, yeah only in the HTML | 23:51 |
LjL | the output it gave now looks much like the output it always gives, but that's (hopefully) just because it hasn't accumulated much history yet | 23:53 |
de-facto | but where does that granularity originate from? upstream or offloop? | 23:53 |
LjL | upstream for jhu, for covidly i'm not sure | 23:54 |
LjL | anyway i am really tempted to play with https://github.com/covidatlas/li | 23:54 |
LjL | it has subregions for a number of countries *and* i can fetch as often as i want until i get banned | 23:55 |
de-facto | because 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 |
CoronaBot | 04/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/jprhnd | 23:58 |
de-facto | nice also for cluster 5? | 23:59 |
Generated by irclog2html.py 2.17.0 by Marius Gedminas - find it at https://mg.pov.lt/irclog2html/!