| DocScrutinizer05 | LjL: that's what I said. I enetered 222 into the box and c&p'ed the generated URL from FF addressbar | 00:04 |
|---|---|---|
| DocScrutinizer05 | and it doesn't create the same result in a second tab where I paste that URL as it does - even after F5 - in the original tab | 00:04 |
| DocScrutinizer05 | there's clearly a silly bug in JS code | 00:05 |
| DocScrutinizer05 | _if_ I was eager to spot ir (which wouldn't help since the source is from server so locally fixing it doesn't work) I'd simply compare leftTrim to rightTrim, the latter *works* as supposed | 00:07 |
| LjL | DocScrutinizer05, but you said leftTrim is getting ignored, i assumed that meant you didn't see a graph respecting it...? i'm just trying to make sure i'm understanding correctly | 00:07 |
| DocScrutinizer05 | it's just annoying since you can't refer to a particular representation of data, which sometimes is needed to make a certain effect visible | 00:08 |
| LjL | i see | 00:08 |
| Brainstorm | Updates for US: +11132 cases (now 9.8 million), +125 deaths (now 239747) since 34 minutes ago | 00:09 |
| LjL | i'm afraid i'm web-incompetent enough i can't even get the site's js code copypasted somewhere i can reformat it | 00:15 |
| LjL | tinwhiskers will have to look at this when he can i guess | 00:15 |
| DocScrutinizer05 | :-D spot the errors | 00:15 |
| DocScrutinizer05 | function trim(dataset) { | 00:15 |
| DocScrutinizer05 | var lTrimVal = parseInt($("#lefttrim").val(),10); | 00:15 |
| DocScrutinizer05 | var rTrimVal = parseInt($("#righttrim").val(),10); | 00:15 |
| LjL | i'm afraid i've no idea. case sensitiveness? | 00:16 |
| LjL | but no because it would go for both | 00:16 |
| DocScrutinizer05 | hint: I don't know either, for sure | 00:16 |
| DocScrutinizer05 | 10 10 maybe | 00:16 |
| LjL | i assume that's a default if the variable can't be read... if that function works similarly to python's .get() | 00:17 |
| LjL | oh no it's the base | 00:18 |
| de-facto | nope thats parse a number to base 10 from a field with id #lefttrim or #righttrim i thought you confirmed the input fields work | 00:18 |
| DocScrutinizer05 | oh | 00:18 |
| tinwhiskers | yeah, I noticed the left trim bug the other day. I haven't been motivated to fix it. | 00:18 |
| tinwhiskers | I thought it used to work and I didn't change anything that I know of, but meh. | 00:18 |
| LjL | tinwhiskers, sounds like Brainstorm | 00:18 |
| tinwhiskers | heh | 00:18 |
| DocScrutinizer05 | then I got no damn idea, I checked all occurrences of "trim" and didn't see any other faintly suspicious stuff | 00:19 |
| DocScrutinizer05 | reserved word? | 00:20 |
| tinwhiskers | ah. ok. found it. Weird it took so long to notice. Anyway, fixed now. | 00:24 |
| tinwhiskers | if($frm{'leftTrime'}>0) { | 00:25 |
| DocScrutinizer05 | lol | 00:26 |
| DocScrutinizer05 | thanks! :-) | 00:26 |
| LjL | tryme | 00:26 |
| DocScrutinizer05 | where was this? I can't find it in page text | 00:28 |
| tinwhiskers | that's in the back-end code that generates the js | 00:28 |
| tinwhiskers | perl | 00:28 |
| DocScrutinizer05 | aaah | 00:28 |
| tinwhiskers | well apparently it's been like that ever since I added that code to update the url as you make changes to the settings, so we just never noticed. I guess left trim wasn't as useful back then as it's becoming now. | 00:40 |
| LjL | tinwhiskers, i only started using it sometimes recently fwiw | 00:41 |
| LjL | and i never really copypasted a url to it | 00:41 |
| tinwhiskers | yeah | 00:41 |
| ghost_rider[m] | Some users here should organize and setup a wiki to organize information they share | 01:07 |
| ghost_rider[m] | Some times I catch really valuable conversations and links | 01:07 |
| LjL | ghost_rider[m], it's not a wiki, but anyone is free to suggest something for adding to https://covid19.specops.network/ if they think it's an important thing that fits right in there. i work on it a fair amount and try to catch many interesting links people post, but i'm not always watching. but i also get the impression barely anyone but me even goes to read it | 01:10 |
| Brainstorm | New from r/Coronavirus: Coronavirus: Coronavirus updates: United States tops 100,000 new coronavirus cases in a day for first time → https://is.gd/nTSvig | 01:13 |
| LjL | the mink thing i have a feeling will turn *big* | 01:20 |
| LjL | they can't be sure every human who has caught the mutation has been tracked down, and they can't be sure every mink carrying it will be killed | 01:20 |
| LjL | and this virus has already shown that when you "can't be sure", it generally can | 01:20 |
| LjL | plus, once this is shown to happen once with one type of animal, what's logically to stop it from happening again, and again, and again... making vaccine efforts maybe not futile, but a lot more complicated than they already are | 01:21 |
| Brainstorm | New from r/WorldNews: worldnews: France registers over 40,000 new COVID-19 cases, warns of under-reporting → https://is.gd/KbIw9t | 01:22 |
| Brainstorm | Updates for US: +4943 cases (now 9.8 million), +55 deaths (now 239802) since an hour ago — Canada: +187 cases (now 247555), +1 deaths (now 10331) since 2 hours ago | 01:24 |
| de-facto | LjL do you have a link describing the mutation? | 01:27 |
| ryouma | having significant trouble dealing with the world status and poential status, mostly pandemic and us politics, even if i were not on the absolute edge personally. detachment used to be possible. rational self-control then was the best i could do. now it is less describable. | 01:28 |
| DocScrutinizer05 | tinwhiskers: re lefttrim, could you support the widespred "<0" approach? leftTrim=-14 == "last two weeks" ? | 01:28 |
| LjL | de-facto, no, all i have is a Danish government press conference that claims, as translated from Danish by someone on Reddit: | 01:28 |
| LjL | On Tuesday, the government received a note from the Statens Serum Institut, which has exposed the mutated coronavirus to antibodies. The result, according to SSI, was deeply troubling because the mutated coronavirus did not respond well to the antibodies. | 01:28 |
| LjL | Thus, there is a risk that a possible vaccine against covid-19 will not have the desired effect if the mutated virus from mink spreads further among humans. | 01:28 |
| LjL | https://www.reddit.com/r/Coronavirus/comments/jnwx9x/denmark_mutated_coronavirus_from_mink_is_a_threat/gb45enn/ | 01:29 |
| de-facto | ugh | 01:29 |
| LjL | i echo your thought | 01:29 |
| ryouma | does it just mean new vaccine? | 01:30 |
| DocScrutinizer05 | the damn friggin terrifying munk thing - I hope they will contain it for good, or they will receive 100 times more bashing than china did | 01:30 |
| DocScrutinizer05 | mink* | 01:30 |
| LjL | de-facto, they have notified the WHO, they are killing every single mink they can get their hands on (and are calling on the army to help), and they are locking down all areas of the country where minks are present. so *they* think this is serious. | 01:31 |
| LjL | ryouma, "just", you say | 01:31 |
| ryouma | that is better than that not meaning that | 01:31 |
| LjL | ryouma, you realize vaccines are already being produced at scale (even before phase 3 trials are over), right? | 01:31 |
| LjL | yes | 01:31 |
| LjL | marginally | 01:31 |
| LjL | it may mean we have to chase this virus forever as it mutates around other animals | 01:32 |
| LjL | so, i'll stick with marginally | 01:32 |
| de-facto | exactly what i was fearing when i first heard of it infecting minks, i think we even talked about it here | 01:32 |
| de-facto | ping-pong-ping | 01:33 |
| de-facto | very bad | 01:33 |
| LjL | well, it's what i feared when i heard it could propagate in cats | 01:33 |
| LjL | it would be nice if sometime what i fear didn't come true | 01:33 |
| LjL | there has been a lack of that lately | 01:33 |
| de-facto | i think we even discussed it at the very beginning when speculating about the natural origin and Drosten mentioning that mink farms could play a role | 01:34 |
| de-facto | that was in spring or such | 01:34 |
| LjL | i was probably busy understanding what a lockdown was, back then | 01:34 |
| LjL | and adjusting to needing to fill in a piece of paper to get out of my door | 01:34 |
| DocScrutinizer05 | %title https://www.reuters.com/article/us-health-coronavirus-denmark-mink/denmark-to-cull-entire-herd-of-mink-due-to-risk-of-coronavirus-mutation-tv2-idUSKBN27K1X6 | 01:35 |
| Brainstorm | DocScrutinizer05: From www.reuters.com: Denmark plans to cull its mink population after coronavirus mutation spreads to humans | Reuters | 01:35 |
| DocScrutinizer05 | then otoh, flu mutates like mad, and we get a vaccination each year, and even if we don't, we still can cope with it better this year since we seen it's sibling last year | 01:40 |
| DocScrutinizer05 | the idea to get rid of sars-cov2 for good is dilusional anyway | 01:41 |
| de-facto | according to nextstrain SARS-CoV-2 got approximately 22-23 mutations per year | 01:44 |
| de-facto | would be neat to know the exact sequence to see its spread in lab data | 01:44 |
| LjL | well the idea of living with this thing, with its current levels of fatality at least, is | 01:45 |
| LjL | i'd rather die of something else sooner if that's going to be the case | 01:46 |
| LjL | also, apparently they have *no idea* how the minks are infecting each other in *different* farms kilometers apart, but so far they are suspecting birds, seagulls. | 01:46 |
| LjL | if it birds, it means that it doesn't matter much if Denmark manages to kill 100% of their minks. birds happen to fly. | 01:47 |
| LjL | de-facto, DocScrutinizer05, ugh, ugh, more translations from Danish | 01:48 |
| LjL | "ECDC, WHO and the EU-commission have been informed of the newly discovered Covid strain. Initial research points to antibodies and treatment being significantly less effective against the new strain." | 01:48 |
| LjL | *and treatment* | 01:48 |
| Brainstorm | New from The Atlantic: A Dreadful New Peak for the American Pandemic: The United States reported 103,087 cases of COVID-19 today, the highest single-day total on record, according to the COVID Tracking Project at The Atlantic . It marks the first time that the country—or any country in the world, for that matter—has documented more than 100,000 new [... want %more?] → https://is.gd/E8XUWj | 01:49 |
| de-facto | its not on nextstrain yet the latest from denmark i could find is https://nextstrain.org/ncov/global?c=country&l=clock&s=Denmark/ALAB-HH-266/2020 | 01:49 |
| de-facto | that would be 2020-05-09 | 01:50 |
| LjL | i haven't even thought to look, i wouldn't understand anything from looking at it anyway... | 01:50 |
| de-facto | neither do i, yet i like to guess things :)) | 01:50 |
| DocScrutinizer05 | LjL: >>living with this thing<< means living, not dying. We live with flu and we gonna live with covid all the same | 01:51 |
| DocScrutinizer05 | this isn't a supervirus, it's just new | 01:52 |
| DocScrutinizer05 | >>and treatment<< well, treatment is what antibodies are zsed for, so it's obvious. They got no better data yet I'd bet | 01:53 |
| LjL | it's significantly worse than the flu. for now, at least, but i don't see a compelling reason why it should quickly become milder in most strains | 01:53 |
| DocScrutinizer05 | used* | 01:53 |
| de-facto | >>“China, Denmark, and Poland should support and extend the immediate and complete ban of mink production,” Sonne and his co-authors wrote last week.<< full ack. | 01:54 |
| DocScrutinizer05 | LjL: I explained already that you "get used to it" | 01:54 |
| LjL | antibodies aren't used very often for treatment. they have been used, they may be a good path to follow, but in this country at least, they are very rarely used in clinical practice | 01:54 |
| de-facto | Fur farms should be ended permanently, they are not essential for anything | 01:54 |
| DocScrutinizer05 | it's not the virus getting milder, it's humans getting tougher | 01:54 |
| LjL | that basically means the ones who don't dying, though | 01:55 |
| LjL | yes, i know it's also known as natural selection | 01:55 |
| LjL | i'm just not a fan of the idea of living through a big spike of that on my species | 01:55 |
| DocScrutinizer05 | I already explained that vaccination serves same purpose as catching and surviving the virus does, in this context | 01:56 |
| LjL | and i already noted how new strains "escaping" antibodies like this one seems to do potentially (but very convincingly, to me) means that one vaccine won't be enough, and we'll have to chase the virus | 01:56 |
| LjL | and yes, we already do that with the flu, but the flu doesn't kill | 01:57 |
| LjL | %cases italy | 01:57 |
| Brainstorm | LjL: In Italy, there have been 790377 confirmed cases (1.3% of the population) and 39764 deaths (5.0% of cases) as of 8 hours ago. 16.5 million tests were performed (4.8% positive). Fatality can be broadly expected to lie between 1.4% (assuming prevalence as in tests) and less than 11.5% (considering only deaths and recoveries). See https://offloop.net/covid19/?default=Italy for time series data. | 01:57 |
| LjL | ... 5% of the people who catch it | 01:57 |
| DocScrutinizer05 | >>flu mutates like mad, and we get a vaccination each year, and even if we don't, we still can cope with it better this year since we seen it's sibling last year<< | 01:57 |
| LjL | meh whatever | 01:57 |
| DocScrutinizer05 | >>flu mutates like mad, and we get a vaccination each year, and ***even if we don't, we still can cope with it better this year since we seen it's sibling last year***<< | 01:57 |
| LjL | ***meh, whatever*** | 01:58 |
| de-facto | btw it does not mean that there is no cross immunity to that strain whatsoever, it just could mean that the antibodies dont protect efficiently against it, yet the immune system already would know the other parts of the virus so i guess its not like being completely naive to SARS-CoV-2 yet we will see what they will find out | 01:59 |
| DocScrutinizer05 | you're negating the perspective of finding a way to coexist with this virus. This means you're resigning and hoping to die fast | 01:59 |
| DocScrutinizer05 | since the virus won'T go away | 01:59 |
| DocScrutinizer05 | and it _will_ mutate | 02:00 |
| DocScrutinizer05 | however our immune system learned to cope with worse virus types | 02:01 |
| de-facto | but we will gain immunity against it (e.g. by annual SARS-CoV-X-vaccinations), so it will be less severe | 02:01 |
| DocScrutinizer05 | and no, this isn't evolution, this is _your_ immune system that learned it | 02:01 |
| DocScrutinizer05 | or what de-facto said | 02:02 |
| de-facto | well actually probably both, mutations that dont cause symptoms will be happily spread by their carriers without them isolating due to feeling sick | 02:02 |
| DocScrutinizer05 | that too, actually. Right | 02:03 |
| LjL | 18<29DocScrutinizer0518> you're negating the perspective of finding a way to coexist with this virus. This means you're resigning and hoping to die fast | 02:03 |
| LjL | how exactly was that not clear when i said | 02:03 |
| LjL | 20<LjL>30 i'd rather die of something else sooner if that's going to be the case | 02:03 |
| de-facto | so i guess both effects would work in our favor | 02:03 |
| DocScrutinizer05 | stress weakens the immune system | 02:05 |
| LjL | de-facto, if our vaccination doesn't target the thing that new year's virus brings, meaning the wrong antibodies get generated, why will that make it less severe? | 02:05 |
| de-facto | and if such a milder strain (potentially with higher transmissibility similar to D614G) also would educate our immune system to develop immunity against more severe strains it may even displace them to some degree | 02:05 |
| ryouma | which parts of the immune system does stress weaken | 02:05 |
| DocScrutinizer05 | that's a highly interesting question, still under evaluation | 02:06 |
| de-facto | LjL, i am not sure but i think its not like black and white but more like gray-ish probabilities e.g. less effective immunity but not completely naive | 02:06 |
| LjL | de-facto, yes, i think maybe researchers should really start working hard on actually designing a human-mutated strain that is innocuous but provides immunity *and* is contagious... even though it would be a difficult and dangerous strategy. but at this point i'd find it better than being haunted by the idea of meeting a mink for the rest of my life (so to speak, meeting a mink is not really the issue) | 02:06 |
| de-facto | the problem is what happens if it recombines with dangerous wild type then? | 02:07 |
| LjL | well, that's why it's difficult and dangerous | 02:07 |
| LjL | i'm just hoping a safe way can be figured out | 02:08 |
| LjL | i have no idea how to make that happen | 02:08 |
| de-facto | but maybe taking essential parts away from its RNA that make it severe to create an attenuated strain e.g. for nose spray vaccination would be neat? | 02:08 |
| de-facto | no idea if that is possible though | 02:09 |
| LjL | de-facto, as long as it's infectious. the problem i see with vaccines, attenuated or not, is are we going to be able to produce them at the needed scale? yes, true, we do it each year with the flu, but now we're starting from scratch and have about 8 billion people who have received no vaccine at all | 02:09 |
| LjL | so i'm thinking about something infectious to let reproduction solve the scaling issue | 02:09 |
| LjL | but speaking of the flu vaccine | 02:10 |
| ryouma | you oppose volunteer infection on ethical grounds, but propose that which is dangerous and non-volunteer | 02:10 |
| LjL | i am not going to get it this year | 02:10 |
| LjL | and not by choice | 02:10 |
| DocScrutinizer05 | this safe method has a name: vaccination. It's the approach that doesn't the ting allow to multiply and spread uncontrolled and that's preferred prolly becazse too many times the "enemy of my enemy" concept turned back at us and bit us | 02:10 |
| de-facto | i think there were such approaches was it smallpox? | 02:10 |
| LjL | simply because my government was incompetent enough that it didn't secure enough supplies | 02:10 |
| LjL | so there is that about the flu, *and* about this | 02:10 |
| dTal | LjL: I think I missed my window on that too | 02:10 |
| LjL | DocScrutinizer05, when has this concept been tried? | 02:11 |
| LjL | i know of variolation, but that was, like, uh, *very* experimental so to speak | 02:11 |
| ryouma | consider rabbits in australia. kudzu in the us. zebra mussels. | 02:12 |
| DocScrutinizer05 | let's see.... ausatralian killer frogs? a zillion more times | 02:12 |
| de-facto | i think variolation was the ancestor to vaccination and may have emerged from China | 02:12 |
| LjL | eh, i was thinking something closer to... viruses | 02:13 |
| LjL | de-facto, that's my understanding too | 02:13 |
| DocScrutinizer05 | the most basic vaccination concept is based on passivated (by heat, radiation, whatever) actual virus | 02:13 |
| DocScrutinizer05 | it's like the first or second ever vaccination done | 02:14 |
| de-facto | β-propiolactone | 02:15 |
| LjL | the first ever vaccination done involved taking the smallpox virus from a cow ("vacca" in latin) after realizing that the cow type was milder, yet protected humans from the human type | 02:15 |
| DocScrutinizer05 | and viruses may have "sex", so beware releasing a supposedly harmless highly infectious sibling of a dangerous virus to the wild | 02:15 |
| LjL | so i'm arguing that's the first ever because it created the term, if nothing else | 02:15 |
| LjL | DocScrutinizer05, that's what de-facto meant when he asked how to deal with recombination | 02:16 |
| Brainstorm | New from ProPublica: For the Postal Service, a Frantic Election Day Turns to Finger-Pointing the Day After: by Maryam Jameel and Ryan McCarthy ProPublica is a nonprofit newsroom that investigates abuses of power. Sign up to receive our biggest stories as soon as they’re published. At a major regional U.S. Postal Service facility in Pennsylvania, [... want %more?] → https://is.gd/wlK1su | 02:16 |
| LjL | i am aware of the issue, i'm just not convinced researchers couldn't/shouldn't work in this direction and see if they can figure out something to prevent it | 02:16 |
| DocScrutinizer05 | n8 | 02:16 |
| LjL | after all, the current vaccine efforts are enormous. maybe we should also have a plan B if simply vaccinating 8 billion people several times turns out to be impractical | 02:16 |
| de-facto | and also current vaccines are developed with very fast methods, so maybe they can be easily modified? | 02:17 |
| tinwhiskers | DocScrutinizer05: OK, I think negative values for leftTrim should do that now | 02:17 |
| de-facto | question would be if they would have to go through full certificaitons again | 02:17 |
| ryouma | you could almost wipe out hte human race with yuour idea | 02:17 |
| tinwhiskers | interestinly when I just wrote leftTrim I actually just write leftTrime :-/ | 02:17 |
| tinwhiskers | but in English | 02:18 |
| de-facto | i remember we even discussed about the phylogenetic tree spreading and if that would translate to a limited window in time where current vaccines would be effective | 02:18 |
| de-facto | so exactly that window may just have been slammed shut with those mink farms | 02:18 |
| de-facto | so maybe we need a two strain vaccination then? | 02:18 |
| LjL | de-facto, and we don't even have a single person vaccinated yet outside of phase 3 trials. so, good job us! | 02:19 |
| de-facto | yeah we are too slow | 02:19 |
| de-facto | with everything, even simple non-pharmaceutical measures | 02:19 |
| LjL | oh well that's even less justifiable | 02:19 |
| DocScrutinizer05 | de-facto: nope, flu vaccines don't | 02:19 |
| LjL | vaccines being slow is... a problem, clearly, but they're going pretty damn fast by any previous standard | 02:19 |
| DocScrutinizer05 | go throu phase2/3 | 02:20 |
| de-facto | DocScrutinizer05, but flu disappears in the summer so its always only the new strains afaik | 02:20 |
| LjL | ryouma, i honestly think this thing could almost wipe out the human race without my help | 02:20 |
| LjL | but i'm flattered if you think my ideas are capable of wiping out the human race | 02:20 |
| de-facto | SARS-CoV-2 did not disappear at all, its phylogenetic tree keeps spreading constantly | 02:21 |
| ghost_rider[m] | LjL: LoL | 02:21 |
| LjL | de-facto, although there *have* been not-easily-explainable surges and stops, as you often noted | 02:22 |
| LjL | not complete stops, but stark slowdowns, often in neighboring areas | 02:22 |
| DocScrutinizer05 | tinwhiskers: thanks, tested and approved :-) | 02:22 |
| de-facto | yes i am a bit puzzled by that since i did never get the feeling that i would understand the cause of those | 02:22 |
| tinwhiskers | :-) | 02:22 |
| LjL | de-facto, well, if we understood the cause of those we may be able to instate lockdowns in advance and avoid filling up hospitals, so please think harder | 02:24 |
| de-facto | well at first we would need to have some "realtime sensors" out there to get a representative picture of current dynamics, something like those REACT studies you linked a few days ago | 02:25 |
| de-facto | we always react only to dynamics, weeks after the fact already happened | 02:25 |
| ryouma | india is worth studying | 02:26 |
| ryouma | they just got better and nobody knows why | 02:27 |
| ryouma | less bad | 02:27 |
| metreo | probably the migrations have subsided | 02:27 |
| metreo | and people are settled and becoming more cautious | 02:27 |
| metreo | are my guesses | 02:27 |
| metreo | also the India numbers are subject to testing limitations | 02:28 |
| de-facto | maybe if combining such representative realtime monitoring with other parameters that may be suspected to have influence (weather, mobility, news, contact rates, your guess is as good as mine...) and feed it into a big data analysis such as a neuronal network it could uncover hidden correlations that may be worth an investigation about it being causative or only happening at the same time (e.g. due to a shared hidden cause in the | 02:28 |
| de-facto | background) | 02:28 |
| metreo | do we know that India isn't running out of tests or reducing testing | 02:28 |
| de-facto | yeah we really do need to base assumptions on representative data, i dont understand at all why not every country dedicates 1% testing capacity to random representative fast track sampling | 02:29 |
| ghost_rider[m] | Reading you guys Resident Evil come again to my mind, it makes sense a "hive" | 02:29 |
| ryouma | if you think the virus could wipe out hte human race, then perhaps a small number of volunteer vsaccine testers, who could mitigate that, would consistute less ethical harm than forcing humanity to particpate in a global experiment that cannot be stopped | 02:29 |
| de-facto | with priority in analysis to get as close as possible to real time projections | 02:29 |
| de-facto | ghost_rider[m], yeah those were really awesome movies indeed :) | 02:30 |
| de-facto | also we need to have solutions that scale a lot better | 02:32 |
| de-facto | its such a huge hassle to get a test done almost a fucking year into the pandemic, this is unacceptable | 02:33 |
| LjL | ryouma, if a human-created, severity-attenuated strain can recombine with the virus in the wild and create something that can wipe out the human race (your claim) then the same thing can also happen with just the virus itself working its way through various animals (my claim) | 02:33 |
| metreo | each test is several hundreds of dollars in costs | 02:33 |
| LjL | what do you call, in ethics, guilt by inaction | 02:33 |
| LjL | metreo, uh no it's not? | 02:33 |
| de-facto | LjL, yeah but what about if only taking away parts of the wild type RNA without adding anything in addition? Not sure but could there anything worse happen than it recombining with the wild type again and regain the ability that was taken away from it? | 02:34 |
| de-facto | i am not sure about that one, like if it recombines in another position or such | 02:35 |
| de-facto | a test is around 30 Euros/Dollars or such if bought in quantities at least a few months ago afaik | 02:36 |
| LjL | also speaking of experiments that cannot be stopped, maybe we *should* have another good look at level 4 bio labs, since it *is* certainly possible that their dangerous mutated strains can cause a deadly experiment on humanity (whether or not that actually happened in Wuhan) | 02:36 |
| ryouma | not capable of arguing sorry but i would | 02:37 |
| tinwhiskers | <de-facto> [...] i dont understand at all why not every country dedicates 1% testing capacity to random representative fast track sampling - YES! we've been saying this since March. Why odes the world ignore us?! | 02:37 |
| LjL | tinwhiskers, I KNOW | 02:38 |
| LjL | let's make a petition on change.org | 02:38 |
| de-facto | still its a huge hassle, a colleague's kid got an outbreak in school class informed last friday, tested on monday and still no fucking result, so we all have to isolate until they get their result, absolutely unacceptable slow | 02:38 |
| LjL | that'll make the world stop ignoring us | 02:38 |
| tinwhiskers | I'm sure the epidemiologists have all been pushing for this and being ignored. It's pretty basic stuff. | 02:38 |
| de-facto | yes its an obvious idea | 02:38 |
| ryouma | perhaps the random testing is limited by accuracy and prevalence | 02:38 |
| de-facto | actually the first idea an epidemiologist would have: get reliable data to base the models upon | 02:38 |
| LjL | ryouma, but accuracy is pretty good, and prevalence is, well, not low :\ | 02:39 |
| tinwhiskers | actually I think NZ does do this now but they have plenty capacity to spare. However given how useful it would be to have real randomised background data it boggles mind mind it isn't considered higher priority. | 02:40 |
| LjL | maybe it's partly for PR reasons | 02:40 |
| tinwhiskers | possibly | 02:40 |
| ryouma | fear of false positive rate | 02:40 |
| LjL | it takes weeks for people to get their swab results. de-facto is understandably annoyed by that. | 02:40 |
| LjL | then people learn that a portion of the tests is being used just randomly | 02:40 |
| LjL | "random" doesn't sound good to people at large, i guesss | 02:41 |
| tinwhiskers | perhaps | 02:41 |
| de-facto | in my opinion getting as close to realtime as possible could avoid many more cases by appropriate action in time than loosing that 1% testing capacity is worth in ending targeted infection chains | 02:41 |
| ghost_rider[m] | LjL: it really started in Whuan or was them the first to flag ? | 02:41 |
| LjL | what | 02:41 |
| LjL | oh | 02:41 |
| LjL | i don't know | 02:41 |
| LjL | there are indications that it was present in Italy, France, Spain and elsewhere in November, but those indications are not certain | 02:41 |
| ryouma | do they not have databases of animal strains and where thye live? | 02:42 |
| LjL | and even if true, it doesn't mean it wasn't present in Wuhan as well | 02:42 |
| tinwhiskers | the data showing it was present in places like France before it was found in Wuhan I'm still pretty sceptical about. | 02:42 |
| de-facto | if it was present there that early, why did they not see a HUGE outbreak in the winter then? | 02:42 |
| LjL | ryouma, of SARS-COV-2? i highly doubt it... | 02:42 |
| de-facto | i would suspect those to be artifacts | 02:42 |
| LjL | de-facto, we did retrospectively learn that doctors were warning us about more pneumonia cases than usual. nothing HUGE, i guess, but something. | 02:42 |
| ghost_rider[m] | Don't matter anyway, but your note on biolabs after so much weapons depots blowing up and that bio in Russia that blowup is a warning to everyone | 02:42 |
| tinwhiskers | hmmm | 02:43 |
| tinwhiskers | that's getting a bit far out on a conspiracy limb for my comfort. Highly speculative. | 02:43 |
| ryouma | well having stuff around can be an issue | 02:44 |
| ryouma | but you can't just tell a major power stop having stuff aorund and know that they will get rid of it | 02:44 |
| tinwhiskers | yeah, it could have escaped from a lab | 02:45 |
| ryouma | not saying it did or addressing htat pointg | 02:45 |
| de-facto | thing is, what difference does it make for now? we would have to deal with it anyhow | 02:46 |
| ryouma | the us did a lot of conspiracy stuff htat is mainstream accepted during cold war | 02:46 |
| ryouma | right | 02:47 |
| LjL | de-facto, understanding things always has the potential of making a difference | 02:47 |
| de-facto | well would it be useful for vaccination development to have its ancestor strain, .e.g from its natural reservoir? | 02:47 |
| LjL | de-facto, "what difference does it make if it stopped in the summer in europe? it's back now" | 02:47 |
| LjL | anyway, i'm reading this | 02:47 |
| LjL | "With regard to the 40 sewage samples collected between October 2019 and February 2020 from the WTPs in Milan, Turin and Bologna, SARS-CoV-2 RNA was detected by nested RT-PCR in 18 samples (amplicon sequences confirmed as SARS-CoV-2 by blast analysis) and in 26 samples by the newly developed real-time RT-(q)PCR (Table 2), with an overall agreement between the two 251 assays of 65.0% (26/40 paired results). In 15 samples, SARS-CoV-2 RNA was detected by both | 02:47 |
| LjL | 252 methods." | 02:47 |
| LjL | from https://www.medrxiv.org/content/10.1101/2020.06.25.20140061v1.full.pdf | 02:47 |
| LjL | can those all just be artifacts? | 02:47 |
| LjL | they used two different methods to run the PCR, and still found it with both methods in 15 samples | 02:47 |
| tinwhiskers | it's certainly interesting but the epidemiology doesn't support it | 02:48 |
| LjL | by the way, it says preprint, but it's published now | 02:49 |
| tinwhiskers | ah. good to know. | 02:49 |
| LjL | %paper doi:10.1016/j.scitotenv.2020.141711 | 02:50 |
| Brainstorm | LjL: An error occurred while searching. | 02:50 |
| LjL | figures | 02:50 |
| tinwhiskers | maybe someone at the lab was infected and the room was full of aerosols for all the tests... who knows. Maybe it's real. | 02:50 |
| tinwhiskers | maybe there were cases in France, etc. but they were not picked up as covid and didn't spread for some reason, but it's a bit whiffy. | 02:51 |
| LjL | yes, and the same happened in similar experiments carried out in Spain, as well as the autopsy in France (iirc) | 02:51 |
| de-facto | interesting paper i did only remember one where they had one sample and we discussed about the cycle threshold | 02:51 |
| de-facto | and why they did not try to confirm it by another way, e.g. obtaining a full sequence or such | 02:52 |
| de-facto | idk if that is even possible form those sewer samples though | 02:52 |
| tinwhiskers | yeah, if we had sequence data so we could place it in the phylogenetic tree that would certainly be compelling. | 02:52 |
| de-facto | would they contain enough information to reconstruct all 30k bases or are they only containing damaged fragments | 02:52 |
| LjL | de-facto, it says "Moreover, as a routine procedure for all conventional 388 PCRs, the identity of all amplified fragments was confirmed by sequencing" | 02:53 |
| tinwhiskers | hrm. So... they should know if it predated other sequences | 02:54 |
| LjL | "Sequences were submitted to NCBI GenBank with the following accession 164 numbers: [a.n. to be assigned]." | 02:54 |
| tinwhiskers | ok | 02:54 |
| LjL | that's from the preprint, hopefully it's assigned in the non-preprint | 02:54 |
| tinwhiskers | that will be very telling | 02:54 |
| de-facto | so if they have sequences they should be able to compare them with current phylogenetic tree and also if they are of more recent strains or ancestors to current tree | 02:54 |
| tinwhiskers | I could well have my mind changed by seeing that | 02:54 |
| Brainstorm | Updates for US: +5280 cases (now 9.8 million), +27 deaths (now 239829) since an hour ago — Canada: +923 cases (now 248478), +17 deaths (now 10348) since an hour ago | 02:54 |
| LjL | MT843229-MT843240 | 02:55 |
| de-facto | so if they would have full sequences they should be able to tell if its contamination from current circulating strains or ancestors of it | 02:55 |
| tinwhiskers | far out | 02:55 |
| tinwhiskers | right | 02:55 |
| tinwhiskers | let's see if we can find in in nextstrain | 02:55 |
| tinwhiskers | that will put this puppy to bed | 02:56 |
| de-facto | LjL, where is that from? | 02:57 |
| de-facto | the MT843229-MT843240 | 02:57 |
| LjL | de-facto, the full text at https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/32835962/ | 02:57 |
| de-facto | thanks | 02:57 |
| LjL | FWIW this study is by now cited by 10 other studies | 02:58 |
| tinwhiskers | Has anyone done the obvious then? | 02:59 |
| tinwhiskers | it seems the NCBI IDs are different to the nextstrain IDs | 03:00 |
| Brainstorm | New from r/WorldNews: worldnews: Mutated variety of coronavirus found in Danish mink → https://is.gd/QgIBVR | 03:00 |
| tinwhiskers | Anyone got access to NCBI Genbank? | 03:00 |
| LjL | no me | 03:00 |
| LjL | not* | 03:00 |
| de-facto | i found some on https://www.biosino.org/ViGTK/virusSearch/list?taxonIdAndMore%5B0%5D=2697049&host=wastewater%20metagenome | 03:01 |
| LjL | i've been saying there were multiple studies about sewage (and the France thing) for months, and i only have so much ability to understand how to find genetic sequences, and that ability is near zero | 03:01 |
| LjL | but you were all saying "it's probably just some fluke" | 03:01 |
| tinwhiskers | well, unless it's placed prior to other samples in the tree is is a fluke | 03:01 |
| de-facto | hmm sequence length 287 | 03:01 |
| tinwhiskers | *it is | 03:01 |
| de-facto | that does not sound like a full one | 03:02 |
| LjL | i wouldn't expect it to be full | 03:02 |
| LjL | it's taken from months old sewage | 03:02 |
| LjL | however refrigerated | 03:02 |
| tinwhiskers | bummer | 03:02 |
| LjL | come on | 03:02 |
| de-facto | yeah thats what i meant | 03:02 |
| tinwhiskers | it may not need to be full to place it, but I'm guessing it was not able to be or someone would have done that. | 03:03 |
| LjL | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7384408/ has a table with some other sewage testing that has been done, but except for Italy and Brazil i think everything else they list is from 2020 | 03:03 |
| LjL | it's a paper from July though so before the Italian paper was even published | 03:04 |
| tinwhiskers | the idea that it was in widespread circulation in several countries just doesn't stack up to me. | 03:04 |
| tinwhiskers | so while it *may* be true it seems unlikely to me and I'd be looking for other explanations unless it can be placed firmly as a progenitor. | 03:05 |
| LjL | we've had very few cases from july to the end of august, in italy as in much of europe | 03:06 |
| ghost_rider[m] | tinwhiskers: before of all this corona-chan I was already suspicious about the e-cigs pneumonia in US | 03:06 |
| tinwhiskers | so it's not that I've discarded it out of hand, just that I'm very sceptical. | 03:06 |
| LjL | and de-facto doesn't quite understand why | 03:06 |
| LjL | so why would it not be possible that we had a similar "undeground" spread before 2020 | 03:06 |
| LjL | considering we don't know the actual reason it slowed down | 03:06 |
| de-facto | oh btw they are listed here https://www.ncbi.nlm.nih.gov/nuccore/MT843229 | 03:07 |
| LjL | and considering that doctors in northern italy *did* retrospectively say "hey, we told you there were a few unexplained pneumonias and you didn't look!" | 03:07 |
| ghost_rider[m] | Well, I'm just curious and I don't close door's so easily, but is just my uber humble opinion | 03:07 |
| tinwhiskers | it would have had to have been quite different since lots of people didn't show up dead or extremely sick with cytokine storm | 03:08 |
| LjL | Adriano Decarli, an epidemiologist and medical statistics professor at the University of Milan, said there had been a “significant” increase in the number of people hospitalized for pneumonia and flu in the areas of Milan and Lodi between October and December last year. | 03:09 |
| LjL | He told Reuters he could not give exact figures but “hundreds” more people than usual had been taken to hospital in the last three months of 2019 in those areas - two of Lombardy’s worst hit cities - with pneumonia and flu-like symptoms, and some of those had died. | 03:09 |
| LjL | https://www.reuters.com/article/us-health-coronavirus-italy-timing-idUSKBN21D2IG | 03:09 |
| tinwhiskers | we should be seeing a different branch in the phylogenetic (unless it dies out??) but all evidence says the tree started in China and there are no outliers that do not come from that strain. | 03:09 |
| LjL | “They [general practitioners] remember having seen very strange pneumonia, very severe, particularly in old people in December and even November,” Giuseppe Remuzzi, the director of the Mario Negri Institute for Pharmacological Research in Milan | 03:10 |
| LjL | , said in an interview with the National Public Radio of the United States. | 03:10 |
| LjL | https://www.scmp.com/news/china/society/article/3076334/coronavirus-strange-pneumonia-seen-lombardy-november-leading | 03:10 |
| LjL | the director of the Mario Negri institute is not supposed to be a dummy, either | 03:10 |
| LjL | although you never know | 03:10 |
| tinwhiskers | it smells really bad to me. I'm not closing the door, but there should still be remnants cycling in the population that don't sit under the chinese strain. | 03:10 |
| de-facto | LjL, i just think if it is that contagious and only a few imports from Wuhan could have triggered such a massive first spike, why would those cases if they really have been around before winter not have causes a similar spike then? | 03:11 |
| LjL | de-facto, i don't know. why were we having no spike in july and august in europe again? | 03:11 |
| tinwhiskers | right, and then they all died out only leaving strains that have chinese ancestry | 03:11 |
| LjL | tinwhiskers, which is possible if that strain had some important evolutionary advantage | 03:12 |
| LjL | just like D614G has been supplanting most everything else | 03:12 |
| de-facto | hmm well people were aware in the summer though and kinda naive to its presence before first spike though | 03:12 |
| tinwhiskers | no, it won't supplant the other strain unless it's in direct competition, which at that early stage there was no host competition. | 03:12 |
| LjL | de-facto, and they are aware now and yet we are having a huge spike now even though almost everyone in italy is wearing masks indoors *and* outdoors | 03:12 |
| LjL | de-facto, i mean, i shouldn't have to argue this with you, you are the one who finds this all strange in the first place | 03:13 |
| de-facto | i do indeed | 03:13 |
| de-facto | ok well maybe it behaves much differently at start with just a few clusters (at begin of 2020 or arguably even end of 2019) than when it already is widespread like "preparing for fall" in the summer | 03:15 |
| de-facto | yet i am puzzled by the fact that it would not explode into the winter then | 03:15 |
| tinwhiskers | and that we haven't ever sequenced it | 03:15 |
| LjL | we have sequenced the pieces of it that were sequenceable from the sewer from what i can see | 03:16 |
| de-facto | yeah and that too | 03:16 |
| LjL | you have just linked to the sequence | 03:16 |
| LjL | what more... | 03:16 |
| LjL | i just don't know | 03:16 |
| tinwhiskers | but it wouldn't immediately just die out because a new strain appears on the scene. It would still maintain clusters until it comes under competitive pressure, which would be about the point we reach herd immunity. | 03:17 |
| LjL | you know, italian researchers are not magical, in fact it's an *endemic* problem in italy that research is *way* underfounded. they sequenced what they could sequence. how much sequencing will assuage you? | 03:17 |
| de-facto | well the sequence was done and submitted in late 2020, so the origin cant be determined for sure to be in 2019, if we could puzzle it into the phylogenetic tree that could be determined potentially i guess | 03:18 |
| de-facto | " 28-AUG-2020" | 03:18 |
| tinwhiskers | if it ever existed at that time it should still have existed when the chinese strain arrived on the scene, and should have been picked up under at least some sequencing of people who were tested. | 03:18 |
| Brainstorm | New from ProPublica: Esto es lo que pasará si Trump intenta lograr una victoria electoral mediante demandas: por Ian MacDougall Read in English. ProPublica es una sala de redacción sin fines de lucro que investiga abusos de poder. Regístrese para recibir nuestras notas principales en cuanto se publiquen. Una audiencia el miércoles para un caso [... want %more?] → https://is.gd/GGPEi7 | 03:18 |
| tinwhiskers | that we never got a sequence of anything that doesn't fit under the chinese strain is highly suggestive such a thing does not exist. | 03:19 |
| de-facto | well to be fair not everyone with pneumonia gets a virus isolated and sequences if nothing unusual is suspected | 03:20 |
| tinwhiskers | yeah, fair | 03:20 |
| ghost_rider[m] | :} | 03:20 |
| tinwhiskers | maybe it just caused very few or minor symptoms so nobody ever noticed it, then it mutated into the much for deadly version that emerged in china. | 03:21 |
| tinwhiskers | *much more | 03:21 |
| de-facto | if it came from a natural reservoir for sure it was around for much longer time already | 03:21 |
| tinwhiskers | but I'm sure you can see why I'm sceptical | 03:21 |
| de-facto | yet if it is that contagious from human to human i dont understand why it would not explode right away when entering human population | 03:22 |
| de-facto | if we had a full sequence we could compare for mutations | 03:22 |
| tinwhiskers | that would clinch it | 03:22 |
| tinwhiskers | reassembly from fragments is not a problem. most sequencing breaks DNA/RNA into fragments anyway | 03:23 |
| de-facto | im not saying they did not try that, maybe its just not possible for some reason, for sure they had the same idea | 03:23 |
| tinwhiskers | perhaps in time we'll get some data | 03:23 |
| de-facto | those samples still should be there, why not bruteforce them? | 03:23 |
| LjL | have an entertaining take of how China's main information organism picks what it counts as scientific evidence. i think maybe we should be entertained but at the same time make sure we don't fall into similar but different traps | 03:24 |
| tinwhiskers | it's not even brute forcing. back when I was at work with the gene guys, they routinely aligned all the fragments of their sequences. | 03:24 |
| LjL | "Currently, we can find no clear evidence on the origin of the virus. It could be China, U.S., Italy or anywhere else. Some may say the current outbreak originated in a Wuhan seafood market. But that could be false since there's no scientific research supporting this claim. [...] A previous example was the outbreak of Spanish flu back in 1918. Despite the name, the flu's actual origin was apparently not the country." | 03:24 |
| de-facto | tinwhiskers, yes its how sequencing works afaik | 03:24 |
| tinwhiskers | LjL: yet, there is strong evidence that all the strains we've found fit tidily into the phylogentic tree that comes from China | 03:25 |
| LjL | tinwhiskers, well i can tell you two things i feel reasonably confident about: 1) reassembly from fragments MAY be a problem in italy's hectic situation and lack of research funding, and 2) if any and all non-Italian researchers seeing this just brushed it off as "pfft, probably some contamination" instead of like offering to analyze the samples, then i wouldn't be surprised it never happened | 03:26 |
| tinwhiskers | so yes, maybe it emerged somewhere else first as a non-deadly (yet virulent) strain and we've just never yet found it. | 03:26 |
| tinwhiskers | reassembly from fragments is normal practice in sequencing. You can even have mixed genetic samples and the alignment will separate and defrag all the samples. | 03:27 |
| LjL | you know, i have no interest or hope to find out that it originated in italy. i'm just a little baffled by how much more weight can be added over time to this research and it's still "pfft, probably a fluke", and i kind of extrapolate your attitude about that to other researchers, and think "well maybe that's why they haven't verified it?" | 03:28 |
| tinwhiskers | It's not pfft. It's certainly interesting, but it doesn't fit quite right as far as I can see it. | 03:28 |
| tinwhiskers | I smell a rat that I can't avoid. | 03:28 |
| LjL | okay | 03:28 |
| ghost_rider[m] | tinwhiskers: let me add some politics: " The Chinese Foreign Ministry on Wednesday refuted the claim by some U.S. politicians that the novel coronavirus originated in a laboratory in Wuhan." | 03:29 |
| LjL | it will never fit into tree if nobody ever makes an effort to put it there though | 03:29 |
| LjL | ghost_rider[m], what does that have to do with this? | 03:29 |
| tinwhiskers | LjL: agreed. I hope we do get to settle this, because it's very curious | 03:29 |
| tinwhiskers | ghost_rider[m]: yeah, really rather not go there | 03:29 |
| tinwhiskers | the data seems pretty rigorous so I can't just discard it entirely but the story doesn't play out well for me. | 03:30 |
| ghost_rider[m] | Anyway, just let me add other interesting sentence: " | 03:32 |
| ghost_rider[m] | "Speaking of the truth, we would like the US government to tell the truth about the US Army Medical Research Institute of Infectious Diseases at Fort Detrick, Maryland to US and the international community," Wang said. | 03:32 |
| LjL | what is interesting about it? | 03:32 |
| tinwhiskers | meh | 03:32 |
| tinwhiskers | I struggle to see how if it was virulent enough to spread around France and Spain, etc, that it just suddenly disappeared. | 03:34 |
| tinwhiskers | Sorry, my head is just 'sploding on that and I can't shake it (or drop it apparently) | 03:34 |
| tinwhiskers | I should go for a walk. | 03:35 |
| ghost_rider[m] | Well, a close family member worked for biological and chemical department, sad he is not around ,,, he died when researching how a biological weapon show up in Africa ... I heard so much at home that now nothing is that strange to me... :} | 03:35 |
| ghost_rider[m] | tinwhiskers: at same time I'm with you | 03:36 |
| ghost_rider[m] | But at same time ... Well, ... Don't know, not even my area if I even have a area | 03:37 |
| ghost_rider[m] | Just a curious guy | 03:37 |
| LjL | tinwhiskers, yes, go for a walk, don't take the (legal or physical) ability to do that for granted ;( | 03:37 |
| tinwhiskers | :-) | 03:37 |
| tinwhiskers | my apologies | 03:37 |
| de-facto | LjL, I agree that there should be made more effort to obtain a full sample of this with international help, afaik such tasks should be done by the WHO in cooperation with local scientists | 03:37 |
| LjL | tinwhiskers, i didn't mean it as expressing a need to apologize. but you're clearly feeling frustrated right now and i can't give you the answer you seek and chances are no one in this particular channel does, so a walk may be a better option | 03:38 |
| tinwhiskers | ah, no, I meant apologies for being insensitive and mentioning I was going for a walk. heh | 03:39 |
| LjL | oh. well... | 03:39 |
| ghost_rider[m] | I'm sorry if I caused something unwanted, I was just no curious to know your opinions | 03:39 |
| LjL | we'd be at a bit of an absurd level of PC if we couldn't mention going for walks just because others may be under lockdown or whatnot | 03:39 |
| tinwhiskers | I don't know what the tongue-in-check emoji is | 03:40 |
| tinwhiskers | *cheek | 03:40 |
| LjL | ghost_rider[m], i am not fully clear on what you think is interesting, and honestly i think there is a bit of a language barrier too. but my general opinion on the topic is: i still find it likely enough that it could have come out of a lab near Wuhan, probably by mistake | 03:40 |
| LjL | tinwhiskers, emoji, now that's something i'd rather do without | 03:40 |
| LjL | more power to walks, less power to emoji | 03:41 |
| tinwhiskers | heh. ok. | 03:41 |
| Brainstorm | New from ProPublica: Tras una jornada electoral frenética, comienzan las acusaciones en el Servicio Postal: por Maryam Jameel y Ryan McCarthy Read in English. ProPublica es una sala de redacción sin fines de lucro que investiga abusos de poder. Regístrese para recibir nuestras historias más importantes tan pronto como se publiquen. En una [... want %more?] → https://is.gd/HkMJHL | 03:45 |
| LjL | when did ProPublica start maching-gunning out articles in Spanish | 03:46 |
| LjL | i've had it in the RSS list for a while and it never did that before | 03:46 |
| ghost_rider[m] | 😀 | 03:46 |
| ghost_rider[m] | Ounce I found a feed with global data from finance, politics etc, all countries, , , instant regret so much data and information that I and rss client got overdose | 03:48 |
| LjL | i hear some people have lived much better after stopping following pretty much any news | 03:51 |
| LjL | i probably don't want to do that, but if it worked for them, maybe it can work for others | 03:51 |
| de-facto | so searching for https://www.ncbi.nlm.nih.gov/nuccore/MT843229 in https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn&QUERY=MT843229.1&DATABASE=nr&MEGABLAST=on&BLAST_PROGRAMS=megaBlast&LINK_LOC=nuccore&PAGE_TYPE=BlastSearch gives a lot of sequences in USA | 03:51 |
| de-facto | not sure what that means | 03:52 |
| de-facto | BLAST can search the databases for sequences in the formats https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp | 03:53 |
| ghost_rider[m] | LjL: I'm the opposite, lack of vats going on make me unhealthy | 03:54 |
| LjL | de-facto, note that what i gave is a range, so there is also https://www.ncbi.nlm.nih.gov/nuccore/MT843230 and https://www.ncbi.nlm.nih.gov/nuccore/MT843231 up to ...40. i don't know if that's enough sequences to splice back together (probably not, or they would have done it, i guess?), but it's more sequences to be followed around | 03:54 |
| de-facto | yeah i know i just wanted to gain some experience with that first one there | 03:55 |
| de-facto | i never used those websites before | 03:55 |
| de-facto | they are quite neat though | 03:55 |
| de-facto | have to admit i barely understand them | 03:56 |
| LjL | it seems, if i understand this correctly, that they picked one protein and they always sampled the same one several times | 03:56 |
| de-facto | they are designed for biotechnology experts | 03:56 |
| LjL | de-facto, i guess nextstrain limits themselves to full sequences? | 03:57 |
| de-facto | hmm not sure i think full sequences with mutations or such | 03:58 |
| de-facto | like when you know position 614 D->G in s-protein or such | 03:58 |
| LjL | right, but so anyway, even if these italian sequences turned out to be prior to the chinese sequences, they wouldn't show up on the nextstrain tree | 04:00 |
| de-facto | probably not, but what if they would show up in the middle of it? | 04:01 |
| de-facto | (speculation of course) | 04:01 |
| LjL | then tinwhiskers would be vindicated in his skepticism | 04:01 |
| LjL | but i think until we can show they are either at the start or in the middle, we just can't say what this means | 04:02 |
| tinwhiskers | agreed | 04:02 |
| de-facto | yes and i have to admit its a bit above of my head to do that, i am no expert with those tools | 04:02 |
| de-facto | they have a tutorial here, but it looks like a lot of work https://nextstrain.org/docs/tutorials/zika | 04:03 |
| tinwhiskers | it *may* also be possible that a progenitor of the wuhan strain could appear as a descendant if it's close enough. | 04:04 |
| tinwhiskers | at least that's what I decided during my walk :-) | 04:04 |
| tinwhiskers | but then if it's that close why was it not deadly... | 04:06 |
| tinwhiskers | hrm | 04:06 |
| tinwhiskers | I wonder if we could get twiv to discuss this? | 04:06 |
| de-facto | yeah if it just would have one link to the first sequence obtained one would not know if it emerged prior or after that, but if it would be included in a chain with its own sequence of ancestors leading to the wuhan strain and also having children itself it would be clear that it came from later mutations | 04:07 |
| tinwhiskers | it was close enough to match on the PCR test obviously. | 04:07 |
| tinwhiskers | so some people should have had a positive test due to having this particular strain | 04:07 |
| tinwhiskers | but maybe it just fell through the crack in terms of any of those people being sequenced. | 04:08 |
| tinwhiskers | *cracks | 04:08 |
| tinwhiskers | added to that most people only got tested if they showed symptoms so if this variant was relatively innocuous maybe it was just never found. | 04:10 |
| tinwhiskers | and yet again, given few places have higher than 20% prevalence of the wuhan descendants it seems unlikely to me it would have vanished entirely yet due to competition, so it *should* show up at some stage. | 04:11 |
| LjL | tinwhiskers, it may also not be a pure progenitor for all i can tell. it may still have come from Wuhan, reached Italy (and possibly other places) from there, and then it took a bit of time brewing underground before the epidemic became obvious, which it still did in Wuhan first because it was there first, and in Lombardy second because it was there second | 04:12 |
| tinwhiskers | yeah, I agree that is possible but it should still be showing up on positive PCR tests now | 04:13 |
| LjL | "why did it take time, if it's so infectious?" i don't know, but again that's the question that we can ask for other non-spikes that we saw later | 04:13 |
| tinwhiskers | yeah | 04:13 |
| LjL | tinwhiskers, do we know anyone who knows anyone from TWIV? | 04:13 |
| tinwhiskers | no, but they do answer questions from listeners | 04:14 |
| tinwhiskers | although being a, err what's it called when you pay them money? | 04:15 |
| LjL | who pays who money? | 04:16 |
| tinwhiskers | You can pay the twiv people money via... umm... hell | 04:16 |
| tinwhiskers | anyway, yuriwho has paid | 04:16 |
| tinwhiskers | not subscriber... but something like that | 04:16 |
| de-facto | yeah i found the first sequence with BLAST in some USA samples i think | 04:18 |
| LjL | supporter? | 04:18 |
| LjL | anyway, you pay them not necessarily for the ability to ask questions, i guess | 04:18 |
| tinwhiskers | right | 04:18 |
| tinwhiskers | Patreon | 04:18 |
| LjL | oh | 04:18 |
| de-facto | e.g. when you click on Analyze this sequence: "Run BLAST" in the right panel of https://www.ncbi.nlm.nih.gov/nuccore/MT843229 | 04:22 |
| yuriwho | yea I send them 20$/month as a patreon... I also took Vincents virology class @ Columbia this summer as a student. | 04:22 |
| tinwhiskers | LjL: ok, point taken about it not being a progenitor. So that would have it brewing underground in China but migrating away to a few other places, presumably as a less lethal strain, then the strain in Wuhan became more lethal. I can buy that. | 04:22 |
| tinwhiskers | yuriwho: cool :-) | 04:22 |
| de-facto | yuriwho, what is your opinion about those mutations occuring in mink farms in North Jutland in Denmark that may evade antibodies from human immunity? | 04:23 |
| LjL | yuriwho, do you have any more clue than we appear to about figuring out whether this short Italian sequence (well, sequences, but apparently always taken from the same gene and protein) that came from sewage samples in Italy pre-dates or post-dates what we understand to be the original Wuhan strain? | 04:23 |
| LjL | also that :( | 04:24 |
| de-facto | https://www.bt.dk/politik/alle-mink-skal-slaas-ihjel-muteret-coronavirus-fra-mink-er-en-trussel-for | 04:24 |
| yuriwho | btw, all it takes is a super spreader to with a particular mutation to start a cluster in an area for that mutant to become regionally dominant. The virus is not evolving so much as being a tracked by these mutations | 04:24 |
| de-facto | https://www.reuters.com/article/us-health-coronavirus-denmark-mink/denmark-to-cull-entire-herd-of-mink-due-to-risk-of-coronavirus-mutation-tv2-idUSKBN27K1X6 | 04:24 |
| yuriwho | gimme some time to look at the articles | 04:24 |
| LjL | yuriwho, the thing here is that these Italian samples (and there are similar studies from Spain and elsewhere i think but we've looked at the Italian one) are supposed to come from sewage from 2019 | 04:25 |
| LjL | they have sequenced https://www.ncbi.nlm.nih.gov/nuccore/MT843231 up to https://www.ncbi.nlm.nih.gov/nuccore/MT843240 | 04:25 |
| LjL | and this is their paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7428442/ | 04:25 |
| yuriwho | well as to the Italian samples of SARS-CoV-2 in wastewater from Nov 2019.... I think that entirely feasible.... for the genetic analyses it was believed to be spreading in China in October and there was tourist traffic from Wuhan to Northern Italy | 04:34 |
| yuriwho | regarding the mink... that does sound potentially dangerous. Do you have a link to the sequences and antibody studies? | 04:35 |
| LjL | yuriwho, i don't know about de-facto, but i don't. what i have is a press release from the Danish government stating that their primary medical institution determined this strain is less or not susceptible to antibodies that were produced with known-strain infection, and so they have decided to cull the entire mink population in the country (mobilized the army to do it more quickly) and also to lock down areas where minks are present | 04:36 |
| ryouma | can you leaborate what do you mean by not so much evolving as "being a tracked"? --- 20:24 <yuriwho> btw, all it takes is a super spreader to with a particular mutation to start a cluster in an area for that mutant to become regionally dominant. The virus is not evolving so much as being a tracked by these mutations | 04:36 |
| ryouma | is the virus mutating less than other similar viruses? | 04:37 |
| LjL | yuriwho, it is stated also that they don't know just how this mutated strain has been jumping from mink farm to mink farm, even at a distance, but for now they suspect seagulls because viral RNA was found on a seagull | 04:38 |
| yuriwho | btw, the Wuhan strain was just the particular mutant that got widely spread 1st... the first virus to cause a cluster of cases will become locally dominant even if it was not the first mutant circulating in the area... It like a first mover advantage | 04:38 |
| LjL | ryouma, i do believe it is mutating less than other RNA viruses, but i think it's due to some characteristic that i'm unable to describe | 04:38 |
| ryouma | yuriwho: just for completeness so could it have been in europe? | 04:39 |
| tinwhiskers | LjL: I can buy this version of events, but I remember that when the news about France and Spain came out people were claiming it arose in Europe before China, and that's what I've always felt smelled like a rat. | 04:39 |
| LjL | tinwhiskers, i don't know if it means it arose in Europe, i'm mostly concerned with whether it was already there or not | 04:39 |
| ryouma | yuriwho: at risk of overwhelming you with dumb questions, does superspreader mean both a person who is like typhoid mary and an event like sturgis rally? | 04:40 |
| de-facto | i dont have the sequence from denmark, i havent found any publications about it yet, i think its all internal for now and the press writing according to that press conference | 04:40 |
| yuriwho | ryouma: do not confuse the terms "mutant" and "strain"... the latter implies a difference in viral phenotype or behavior... the former is just an inconsequential mutation | 04:40 |
| LjL | tinwhiskers, of course CCTV immediately tried to use it as a "weapon" to show it may not have originated in China at all. that's why i showed the snippet earlier, to show how obvious a game they played. but that should not taint the science | 04:40 |
| de-facto | "According to Politiken, the memo was prepared by virologist Anders Fomsgaard and chief epidemiologist at the Statens Serum Institut Kåre Mølbak. It should show how the virus in ten people in North Jutland who are infected with mink has changed to a degree that can threaten the effect of a potential future vaccine." | 04:40 |
| tinwhiskers | LjL: ok | 04:41 |
| LjL | de-facto, it does seem to be kill the mink first, publish about it later | 04:42 |
| tinwhiskers | I wonder if they will still get to use the fur? | 04:42 |
| LjL | no, they will be cremated | 04:42 |
| tinwhiskers | ah | 04:42 |
| de-facto | but still is it not already too late if it appeared in human population? | 04:43 |
| LjL | it said somewhere they tried to secure more crematoriums aside from mobilizing the army. it's about 15 to 17 million mink apparently | 04:43 |
| LjL | de-facto, that's why they are locking down the areas with mink, presumably | 04:43 |
| LjL | but yeah, if i had to guess, i'd say it's late | 04:43 |
| tinwhiskers | wow | 04:43 |
| yuriwho | "super spreader" is used loosely by the media... it refers to an infected person that has an unusually high viral load and can infect others rapidly because every droplet they emit contains an unusually high dose of virus... many of these super spreaders are asymptomatic young people | 04:43 |
| LjL | tinwhiskers, they are the world biggest mink producers :\ | 04:43 |
| LjL | yuriwho, yeah, the media sometimes talks about "super spreading events" where the high spreading is not really so much due to the spreader being "super", but the event being at high risk | 04:44 |
| tinwhiskers | I used to keep ferrets back home, which are pretty much mink that aren't white :-) | 04:44 |
| yuriwho | yes LjL | 04:44 |
| LjL | tinwhiskers, i do seem to recall it has been shown to infect ferrets | 04:44 |
| tinwhiskers | All my ferrets met untimely deaths too (except one pet one called stinky) | 04:44 |
| yuriwho | if the data is true, there is no time to wait to publish re the mink | 04:45 |
| LjL | that's what worries me :\ | 04:45 |
| yuriwho | there has been many examples of it being transmitted from humans to mammals, few examples of the virus getting transmitted back | 04:45 |
| tinwhiskers | great, so ferrets are a reservoir host of bovine Tb in NZ. So now we might get feral ferrets being a reservoir for covid too. that's not funny! | 04:46 |
| yuriwho | every time a virus hops species, it undergoes a rapid evolution to adapt to the new host | 04:46 |
| LjL | yuriwho, i had already heard of mink back-infecting though, i think, and of mink farms getting infected at very high rates. but before now they hadn't found a whoopsies in the mutations | 04:46 |
| de-facto | yuriwho, what would be the worst case to expect from such a ping-pong-event between humans and minks? totally new virus where everyone recovered or vaccinated appears completely naive or just a less efficient immunity that still may have milder trajectories but potentially may be contagious to others again, e.g. resetting vaccination efforts in an epidemiological but not medical perspective? | 04:47 |
| tinwhiskers | *noting I'm using "covid" colloquially to refer to the virus, not the disease. | 04:47 |
| yuriwho | so species jumps cause large changes in the virus sequence usually | 04:47 |
| de-facto | it evolved under completely different immunologic pressure in minks i guess | 04:47 |
| yuriwho | yes\ | 04:47 |
| LjL | yuriwho, maybe we're just a lot like mink | 04:47 |
| yuriwho | it's likely our ACE-2 receptors are very similar | 04:48 |
| tinwhiskers | I'm a bit like a mink if I heavn't showered for a few days | 04:48 |
| de-facto | afaik minks are quite a good model for human respiratory diseases i read somewhere | 04:48 |
| LjL | heh | 04:48 |
| LjL | yuriwho, the thing is, they can hurry up and kill them all before publishing anything, but if their hunch is right that *birds* are the vectors... good luck getting that contained | 04:49 |
| de-facto | i am just trying to understand if those potentially are just slightly bad news or really bad news | 04:49 |
| yuriwho | it the virus has jumped twice (ping pong) it has also had 2 rounds of rapid evolution... is there evidence of human to human spread of the new strain? | 04:49 |
| LjL | yuriwho, i think there is evidence of only 12 infected humans so far, although that doesn't directly answer your question | 04:50 |
| de-facto | im not sure, but they say that many infections in Denmark are related to mink farms | 04:50 |
| LjL | i mean with this mutation verified | 04:50 |
| de-facto | "Health Minister Magnus Heunicke said half the 783 human coronavirus cases in northern Denmark ''are related'' to mink." | 04:50 |
| yuriwho | if there is evidence of human to human transmission of a new strain that is resistant to neutralizing antibodies that could be bad news | 04:50 |
| de-facto | from https://www.dw.com/en/denmark-to-cull-all-farmed-minks-over-coronavirus-mutation/a-55501832 | 04:50 |
| ryouma | why are birds related to mink | 04:51 |
| ryouma | what aboutg humans | 04:51 |
| yuriwho | are they also going to institute a travel ban for humans from northern denmark? | 04:51 |
| de-facto | i havent read about human to human transmission but about somewhat evading human antibodies hence vaccinations, yet why would it not be human to human transmissible if minks are so similar? | 04:51 |
| LjL | de-facto, honestly i think the tone of that DW article answers your question on whether it's a bit bad or very bad | 04:52 |
| de-facto | hopefully... | 04:52 |
| yuriwho | the birds would likely not be infected... but may transmit it via flesh on their talons | 04:52 |
| LjL | yuriwho, yes, they found it on a foot, not infected | 04:52 |
| yuriwho | this is worth following closely | 04:53 |
| de-facto | and then i have seen pictures of culled minks laying around in open skies | 04:53 |
| de-facto | very bad idea if birds can transmit it like that | 04:53 |
| tinwhiskers | d'oh | 04:53 |
| LjL | great, https://en.wikipedia.org/wiki/COVID-19_pandemic_in_Denmark (which does not cover recent months) is not available in Danish | 04:54 |
| de-facto | https://www.bt.dk/politik/alle-mink-skal-slaas-ihjel-muteret-coronavirus-fra-mink-er-en-trussel-for | 04:55 |
| de-facto | https://bt.bmcdn.dk/media/cache/resolve/image_1240/image/156/1564385/23568501-mink2.jpg | 04:55 |
| de-facto | bad idea. | 04:55 |
| LjL | yuk | 04:57 |
| de-facto | why not put them into a big hole and cover them with earth? | 04:57 |
| LjL | https://www.reddit.com/r/COVID19/comments/jo2muy/mink_and_covid19/gb5atmz/ | 04:57 |
| tinwhiskers | probably health restrictions | 04:57 |
| tinwhiskers | we're no longer allowed to bury dead livestock in NZ. Maybe it's the same there. | 04:58 |
| de-facto | yet seagals may want to try their flesh and give the new mutant virus a ride to the next host | 04:58 |
| tinwhiskers | I think the reasoning is groundwater contamination or some such. | 04:58 |
| de-facto | whatever then burn them in a big fire or such, but having them laying around in open skies is the worst idea possible when knowing birds are around frequently there | 04:59 |
| tinwhiskers | yeah | 05:00 |
| LjL | this twitter thread https://twitter.com/BallouxFrancois/status/1324085761449304067?s=19 has been linked in r/COVID19 in a "rare" move (they normally don't allow Twitter links), but i am already reading "Minks are highly susceptible to #SARSCoV2, as are most carnivores including dogs and domestic cats." ← what? dogs aren't "highly" susceptible. they can get a mild form that is not transmissible, last i checked. cats are another story. | 05:01 |
| de-facto | oh LjL good find :)) | 05:01 |
| LjL | "#SARSCoV2 mutations acquired in minks are not concerning. We already knew that #SARSCoV2 can transmit from minks to humans. Though, this should be of no concern in terms of the evolution of the transmissibility of the virus." ← so the Danish government is just totally overreacting? | 05:02 |
| de-facto | https://translate.google.com/translate?sl=auto&tl=en&u=https://coronasmitte.dk/-/media/mediefiler/corona/mink/risikovurdering-af-human-sundhed-ved-fortsat-minkavl_03112020.pdf | 05:02 |
| tinwhiskers | better safe than sorry? | 05:02 |
| LjL | "If they were beneficial for the virus to infect its human host, they would be at high frequency already." ← uh well, at some point it needs to start, it starts when it starts, which could be now | 05:03 |
| tinwhiskers | I mean the mink weren't going to live long, fulfilling lives anyway. | 05:03 |
| LjL | "An interesting observation gets misunderstood and blown out of proportion and ends up as a silly and confusing story fuelling further fear and confusion in the public." ← this is not just a "story". there are extremely concrete actions Denmark is taking about this | 05:03 |
| yuriwho | read this twitter thread: https://twitter.com/LucyvanDorp/status/1324088676624773123 | 05:03 |
| tinwhiskers | still, gotta hurt the economy that little bit extra at a time it's really not needed. | 05:04 |
| de-facto | well why would that not be bad news? if transmissibility did not change it means that it would spread from human to human similar to the variant we know already except that we arent immune or vaccinated against this one? | 05:04 |
| LjL | de-facto, you are right as far as i can guess | 05:04 |
| yuriwho | the mutant strain has only been found in 12 humans | 05:05 |
| LjL | i don't know who this person is, he may be the world's leading expert, but to play the tinwhiskers here for a moment, i find *his* story is a bit at odds with what Denmark is doing in response to this. okay, politicians can be crazy, but still | 05:05 |
| tinwhiskers | This mutation, falling within the receptor binding domain, may be a good candidate for adaptation of #SARSCoV2 to #mink hosts. While this mutation has been seen in #SARSCov2 in human circulation it is rare. Currently available mink genomes fall in the diversity of human #SARSCoV2 | 05:05 |
| LjL | yuriwho, but it's not like they sequence all cases | 05:05 |
| tinwhiskers | but presumably they think there is heightened risk of a more dramatic change?? | 05:06 |
| LjL | they will now, in those parts of Denmark, maybe, hopefully | 05:06 |
| yuriwho | we do not have enough info to assess the risk here | 05:06 |
| de-facto | from above PDF | 05:12 |
| de-facto | "Because of the changes that occur in the spike protein in several of the mink variants of the virus, there is a risk that vaccines targeting the spike protein will not provide optimal protection against the new viruses, occurring in mink, and the immunity from past COVID-19 infection may provide less protection against the new virus variants." | 05:12 |
| yuriwho | https://science.sciencemag.org/content/370/6516/539.1 | 05:13 |
| de-facto | "Among the mink varieties, seven have been seen different mutations in the Spike protein and examples of up to 4 different changes in Spike the protein in the same virus. A specific virus with 4 changes in the genes for spike protein has been detected in five North Jutland mink farms and in 12 patient samples, of which 4 with direct connection to three of these farm (cluster 5)." | 05:13 |
| yuriwho | %T | 05:13 |
| Brainstorm | yuriwho: From science.sciencemag.org: Ban unsustainable mink production | Science | 05:13 |
| de-facto | "Preliminary studies suggest that this virus exhibits decreased susceptibility to neutralizing antibodies from several people with a history of infection. This is proven in a laboratory experiments where it is seen that the particular mink virus is not inhibited to the same extent in the growth of human antibodies that have been infected with a non-mink-related variant of SARS-CoV Ongoing studies will further uncover the issue. | 05:15 |
| de-facto | Additional variants are identified by sequencing but not yet investigated for neutralization." | 05:15 |
| de-facto | "This is worrying, as it could potentially affect the efficacy of a future COVID-19 vaccine against infection with new mink variants, and involve a risk of impaired immunity to these after over COVID-19 infection, which is important for the individual and for herd immunity in society." | 05:16 |
| LjL | yuriwho, it does seem that this has been a growing concern for a while, in Denmark and not exclusively there, and maybe the current actions are just an "okay, enough is enough" sort of situation. but still, they seem to be taking it extremely seriously | 05:16 |
| yuriwho | LjL: I agree | 05:16 |
| yuriwho | I do not believe this will have any big impact on vaccines unless this strain is allowed to propagate widely.. I hope they are isolating mink farmers while the culling takes place | 05:17 |
| de-facto | Drosten mentioned that mink farms could be a candidate for a potential reservoir right at the begin of the first wave, was it March or such? | 05:17 |
| ghost_rider[m] | At start top Russian virologist said a vax wold be impossible due to mutations, ... | 05:18 |
| yuriwho | de-facto: yes, the virus now has many possible animal resevoirs.... not just bats | 05:18 |
| LjL | yuriwho, i don't know, this virus has shown it has quite an ability to define containment efforts :\ | 05:18 |
| LjL | to defy* | 05:19 |
| de-facto | yuriwho, do you remember we discussed about the phylogenetic tree spreading with time and that this could mean a window in time for vaccination with a single vaccine could close? that was also several months ago in #coronavirus | 05:19 |
| ghost_rider[m] | I see it as a advanced computer worm that patterns to match it can't be used ... | 05:19 |
| yuriwho | as I have said for a very long time... this virus will never be eradicated and we will be playing cat and mouse with it like we do with the common flu... expect to have an annual vaccination for the rest of your life | 05:20 |
| LjL | :( | 05:20 |
| LjL | and also intermittent lockdowns for the rest of our lives as new variants emerge from animal reservoirs? | 05:21 |
| yuriwho | there will always be strains resistant to the immunity of any given vaccine to re-start a new cycle | 05:21 |
| LjL | what a bright future | 05:21 |
| ghost_rider[m] | Da Fuk, and that nano bot's yada is the virus to small or that nano bot's are of no use to this ? | 05:22 |
| LjL | what | 05:23 |
| yuriwho | the vaccines will evolve and become combinatorial like the flu vaccines are | 05:23 |
| de-facto | well but to be fair we dont know if reinfections with such mutant variants would be as severe as first infections to naive susceptible | 05:23 |
| LjL | de-facto, so far we already know that even re-infection with the "usual" strains can be worse than first infections (although there is almost certainly bias in finding those), so... | 05:23 |
| yuriwho | de-facto: correct..... I suspect the current strains have already maximized transmission | 05:24 |
| de-facto | yuriwho, but flu comes in waves, right? like disappearing in the summer, that obviously is not the case with SARS-CoV-2 so it may be more of a continuous drift than coming in distinct yearly waves | 05:24 |
| yuriwho | de-facto: SARS-CoV-2 shows the same seasonal pattern as flu, just not quite as pronounced | 05:25 |
| de-facto | LjL, yes there are those cases reported, but we really dont know how representative they are, maybe they only get attention because they are noticed by the bias of being symptomatic or even worse | 05:25 |
| Brainstorm | New from CNBC Health: Immune cells are responding to Covid six months after infection, study finds: Cellular, or "T-cell," immunity against Covid-19 is likely to be present within most adults six months after primary infection, a new study said. → https://is.gd/1Y5FJg | 05:25 |
| de-facto | ^^ so maybe those cellular immunity responses also get triggered by the mutant variants making progressions milder? | 05:26 |
| yuriwho | we will soon have coronavirus surveillance systems for high throughput sequencing and antibody characterization randomly testing samples near airports... A friend of mine is working on this | 05:27 |
| de-facto | they dont only react to s-proteins but all of the other ones too | 05:27 |
| de-facto | so if we need to quickly "adjust" vaccinations to the new mutant variants emerging in such screenings, would those be directly be available to the population once a "pipeline concept" was tested with trials or would each single little "patch" have to go through all the phases I, III, III? | 05:29 |
| LjL | yuriwho, how is whatever you were working on in relation to COVID going? | 05:29 |
| yuriwho | we are still learning about how to obtain durable immune responses with vaccines. | 05:29 |
| yuriwho | LjL: it's been a lot slower than I expected.. the gov said they would fund me then they ran out of money | 05:30 |
| LjL | sounds like a government :\ | 05:30 |
| yuriwho | I need to wait till next April (new budget) to get fully funded.... working away with a small team now | 05:31 |
| yuriwho | also with Biden as President new year, I expect the NIH will get a large budget increase | 05:32 |
| yuriwho | s/new/next | 05:32 |
| LjL | either that, or some civil war | 05:33 |
| yuriwho | nah, it's almost guaranteed that Biden will win | 05:33 |
| yuriwho | I expect it to be announced by midnight tomorrow | 05:34 |
| LjL | yuriwho, sure, what's not guaranteed is that Trump and his followers will accept the result as valid, and then you have a supreme court that's now mostly Trump-sympathetic | 05:35 |
| LjL | Biden won't win with the large margin that was being predicted earlier | 05:35 |
| LjL | he'll win by a relatively tight margin, it looks like | 05:35 |
| LjL | and that's not good when it comes to fueling the fire | 05:35 |
| yuriwho | it will be a solid win | 05:35 |
| de-facto | id guess Biden will win with just two state votes | 05:36 |
| de-facto | like 270:268 or such | 05:36 |
| yuriwho | no, a much bigger win | 05:36 |
| yuriwho | gimme a sec, I'll put my electoral college prediction on paper | 05:37 |
| de-facto | ay damn +19990 daily new infections for Germany | 05:38 |
| de-facto | every day a new record | 05:38 |
| de-facto | :((( | 05:38 |
| de-facto | +118 dead | 05:38 |
| yuriwho | here my prediction: 302 EC votes for Biden-232 EC votes for Trump: https://projects.fivethirtyeight.com/trump-biden-election-map/#TN:1,KY:1,IN:1,WV:1,OK:1,MD:0,NJ:0,CT:0,MA:0,VT:0,DE:0,FL:1,VA:0,NY:0,NH:0,ME:0,ND:1,SD:1,NE:1,KS:1,MO:1,IA:1,WY:1,MT:1,ID:1,UT:1,NV:0,CA:0,OR:0,WA:0,WI:0,MN:0,MI:0,IL:0,NM:0,CO:0,HI:0,AK:1,GA:0,NC:1,SC:1,AL:1,MS:1,AR:1,LA:1,TX:1,AZ:0,DC:0,M1:0,N2:0,N1:1,N3:1,M2:1,PA:0,OH:1 | 05:40 |
| tinwhiskers | Biden currently has 253. If he gets Nevada, Arizona and Pennsylvania he goes to 290. He might get Georgia too, but 302 seems a little optimistic to me. | 05:41 |
| metreo | you think he wins Georgia? | 05:41 |
| yuriwho | click my link | 05:41 |
| tinwhiskers | no | 05:41 |
| yuriwho | I do | 05:41 |
| AimHere | I think he scrapes Georgia | 05:41 |
| tinwhiskers | mail-in might have him scrape in | 05:41 |
| yuriwho | it will involve a recount | 05:41 |
| AimHere | Isn't it all mail-in fvrom here on out | 05:42 |
| yuriwho | yep | 05:42 |
| tinwhiskers | yeah | 05:42 |
| AimHere | Basically he's on 30k short, with 90k to count | 05:42 |
| de-facto | i guess we will see hopefully soon | 05:42 |
| yuriwho | I have analyzed this carefully | 05:42 |
| metreo | he's 200K behind in PA as well | 05:42 |
| AimHere | With mail-in votes in Urban counties, it looks very doable | 05:42 |
| metreo | well 170K | 05:42 |
| yuriwho | mark my words | 05:42 |
| tinwhiskers | There's 5% remaining and Trump is leading by 0.6% but it's possible with a mail-in surge. | 05:42 |
| metreo | orange man will sue against the mail in votes? | 05:43 |
| yuriwho | he will lose those lawsuits | 05:43 |
| tinwhiskers | anyway, it looks good for Biden and the world :-) | 05:43 |
| AimHere | It's his only chance of winning | 05:43 |
| AimHere | Other than a super-slim one | 05:43 |
| yuriwho | the only lawsuits that can have any impact need to address a constitutional law question..... he does not have one | 05:44 |
| LjL | i'm about to go to bed. i don't mind if you talk about the elections a bit, but can i be confident it won't turn entirely into an elections channel? | 05:44 |
| tinwhiskers | lol. sure :-) | 05:44 |
| yuriwho | it is relevant to how COVID-19 will be handled in the coming year | 05:45 |
| metreo | look at this: https://projects.fivethirtyeight.com/trump-biden-election-map/#TN:1,KY:1,IN:1,WV:1,OK:1,MD:0,NJ:0,CT:0,MA:0,VT:0,DE:0,FL:1,VA:0,NY:0,NH:0,ME:0,ND:1,SD:1,NE:1,KS:1,MO:1,IA:1,WY:1,MT:1,ID:1,UT:1,CA:0,OR:0,WA:0,WI:0,MI:0,IL:0,NM:0,CO:0,HI:0,AK:1,NC:1,SC:1,AL:1,MS:1,AR:1,LA:1,TX:1,AZ:0,DC:0,M1:0,N2:0,N1:1,N3:1,M2:1,OH:1,PA:1,NV:1,GA:1 | 05:45 |
| AimHere | Why is Minnesota uncalled? | 05:46 |
| metreo | Biden has it | 05:46 |
| tinwhiskers | yeah | 05:46 |
| AimHere | That's what I mean | 05:46 |
| yuriwho | I do not see that as possible.... the remaining votes in Nevada come from Las Vegas and Reno | 05:46 |
| AimHere | That's like Trump's only path to victory | 05:46 |
| tinwhiskers | 52.4 to 45.4 with 95% complete | 05:46 |
| AimHere | He has to win every single outstanding state, witht he possible exception of maybe one of them | 05:47 |
| yuriwho | you need to examine where the remaining ballots to be counted come from | 05:47 |
| metreo | Biden is ahead 8k in NV with 75% counted | 05:47 |
| yuriwho | I bet $500 with a Trump supporter friend of mine.... | 05:48 |
| tinwhiskers | score! | 05:48 |
| metreo | NV is deciding the election | 05:48 |
| yuriwho | yep | 05:49 |
| yuriwho | no need to wait for Pennsylvania | 05:49 |
| de-facto | yeah i think so too, NV will be critical | 05:49 |
| yuriwho | also, there was almost no violence today | 05:50 |
| tinwhiskers | Biden will get NV | 05:50 |
| de-facto | then he gets US | 05:50 |
| yuriwho | however, the Republicans will likely control the senate | 05:50 |
| metreo | Clinton lost NV last election | 05:50 |
| tinwhiskers | will PA take longer than NV? | 05:51 |
| AimHere | It's pretty much any of the uncalled states that decides this election | 05:51 |
| metreo | fewer non-college graduates voted Trump this election | 05:52 |
| AimHere | First one to go Biden | 05:52 |
| yuriwho | I expect this will translate into a big infusion of $ next year to fight COVID | 05:52 |
| de-facto | that would be awesome | 05:52 |
| metreo | yes they are expecting a large stimulus with Biden | 05:52 |
| tinwhiskers | let's hope | 05:52 |
| yuriwho | PA could take a week to decide | 05:52 |
| tinwhiskers | it's been piss-poor so far | 05:52 |
| de-facto | we need really to speed up COVID response to hit it with a bigger hammer | 05:52 |
| metreo | PA can shut the heck up and count :P | 05:52 |
| de-facto | right now i got the feeling we are not doing enough on all fronts | 05:52 |
| yuriwho | here-here | 05:52 |
| tinwhiskers | Dems will really have their work cut out for them winning the cooperation of the republicans though. | 05:53 |
| tinwhiskers | I mean the republican-supporting public | 05:53 |
| tinwhiskers | they are going to be a bit miffed | 05:53 |
| yuriwho | yep, it's a mutual hostage negotiation | 05:53 |
| metreo | Nah they love spending money | 05:53 |
| tinwhiskers | yeah :-) | 05:53 |
| metreo | Trumps the outliers | 05:53 |
| metreo | out-liar* | 05:54 |
| tinwhiskers | heh | 05:54 |
| metreo | he's an out-liar hehe | 05:54 |
| metreo | outta-here-liar | 05:54 |
| yuriwho | Biden and Nancy will be able to negotiate with just a handshake though.... thats the thing with Trump, you cannot trust him to hold up his end of a bargain.... thus no deals | 05:55 |
| de-facto | yeah we will see, i just hope everything will be peaceful and they will take control over COVID again to bring it down | 05:55 |
| de-facto | same here, even more urgently in EU | 05:55 |
| tinwhiskers | yuriwho: yes | 05:55 |
| yuriwho | anyway, I am optimistic | 05:56 |
| tinwhiskers | yeah. it looks like the election is in the bag at least. From there... still quite a bit of uncertainty. | 05:57 |
| yuriwho | the next 2-½ months will be brutal..... Trump will try to sabotage everything | 05:58 |
| tinwhiskers | yeah | 05:58 |
| de-facto | what does that mean for COVID in USA? | 05:58 |
| tinwhiskers | well, maybe the individual states will recognise the right way forward is lock downs. Some will, some won't. | 05:59 |
| yuriwho | it means a National plan.... testing and tracing..... fact based society... funding for Science | 05:59 |
| tinwhiskers | wow | 05:59 |
| tinwhiskers | that would be nice | 05:59 |
| de-facto | that would be good, probably they are triggered by what is going wrong in EU right now | 05:59 |
| yuriwho | each Governor will have to chose to either deny federal money for COVID or follow the plan | 06:00 |
| tinwhiskers | ahh I see | 06:00 |
| tinwhiskers | the thing is they really need to lock down before Jan | 06:00 |
| yuriwho | agreed | 06:01 |
| yuriwho | sadly, I only expect that to happen in Blue states | 06:01 |
| tinwhiskers | yeah. So there will be some control treatments to compare to. | 06:02 |
| yuriwho | we are discussing lockdowns here in Canada, and our numbers are way better | 06:02 |
| de-facto | i still wonder why incidence is not going up as dynamically in USA as it does in EU, is that already an effect from part of the population being removed from susceptible or due to USA getting used to dealing with it and not overrun like EU did after a summer of carelessness? | 06:02 |
| LjL | de-facto, it almost seems... i don't want to diss lockdowns... but it almost seems like a "spring loaded" effect from lockdowns | 06:03 |
| LjL | in the US they just had a more or less linear trajectory, without real lockdowns | 06:03 |
| metreo | yuriwho, I think lockdowns are being scaled back in Ontario | 06:03 |
| LjL | in europe, we stopped it for a while, but then it came back *much* quicker | 06:03 |
| de-facto | yeah | 06:03 |
| de-facto | people thought its over and they would not have to care about it anymore | 06:04 |
| de-facto | despite officials saying the opposite | 06:04 |
| yuriwho | The EU let everyone go on holiday during August | 06:04 |
| metreo | yuriwho, we certainly aren't talking about lockdowns in Atlantic Canada there are only 16 active cases | 06:04 |
| de-facto | yeah that was a HUGE mistake | 06:04 |
| de-facto | they thought tourism industry needed to earn money | 06:04 |
| de-facto | well they do but now we pay the price | 06:05 |
| yuriwho | Atlantic Canada has done very well in containing the virus.... I ever heard rumor of you opening up your bubble for Cuba | 06:05 |
| metreo | the only tourists showing up would be the really crazy people | 06:05 |
| metreo | yuriwho, yeah a travel agency is setting that up, it's a bubble-2-bubble arrangement | 06:06 |
| yuriwho | https://www.country94.ca/2020/10/31/is-atlantic-canada-cuba-travel-bubble-feasible/ | 06:06 |
| yuriwho | %T | 06:06 |
| Brainstorm | yuriwho: From www.country94.ca: Is Atlantic Canada-Cuba Travel Bubble Feasible? | Country 94 | 06:06 |
| metreo | it's a nice thought but I won't go | 06:06 |
| yuriwho | which Province are you in? | 06:07 |
| metreo | NS, you? | 06:07 |
| yuriwho | Ontario, GTA west | 06:07 |
| metreo | been here 3 years, got lucky with Covid | 06:07 |
| metreo | I've lived in Aurora before | 06:07 |
| yuriwho | I know that area | 06:08 |
| yuriwho | I live in Halton and have a Cottage on the western edge of Algonquin Park | 06:08 |
| metreo | beautiful parts of the world to be sure | 06:09 |
| LjL | yuriwho: my point is kinda, the US didn't really *stop* anyone from going on holiday either (save for some specific states), but having had no lockdowns, their curve stayed bad but constant. Instead in the EU it's now rising at levels beyond exponential | 06:09 |
| LjL | Look at Belgium | 06:10 |
| Brainstorm | New from This Week In Virology: TWiV 678: Fishing for viruses with Nels Elde: Nels joins TWiV to reveal the discovery of a picornavirus of zebrafish by measuring immune responses in the host, genome sequence analysis of the White House COVID-19 outbreak, and a six-fold higher SARS-CoV-2 exposure rate than reported cases in German children. → https://is.gd/gP79ds | 06:10 |
| yuriwho | that is related to general warmth and sunlight and people being outdoors in wide open spaces | 06:10 |
| LjL | yuriwho: well, okay, now that has stopped and it's cold and we're indoors so things get bad. But why *worse* growth than the US? | 06:11 |
| yuriwho | as the Northern Hemisphere goes into winter, temperature, sunlight and humidity all have a significant effect on viral spread | 06:11 |
| de-facto | i also think with the pathogen constantly in circulation US citizens were forced to learn to live with it, while in EU people simply ignored it in the summer because prevalence was brought down so far with the first lockdowns | 06:11 |
| LjL | de-facto: that's almost an argument against lockdowns | 06:12 |
| de-facto | well not if you look at their constantly high fatalities | 06:12 |
| de-facto | but yeah now we got the explosion here, so we really do need to contain it brutally | 06:12 |
| LjL | Wait until our fatalities match the case numbers we're witnessing... :/ | 06:13 |
| yuriwho | Imagine a droplet of virus emanating from your mouth..... in the humid summer, the droplet maintains it's size or grows, gets irradiated by sunlight and falls to the ground over a small distance | 06:13 |
| LjL | We can't do anything about those now, they are bound to happen | 06:13 |
| ghost_rider[m] | LjL: In Portugal was strange, during August we had 1000 car's getting in in just one small road, party everywhere, I was expecting in 15/30 days a rise in numbers, but only now we are getting that rise in infection's. That confuses me, ... | 06:14 |
| de-facto | we need to hammer it down with non-pharmaceutical measures as we still dont have effective pharmaceutical interventions available | 06:14 |
| LjL | Well good night for now | 06:14 |
| ghost_rider[m] | yuriwho: I see, explain a bit what I said, but during the night ... | 06:15 |
| de-facto | yeah gn8 | 06:15 |
| ghost_rider[m] | LjL: GG √} | 06:15 |
| metreo | night night Ljl | 06:15 |
| yuriwho | Imagine a droplet emanating from your mouth in the cold of winter (below freezing) with low humidity and low sunlight.... the virus shrinks, increasing the viral concentration per droplet, the smaller droplet travels further... everyone is indoors... due to the colder temperature, the virus survives longer on surfaces | 06:15 |
| ghost_rider[m] | yuriwho: I see, thanks... | 06:17 |
| LjL | yuriwho: I've seen only one study correlating the virus with temperatures, at a coarse country level (you probably linked that one). I haven't seen studies linking it to temperature AND humidity, and a bit more granular... Maybe I've just missed it, but it almost seems like among the flood of preprints, some important findings are still not being determined | 06:18 |
| ghost_rider[m] | I was thinking temperature is irrelevant since in Brasil is like wild fire both dense and deep country... Even in remote natives showed up unexplained | 06:18 |
| yuriwho | gimme a sec | 06:19 |
| yuriwho | https://www.hindawi.com/journals/av/2011/734690/ | 06:20 |
| yuriwho | %T | 06:20 |
| Brainstorm | yuriwho: From www.hindawi.com: The Effects of Temperature and Relative Humidity on the Viability of the SARS Coronavirus | 06:20 |
| yuriwho | thats from Scientists in Hong Kong | 06:20 |
| yuriwho | FYI, most virologists are employed in Departments of Microbiology | 06:23 |
| LjL | I'll check it out tomorrow, I'm awake with one eye only | 06:24 |
| ghost_rider[m] | LjL: I bet there is a study that relates lack of sleep with weaker immune system :} goooo | 06:25 |
| Brainstorm | New from The Indian Express: World: Indonesia sees first recession in over two decades as coronavirus hits → https://is.gd/ltVJfp | 06:46 |
| Brainstorm | New preprint: COVID-19 in Hospitalized Ethiopian Children: Characteristics and Outcome Profile by Tigist W. Leulseged et al, published on 2020-11-04 at https://medrxiv.org/cgi/content/short/2020.10.30.20223115 [... want %more?] | 07:20 |
| Brainstorm | Updates for Belgium: +14903 cases (now 468213), +205 deaths (now 12331) since 18 hours ago — France: +4510 cases (now 1.5 million) since 8 hours ago — Canada: +112 cases (now 248590), +1 deaths (now 10349) since 4 hours ago — New Zealand: +2 cases (now 1973) since a day ago | 07:20 |
| CoronaBot | 04/r/coronavirus: Coronavirus updates: United States tops 100,000 new coronavirus cases in a day for first time (10080 votes) | https://www.washingtonpost.com/nation/2020/11/03/covid-coronavirus-updates-2/ | https://redd.it/jo6rgb | 07:25 |
| kara[m] | czech question | 07:49 |
| kara[m] | <ghost_rider[m] "LjL: I bet there is a study that"> i have heard this too | 07:49 |
| Brainstorm | New from BMJ: Seven days in medicine: 28 Oct to 3 Nov 2020: Covid-19Healthcare workers report rise in abuseOver a third (35%) of 1250 UK healthcare professionals surveyed by the Medical Protection Society said that they had experienced verbal or physical... → https://is.gd/fQsH8I | 07:57 |
| Brainstorm | Updates for US: +616 cases (now 9.8 million), +13 deaths (now 239842) since 5 hours ago | 08:21 |
| Brainstorm | New from WHO Euro: New agreement between WHO/Europe and Welsh Government launched to accelerate action on health equity: WHO/Europe and the Welsh Government have agreed to work more closely together to promote health equity and rights and to ensure prosperity for all. Discussions with Public Health Wales and National Health Service (NHS) Wales, held at [... want %more?] → https://is.gd/TEIYhC | 08:33 |
| Brainstorm | Updates for France: +19318 cases (now 1.6 million), +27 deaths (now 38701) since an hour ago — Lombardy, Italy: +7758 cases (now 224191), +96 deaths (now 17848) since a day ago — United Kingdom: +1623 cases (now 1.1 million), +45 deaths (now 47787) since 15 hours ago — Netherlands: +1388 cases (now 384911), +7 deaths (now 7689) since 17 hours ago | 08:36 |
| Brainstorm | New from r/WorldNews: worldnews: US records more than 100,000 new coronavirus cases in a single day for the first time → https://is.gd/MlUqqA | 09:26 |
| Brainstorm | New from CNBC Health: Covid vaccine maker AstraZeneca expects to release trial data by year-end: British pharmaceutical giant AstraZeneca said Thursday it expects vaccine data to be available this year as it reported a solid rise in third-quarter sales. → https://is.gd/2SFb1D | 09:44 |
| Brainstorm | New from Medical Xpress: Beijing bars arrivals from UK, Belgium due to second COVID-19 waves: China has imposed fresh travel bans on non-Chinese arrivals from Britain and Belgium, as it guards against a resurgence of the coronavirus by refusing entry to people from two of Europe's worst-hit nations. → https://is.gd/qgkvTF | 09:53 |
| Brainstorm | New from Medical Xpress: US daily COVID-19 cases hit new record, topping 99,000: Johns Hopkins: More than 99,000 novel coronavirus cases were recorded in the United States in the past 24 hours, a new daily record, according to a tally by Johns Hopkins University. → https://is.gd/3OGEMM | 10:02 |
| pwr22 | UK lockdown starts today! | 10:14 |
| pwr22 | I'm unsure if anyone will actually adhere to it | 10:16 |
| Brainstorm | Updates for US: +403 cases (now 9.8 million) since 2 hours ago — Canada: +283 cases (now 248873), +2 deaths (now 10351) since 3 hours ago | 10:21 |
| Brainstorm | New from StatNews: Opinion: Far more transparency is needed for Covid-19 vaccine trials: The U.S. public has already endured repeated missteps in the pandemic response. Transparency in the research on Covid-19 vaccines will help ensure that Americans trust safe, effective vaccines — and… → https://is.gd/0W6Fxs | 10:48 |
| Brainstorm | New from Reddit (test): CoronaVirus_ITALIA: La Danimarca abbatterà 15milioni di visoni per via del covid-19, poiché una mutazione del virus rischia di invalidare il futuro vaccino → https://is.gd/rjn4qF | 11:43 |
| Brainstorm | New from BMJ: Covid-19: NHS is placed on highest alert level as intensive care beds fill up: The NHS has been placed on the highest alert level amid warnings that some hospitals are now seeing more patients with covid-19 than they did at the height of the pandemic in April.Intensive care... → https://is.gd/81NRTd | 12:01 |
| Brainstorm | New from BBC Health: (news): Covid: The new lockdown rules for England, Wales, Scotland and Northern Ireland → https://is.gd/KDgKoi | 12:10 |
| Brainstorm | New from CNBC Health: U.S. daily coronavirus cases surpass 100,000 for the first time: The number of new daily coronavirus cases recorded in the U.S. surpassed 100,000 for the time Wednesday, according to a tally by Johns Hopkins University. → https://is.gd/yrcX21 | 12:28 |
| Brainstorm | Updates for Switzerland: +10128 cases (now 202504), +25 deaths (now 2580) since 13 hours ago | 12:52 |
| Brainstorm | New from Medical Xpress: Greece to re-enter virus lockdown from Saturday: Greece will re-enter a lockdown from Saturday for three weeks to battle a second wave of the coronavirus, Prime Minister Kyriakos Mitsotakis announced. → https://is.gd/qkEk5t | 13:04 |
| rpifan | yea | 13:28 |
| DocScrutinizer05 | tinwhiskers: "alternative source" doesn't prpagate into URL at all. Maybe a little rework regarding making it a checkbox and add altSource=1 to URL? | 13:38 |
| DocScrutinizer05 | or s/alt// if that makes sense? | 13:40 |
| DocScrutinizer05 | I don't suggest sources=RKI,JHU,FooBar,... for known reasons | 13:41 |
| DocScrutinizer05 | um wait | 13:53 |
| DocScrutinizer05 | aaah legacy=no - sorry, nevermind | 13:53 |
| DocScrutinizer05 | https://offloop.net/covid19/?default=Germany&cumulative=no&miscType=Reff&leftTrim=-30&legacy=no is the RKI obviously (which btw is not encumbered by any copyright issues), compare to the weird numbers https://offloop.net/covid19/?default=Germany&cumulative=no&miscType=Reff&leftTrim=-30 | 13:58 |
| DocScrutinizer05 | just for reference https://i.imgur.com/9A5xmUf.png | 14:09 |
| DocScrutinizer05 | which however is based on publishing date, not reporting date or start of symptoms | 14:11 |
| DocScrutinizer05 | tinwhiskers: which smoothing algo do you apply? it seems quite good | 14:14 |
| Brainstorm | New from BMJ: Covid-19: Care home residents in England should have “safe spaces” for visits from family and friends, says guidance: All care home residents in England should be allowed to receive visits from family and friends in a covid secure way despite new lockdown restrictions coming into force on 5 November, the Department... → https://is.gd/mQpnIE | 14:25 |
| DocScrutinizer05 | >>Healthcare workers report rise in abuseOver a third (35%) of 1250 UK healthcare professionals surveyed by the Medical Protection Society said that they had experienced verbal or physical... << depressing how idiotic human beings can act, a disgrace for whole human race | 14:26 |
| Brainstorm | New from Medical Xpress: What can smartphone location data tell us about the pandemic?: Kevin Williams, an associate professor of economics at Yale SOM, was in the middle of a study of consumer retail behavior using real-time cell phone location data when COVID-19 hit. Shelter-in-place orders rolled across the country. Foot traffic at stores froze. → https://is.gd/zleunF | 14:34 |
| Brainstorm | New from Medical Xpress: Delhi battling dual crises of pollution and coronavirus: India's capital is reeling from the double impact of the coronavirus and severe air pollution, New Delhi's chief minister warned Thursday, as the megacity reported a record jump in cases and its worst smog in a year. → https://is.gd/tyZeb4 | 14:52 |
| Brainstorm | New from NIH Director's blog: Speeding COVID-19 Drug Discovery with Quantum Dots: These round, multi-colored orbs in the illustration above may resemble SARS-CoV-2, the coronavirus responsible for COVID-19. But they’re actually lab-made nanocrystals called quantum dots. They have been specially engineered to look and, in some ways, act like the [... want %more?] → https://is.gd/03dWLp | 15:01 |
| Brainstorm | Updates for Netherlands: +5577 cases (now 390488), +84 deaths (now 7769) since 6 hours ago — US: +1366 cases (now 9.8 million), +11 deaths (now 239853) since 4 hours ago | 15:08 |
| Brainstorm | New from Medical Xpress: Data analysis identifies the 'mother' of all SARS-CoV-2 genomes: In the field of molecular epidemiology, the worldwide scientific community has been sleuthing to solve the riddle of the early history of SARS-CoV-2. → https://is.gd/Tm0Egc | 15:20 |
| drsatan | ***COUGH*** | 15:33 |
| Brainstorm | New from Medical Xpress: Using machine learning to track the pandemic's impact on mental health: Dealing with a global pandemic has taken a toll on the mental health of millions of people. A team of MIT and Harvard University researchers has shown that they can measure those effects by analyzing the language that people use to express their anxiety online. → https://is.gd/WMASTg | 15:37 |
| CoronaBot | 04/r/covid19: Startling Case Study Finds Asymptomatic COVID-19 Carrier Who Shed Virus For 70 Days (83 votes) | https://www.sciencealert.com/case-study-reveals-rare-patient-who-showed-no-symptoms-but-shed-infectious-sars-cov-2-for-70-days | https://redd.it/joiz4b | 15:45 |
| Brainstorm | New from CNBC Health: Sony's new PS5 game console won't be sold in stores on Nov. 12 release day: Sony said its new PS5 game console won't be sold in stores due to the spread of coronavirus, so customers should plan to buy online. → https://is.gd/5ew2Wn | 15:55 |
| Brainstorm | New from Medical Xpress: European virus 'explosion' as England locks down: England became the latest European country to enter a second coronavirus lockdown on Thursday as the continent emerged as the region with the most infections and the United States set a new daily record with nearly 100,000 cases. → https://is.gd/UYHzNw | 16:23 |
| Brainstorm | Updates for US: +3139 cases (now 9.8 million), +38 deaths (now 239891) since an hour ago | 16:23 |
| Brainstorm | New from Medical Xpress: Swedish PM sounds alarm as virus deaths top 6,000: Swedish Prime Minister Stefan Lofven went into self-isolation on Thursday and warned that the soaring coronavirus cases had created a "serious situation" again, as the country's deaths passed 6,000. → https://is.gd/x36Fzn | 16:32 |
| rpifan | nice | 16:47 |
| Brainstorm | New from Medical Xpress: Europe now region hardest hit by virus infections: Europe has become the region with the highest number of registered cases of the new coronavirus, according to a tally by AFP at 1100 GMT on Thursday based on health authority data. → https://is.gd/9HspLQ | 16:49 |
| rpifan | yea | 16:56 |
| rpifan | we all knew there'd be a harder second wave | 16:57 |
| Brainstorm | New from The Indian Express: World: Head of Serbian Orthodox Church in hospital with coronavirus → https://is.gd/eV69gk | 16:58 |
| DocScrutinizer05 | wo covered virus causing autoimmune, at Oct. 28, but did we cover https://www.sciencemag.org/news/2020/09/hidden-immune-weakness-found-14-gravely-ill-covid-19-patients et al suggesting that interferon related autoimmune may cause severe covid. Studies found a 15% in those with severe vs 0% in mild or asymptomatic, and a 0.3% in uninfected control group | 17:03 |
| DocScrutinizer05 | we* | 17:03 |
| DocScrutinizer05 | %title | 17:07 |
| Brainstorm | DocScrutinizer05: From www.sciencemag.org: Hidden immune weakness found in 14% of gravely ill COVID-19 patients | Science | AAAS | 17:07 |
| DocScrutinizer05 | %title https://science.sciencemag.org/content/370/6515/eabd4585 | 17:07 |
| Brainstorm | DocScrutinizer05: From science.sciencemag.org: Autoantibodies against type I IFNs in patients with life-threatening COVID-19 | Science | 17:07 |
| DocScrutinizer05 | sidenote factoid: in Germany ~22mio are "high risk", so more than oen out of four. | 17:08 |
| Brainstorm | Updates for US: +4051 cases (now 9.8 million), +52 deaths (now 239943) since 51 minutes ago | 17:09 |
| Brainstorm | New from Medical Xpress: Rapid changes in biomarker of inflammation may be a key predictor of COVID-19 outcomes: Predicting the course of a COVID-19 patient's disease after hospital admission is essential to improving treatment. Brigham and Women's Hospital researchers analyzed patients' levels of inflammation, known to be associated with severity of [... want %more?] → https://is.gd/gjsRJa | 17:16 |
| ghost_rider[m] | DocScrutinizer05: Germany 22 what ? Million ? | 17:18 |
| ghost_rider[m] | Imaginary Jeebus, if yes | 17:18 |
| tinwhiskers | DocScrutinizer05: smoothing algo is something like a "diminishing 7 day centered moving average". That is, an average of the current day's value and three days prior and post, except that two days from the end of the series it becomes a five day centered average, one day before the end, a three day centered average and the end value of the series is unaffected. | 17:21 |
| tinwhiskers | Moving averages introduce an annoying lag effect so centering them takes that away but leaves you with the problem of what to do when you run out of data at the end of the series. | 17:22 |
| Brainstorm | New from Medical Xpress: Fit, 35 and hospitalized with COVID, woman donates plasma to help others: (HealthDay)—If you've recovered from a COVID-19 infection, you can help as many as four other COVID-19 patients get better, simply by donating your plasma. → https://is.gd/eJcvSX | 17:26 |
| tinwhiskers | If you're following a climbing or falling trend a moving average suppresses the trend and is pretty damn useless. | 17:26 |
| DocScrutinizer05 | ~22mio | 17:32 |
| ghost_rider[m] | Sad of me, don't understand that unit | 17:35 |
| DocScrutinizer05 | million | 17:37 |
| de-facto | tinwhiskers, nice so you do a symmetric window evenly weighted moving average with dynamic shrinking window a the edges? | 17:37 |
| tinwhiskers | Right | 17:38 |
| tinwhiskers | That's a much more succinct way to put it :-) | 17:38 |
| Brainstorm | Updates for Italy: +34502 cases (now 824879), +428 deaths (now 40192) since a day ago — US: +402 cases (now 9.8 million), +4 deaths (now 239947) since 35 minutes ago | 17:39 |
| ghost_rider[m] | DocScrutinizer05: WoW | 17:40 |
| DocScrutinizer05 | tinwhiskers: butt ugly but look at folded phase (7d phase period) filtering for smoothing in the red fat line of http://reisenweber.net/et_al/covid/covid19_statistics.htm | 17:40 |
| DocScrutinizer05 | it has no system immanent inertia or lag at all | 17:41 |
| tinwhiskers | Right | 17:41 |
| tinwhiskers | How's that done? | 17:42 |
| tinwhiskers | You mean the fat blue line in the top graph? | 17:43 |
| LjL | :( | 17:43 |
| DocScrutinizer05 | basically I do a pattern memory by calculating a emphasize-on-new average of ratio between 7day moving average and current raw value. This gives an anjustment factor for each day of week by which I multiply the raw value | 17:44 |
| tinwhiskers | *blink blink* | 17:45 |
| DocScrutinizer05 | the blue line is 7d moving avwerage | 17:45 |
| de-facto | solid red on second graph | 17:45 |
| DocScrutinizer05 | [3 Nov 2020 21:25:58] <DocScrutinizer05> de-facto: https://i.imgur.com/P44JI7E.png rot = faelle_heute / wichtung_heute; wichtung_heute = (wichtung_-7d * 3 + verhaeltnis_heute)/4; verhaeltnis_heute = faelle_heute / avg[N=heute .. -6d](faelle[N]) | 17:46 |
| DocScrutinizer05 | yes | 17:46 |
| DocScrutinizer05 | solid red on second graph | 17:46 |
| tinwhiskers | Oh, folded phase in second graph. Ok | 17:46 |
| DocScrutinizer05 | fotted red is R_eff based on that but it's too jittery | 17:47 |
| DocScrutinizer05 | dotted* | 17:47 |
| metreo | I wonder what plotting tool is being used? | 17:48 |
| tinwhiskers | So that's more about removing weekly patterns than smoothing per se? | 17:49 |
| de-facto | so to translate for tinwhiskers he uses solid_red = cases_today / weighting_today with weighting_today = (3*weighting(-7days) + ratio_today) / 4 with a ratio_today = cases_today / average(today ... today-6days) | 17:51 |
| de-facto | as far as i understood his equations | 17:51 |
| tinwhiskers | Thanks :-) | 17:52 |
| LjL | Calls to emergency services for respiratory reasons in Lombardy: https://lab24.ilsole24ore.com/coronavirus/#box_15 so much for "it's not worse than spring, we're just testing a lot more" (they are testing so much that they have now instructed contacts of positives NOT to request a test) | 17:53 |
| Brainstorm | Updates for US: +2736 cases (now 9.8 million) since 21 minutes ago — Switzerland: +28 deaths (now 2608) since 5 hours ago | 17:54 |
| de-facto | tinwhiskers, yes thats how i understood it too | 17:55 |
| de-facto | LjL, for some reason that website removes id from links when loading at least for me | 17:57 |
| LjL | Oh | 17:57 |
| LjL | Well go to the thing where it says 118... | 17:58 |
| DocScrutinizer05 | sorry, PC crashed | 18:00 |
| de-facto | damn so at 2/3 of the first peak already | 18:00 |
| DocScrutinizer05 | at 17:48:42 CET | 18:00 |
| LjL | de-facto: and much thicker in Milan | 18:03 |
| de-facto | interesting the lockdown date at 2020-03-9 and the decline of the first peak starting at 2020-03-25 | 18:04 |
| de-facto | probably people began to be careful before lockdown date though | 18:04 |
| DocScrutinizer05 | tinwhiskers: row24 H=B24/C24 I=(H17*$I$1+H24*$I$2)/($I$1+$I$2) J=B24/I24 redline=J | 18:05 |
| Jigsy | 3>In line with the new COVID-19 guidance, travel outside of home, with the exception of a limited number of reasons including work or education, is not permitted during lockdown. | 18:08 |
| Jigsy | Guess I'll just starve? | 18:08 |
| LjL | de-facto: 15 days checks out though, doesn't it? I'd take this graph as a more realtime indicator than the case graph | 18:08 |
| rpifan | you should | 18:09 |
| LjL | Jigsy: I'm sure the limited number of reasons includes grocery shopping as it did in all other countries under lockdown... Including doesn't mean limited to | 18:09 |
| LjL | rpifan: excuse me? | 18:09 |
| rpifan | yea | 18:09 |
| rpifan | Jigsy, you should starve i bet you could loss some weight | 18:10 |
| rpifan | good time to do so | 18:10 |
| Jigsy | I'm not overweight... | 18:10 |
| LjL | rpifan: that is not funny. Also starving means dying of hunger | 18:10 |
| de-facto | yeah looks like ~16 days into lockdown until the peaks maximum began to decline and lockdown continued from that decline for 53 days, so all in all 69 days lockdown for the first peak there | 18:11 |
| DocScrutinizer05 | LjL: we had a tightening of measures 2 weeks before lockdown | 18:11 |
| LjL | Jigsy: when did the UK issue new guidance anyway? When Johnson announced the thing, my understanding, although paper articles were conflicting, was that leaving home was still okay | 18:11 |
| metreo | actually the concern here is inactivity and people gaining weight | 18:11 |
| DocScrutinizer05 | de-facto: ^^^ | 18:11 |
| rpifan | Jigsy, r u sure, many ppl think they arent but they are, whats your BMI | 18:11 |
| metreo | I've never been less active personally | 18:12 |
| LjL | rpifan: just stop. Now. | 18:12 |
| DocScrutinizer05 | nevermind, meh, March | 18:12 |
| rpifan | metreo, ive been doing 100 pushups | 18:13 |
| rpifan | since corona started | 18:13 |
| rpifan | plus | 18:13 |
| rpifan | weight training at home | 18:13 |
| rpifan | and dips | 18:13 |
| metreo | rpifan: 100 at once!? I can do 30 weighing 185lbs | 18:13 |
| LjL | de-facto: I think of you take into account how much further into the 118 call peak we already are before full lockdown this time (which begins tomorrow), yikes, we can predict that graph going much higher than last time | 18:13 |
| rpifan | 100 in sets of 20 | 18:14 |
| rpifan | i mean | 18:14 |
| rpifan | 20 reps | 18:14 |
| metreo | ^ how I do | 18:14 |
| rpifan | per set | 18:14 |
| metreo | yeah that's what I try to do everyday | 18:14 |
| LjL | Also that mink farm business really destroyed my already very limited optimism, I feel like... | 18:14 |
| rpifan | good metreo | 18:15 |
| de-facto | LjL huh but the first wave lockdown looks like it began at ~1000 second wave graph looks like it was at ~800 at 2020-11-02 so it may be similar? | 18:16 |
| de-facto | yet if now prevalence is more in the young people less of them may call 118 if not symptomatic or such | 18:18 |
| de-facto | not sure | 18:18 |
| LjL | de-facto: maybe you're right. Well I wouldn't take that graph as estimating prevalence at all. But I think it's a good proxy for hospitalizations | 18:18 |
| metreo | .title https://arxiv.org/abs/2010.13381 | 18:19 |
| Brainstorm | metreo: From arxiv.org: [2010.13381] Secure and Efficient Trajectory-Based Contact Tracing using Trusted Hardware | 18:19 |
| de-facto | LjL, yeah that makes sense indeed and also probably more current indicator in time than testing numbers | 18:19 |
| metreo | .title https://arxiv.org/abs/2011.02309 | 18:21 |
| Brainstorm | metreo: From arxiv.org: [2011.02309] Towards Privacy in Geographic Message Dissemination for Connected Vehicles | 18:21 |
| metreo | just browsing :) | 18:21 |
| Brainstorm | Updates for US: +5217 cases (now 9.8 million), +69 deaths (now 240016) since 52 minutes ago — Arizona, US: +2135 cases (now 252768), +28 deaths (now 6087) since a day ago | 18:39 |
| LjL | 8,99CarlSagan:99,99 [4,99NPR - Science99,99] Clots, Strokes And Rashes. Is COVID-19 A Disease Of The Blood Vessels?99,99 https://www.npr.org/sections/health-shots/2020/11/05/917317541/clots-strokes-and-rashes-is-covid-19-a-disease-of-the-blood-vessels?utm_medium=RSS&utm_campaign=science 2020-11-05T12:02:03 | 18:41 |
| CoronaBot | 04/r/covid19: Case Study: Prolonged infectious SARS-CoV-2 shedding from an asymptomatic immunocompromised cancer patient. (83 votes) | https://www.cell.com/cell/fulltext/S0092-8674(20)31456-2 | https://redd.it/jok6sw | 18:41 |
| LjL | Nothing new, I guess, but the article contains a few links | 18:41 |
| Brainstorm | Updates for Spain: +9097 cases (now 1.4 million), +368 deaths (now 38486) since 23 hours ago — US: +8354 cases (now 9.8 million), +72 deaths (now 240088) since 21 minutes ago | 18:54 |
| Brainstorm | New from r/WorldNews: worldnews: Denmark's mink cull a 'black day' for farmers, tighter COVID lockdown planned → https://is.gd/nTt4Sf | 18:56 |
| de-facto | hopefully they will go bankrupt and do something more useful in their future | 19:02 |
| LjL | yuriwho: in a late answer to a question you had yesterday, "Municipalities in northern Denmark, home to most of the country’s mink farms, will face restrictions on movement across county lines, while restaurants and bars will be forced to close, the mayor of Vesthimmerland Municipality, Per Bach Laursen, told Reuters." - I'd assume no movement across county lines implies no movement abroad. https://www.reuters.com/article/us-health-coronavirus-denmark-mink-lock | 19:03 |
| LjL | d/denmarks-mink-cull-a-black-day-for-farmers-tighter-covid-lockdown-planned-idUSKBN27L1HD | 19:03 |
| de-facto | and even more hopefully spread of the new mutant strain could be contained with lockdown | 19:03 |
| LjL | I can't see how to be honest... Lockdowns are never airtight, unless you're China maybe | 19:04 |
| de-facto | the more aggressive the containment methods the tighter it will be | 19:05 |
| Brainstorm | New from Medical Xpress: Delaying cancer care costs lives: (HealthDay)—Even as the coronavirus pandemic has postponed the delivery of many kinds of health care, a new study suggests that delaying cancer treatment by even a month can raise your risk of dying by 6% to 13%, and that risk keeps rising the longer treatment is delayed. → https://is.gd/1plVAD | 19:06 |
| LjL | de-facto: and that also doesn't consider the fact that they don't know how mink farms could be infected at a distance, so it's likely that mink in other countries, or other animals even, have caught this strain by now | 19:07 |
| Arsanerit | mink farming should be banned | 19:07 |
| de-facto | yes indeed thats a good question | 19:07 |
| LjL | Arsanerit: yes but to avoid spread it should be banned worldwide in a matter of days | 19:08 |
| Arsanerit | A ban had already announced been in The Netherlands when this happened. | 19:08 |
| LjL | Which I find unlikely | 19:08 |
| de-facto | i also think having pelts and fur is not essential, its luxury items that should be made artificially and mink farming should be banned globally | 19:08 |
| de-facto | and it was known for many many months already that this will be a problem | 19:08 |
| de-facto | that is what makes me angry, why did they not react according to the knowledge becoming available | 19:09 |
| Brainstorm | Updates for US: +3114 cases (now 9.8 million), +24 deaths (now 240112) since 20 minutes ago — Switzerland: +14 deaths (now 2622) since an hour ago | 19:09 |
| Arsanerit | economic interests | 19:09 |
| LjL | de-facto: devil's advocate - we've been finding out lately that plastic, including that used for clothing, has extreme and unforeseen ecological impact on animals, and whenever you wash, say, a pile fabric cloth, or microfiber, you are releasing a lot of microplastic into the water. That could be used as an argument for natural fabrics over artificial alternatives | 19:10 |
| de-facto | well yeah if a problem becomes apparent address and solve it | 19:11 |
| de-facto | especially if its a problem related to pandemics because it easily can become amplified exponentially | 19:12 |
| de-facto | but yeah climate change is a much bigger problem that is ignored for too long | 19:12 |
| de-facto | yet thats offtopic | 19:13 |
| LjL | Plastic issues run a bit parallel to climate change | 19:14 |
| Brainstorm | New from Medical Xpress: Paris tightens screws on virus lockdown: Paris will order food shops to close at 10:00 pm and outlaw nighttime food deliveries and alcohol sales, officials said Thursday, hoping to prevent crowds that have gathered at some restaurants and grocery stores despite a new coronavirus lockdown. → https://is.gd/OmuCy6 | 19:15 |
| LjL | Yes, get fewer crowds by cramming them into smaller timeslots, way to go | 19:17 |
| tinwhiskers | Heh | 19:17 |
| de-facto | lol | 19:18 |
| de-facto | sometimes its almost comical if it was not so tragic | 19:19 |
| de-facto | why not concentrate tracing efforts to uncover the infection origins of a randomly selected group of cases | 19:20 |
| de-facto | try everything to determine this information | 19:20 |
| de-facto | then make statistics about it and modify containment accordingly | 19:21 |
| de-facto | otherwise there always will be bias in the stats, the easily known infection origins (such as family at home) will be overexposed in the stats | 19:22 |
| de-facto | but those cant be avoided anyhow since households life together, it would be much more important to know more about the unknown infection origins | 19:23 |
| de-facto | like in Germany 75% of infection origins are unknown | 19:24 |
| de-facto | only if we knew more about those we can target them specifically with containment | 19:24 |
| Brainstorm | Updates for US: +8474 cases (now 9.8 million), +91 deaths (now 240203) since 23 minutes ago | 19:24 |
| Brainstorm | New from Medical Xpress: Blood cell mutations confound prostate cancer liquid biopsy results: Unrelated mutations, when present in the blood, can lead to false positive results in men with advanced prostate cancer who are undergoing liquid biopsies. Such tests, which look for variants in the cell-free DNA that tumors shed into the blood plasma, help [... want %more?] → https://is.gd/vKD93P | 19:24 |
| Brainstorm | New from Gazzetta Ufficiale italiana: MINISTERO DELLA SALUTE - ORDINANZA 4 novembre 2020: Ulteriori misure urgenti in materia di contenimento e gestionedell'emergenza epidemiologica da COVID-19. (20A06144) → https://is.gd/YGWWpR | 19:34 |
| Brainstorm | New from Medical Xpress: Diseases, Conditions, Syndromes: Emotional moment shows health care workers feel COVID-19 fatigue too. 'We feel trapped in many ways' → https://is.gd/8QAXOm | 19:43 |
| Brainstorm | Updates for France: +34218 cases (now 1.6 million), +363 deaths (now 39037) since 11 hours ago — US: +11314 cases (now 9.9 million), +119 deaths (now 240322) since 35 minutes ago — Canada: +1486 cases (now 250359), +35 deaths (now 10377) since 9 hours ago | 19:54 |
| de-facto | %title https://www.youtube.com/watch?v=q9EwA8w-jP8 Interesting talk from Drosten in German for the general public about current situation and strategies | 20:03 |
| Brainstorm | de-facto: From www.youtube.com: MENSCHEN | WINDTHORST-ABEND MIT CHRISTIAN DROSTEN | AUS DEM JAM MEPPEN - YouTube | 20:03 |
| Brainstorm | New from In The Pipeline: Don’t Make Mine Mink: There’s a situation in Denmark that deserves some epidemiological attention. Now, put me in the (rather large) category who did not realize how large the Danish mink industry is – or that a Danish mink industry existed at all – but there are plenty of mink farmers there and millions of mink. 40% [... want %more?] → https://is.gd/ww4pdT | 20:11 |
| LjL | today i talked to a MOLECULAR BIOLOGIST https://np.reddit.com/r/worldnews/comments/jnyh30/denmark_to_cull_entire_13_million_mink_herd_as/gb5sngs/ | 20:15 |
| bin_bash | whoa | 20:16 |
| bin_bash | glad theyre doing the right thing but damn | 20:16 |
| bin_bash | lol that guy is butthurt | 20:18 |
| tinwhiskers | lol | 20:18 |
| bin_bash | i kind of doubt that he's a molecular biologist | 20:18 |
| tinwhiskers | RE Mink: Derek says, "The article also says, rather alarmingly, that “The Serum Institute estimates that five percent of the viral infections among people in North Jutland are of the new type of virus mutation“, and I would very much like to hear some more about that." So that cat is well out of the bag now. :-( | 20:24 |
| LjL | yes | 20:24 |
| tinwhiskers | s/cat/mink/ | 20:24 |
| Brainstorm | Updates for US: +6343 cases (now 9.9 million), +56 deaths (now 240378) since 41 minutes ago | 20:25 |
| LjL | well i am concerned about cats too, personally | 20:25 |
| bin_bash | ya i wish we could just cull all strays/ferals | 20:25 |
| LjL | sustained transmission in cats has been shown. i guess unless i forget, though, a jump back to humans has not yet been shown. but honestly i'm a bit tired of people assuming things won't happen just because "it hasn't been shown", considering how struggling we are with keeping on top of things | 20:26 |
| LjL | bin_bash, at this pace we'd probably end up culling all mammals | 20:26 |
| LjL | maybe we should start with us | 20:26 |
| tinwhiskers | yes, we've already got ourselves into enough trouble due to "there is no evidence that suggests..." | 20:27 |
| bin_bash | LjL: nah i think starting with invasive felines is the best step | 20:27 |
| de-facto | yes cats too but afaik there are not mass breeding for cats similar to those stupid mink farms | 20:27 |
| LjL | i saw that 5% figure yesterday. i said nothing because i didn't have a solid source and people here were being like, calm down for now, it's just 12 people. | 20:27 |
| tinwhiskers | cows, sheep, pigs? | 20:27 |
| de-facto | btw also hamsters | 20:27 |
| dTal | there is no evidence to suggest that those who say "there is no evidence to suggest" are correct | 20:28 |
| tinwhiskers | dTal: heh | 20:28 |
| LjL | :) | 20:28 |
| dTal | (checkmate atheists) | 20:28 |
| LjL | tinwhiskers, if it gets into an animal that's heavily domesticated for food, we're going to be in deep trouble. | 20:28 |
| dTal | ..thanks for the nightmare | 20:29 |
| tinwhiskers | but I don't wanna be a vegetarian :-( | 20:29 |
| LjL | dTal, it's a bit difference. there has been no evidence to suggest god exists... for thousands of years. that there is no evidence for this or that about COVID for a month or two is a little less comforting | 20:29 |
| LjL | dTal, well i had nightmares about the mink thing already, so you're welcome ;( | 20:30 |
| de-facto | tinwhiskers, nope cattle is not so susceptible it seems fortunately https://www.biorxiv.org/content/10.1101/2020.08.25.254474v1 | 20:30 |
| de-facto | %T | 20:30 |
| tinwhiskers | \o/ | 20:30 |
| Brainstorm | de-facto: From www.biorxiv.org: Experimental infection of cattle with SARS-CoV-2 | bioRxiv | 20:30 |
| tinwhiskers | although I eat mostly sheep... | 20:30 |
| tinwhiskers | (back home, that is) | 20:31 |
| dTal | sheep are good at social distancing | 20:31 |
| LjL | i'd be more concerned with pigs | 20:31 |
| dTal | gonna freeze a bunch of bacon | 20:31 |
| dTal | gonna be a bacon millionarie | 20:31 |
| tinwhiskers | invest in bacon now | 20:31 |
| dTal | and maybe a ham, for christmas | 20:32 |
| LjL | if it happens it would not be a problem just for pork. those normally eating porks will end up eating something else | 20:32 |
| tinwhiskers | yeah, the relatively intensive practices used for pig farming are concerning | 20:32 |
| LjL | anyone have a good source about the Danish mink situation that includes that 5% figure (if it really comes from health officials) and is decent and is in English, to add to the links list? | 20:34 |
| tinwhiskers | There was that comment we saw yesterday that the variation found in the mink strain is within the variation found among humans, so it may not be bad news, and at least nipping this in the bud now might mean we won't get far worse news. | 20:35 |
| tinwhiskers | I took it to mean all the mutations found in the mink strain have also been found in humans strains. | 20:35 |
| LjL | but again their SSI was like "this doesn't convincingly respond to antibodies or treatment, KILL THEM ALL QUICK". i am not comforted by the not-yet-published science that's probably behind such a decision | 20:36 |
| ghost_rider[m] | LjL: please, I lost your wiki, so sorry | 20:36 |
| LjL | ghost_rider[m], it's in the room's topic... | 20:37 |
| tinwhiskers | LjL: yeah, that's a concern but not really clear what it means. | 20:37 |
| ghost_rider[m] | Oh, I see now, sorry | 20:37 |
| LjL | tinwhiskers, besides how would anyone know that this mutation has all been found in human strains? no sequences were published yet afaik... | 20:37 |
| tinwhiskers | oh. umm... huh. | 20:38 |
| tinwhiskers | well, that doesn't stack up then. | 20:38 |
| de-facto | "Until now, natural or experimental infections demonstrated the susceptibility of fruit bats (Rousettus aegyptiacus), ferrets, felids, dogs and minks, while pigs, chicken and ducks could not be infected (4-6). Besides ducks, chicken and pigs, major livestock species with close contact to humans are ruminants including a global population of ca. 1.5 Billion of cattle. In bovines, non-SARS betacoronaviruses are widespread (7, 8) with | 20:38 |
| de-facto | seroprevalences reaching up to 90% (9). The course of infection is usually subclinical (7). However, it is yet unknown whether any ruminant species including cattle is susceptible to SARS-CoV-2 infection or whether there is any cross-reactivity of antibodies against bovine coronaviruses (BCoV) to SARS-CoV-2." | 20:38 |
| Brainstorm | New from Medical Xpress: Researchers use genomics to reconstitute yellow fever outbreak in Sao Paulo: Yellow fever virus is normally confined to the Amazon region, but the virus circulated in the Southeast of Brazil between 2016 and 2018, causing the worst epidemic and epizootic outbreaks there for decades. The Ministry of Health confirmed 2,251 cases [... want %more?] → https://is.gd/YMYiFE | 20:38 |
| LjL | de-facto, that's good | 20:39 |
| de-facto | "All animals tested negative for the presence of SARS-CoV-2 RNA in swab samples and SARS-CoV-2-specific antibodies in serum prior to infection. None of the inoculated cattle, nor any of the contact animals showed any clinical, disease-related symptoms. Body temperature, feed intake and general condition remained in a physiological range throughout the study. However, two of the inoculated animals became productively infected demonstrated | 20:40 |
| de-facto | by the detection of viral RNA in nasal swabs." | 20:40 |
| LjL | %papers susceptibility of ferrets, cats, 129 dogs, and other domesticated animals to SARS–coronavirus 2 | 20:41 |
| Brainstorm | LjL: An error occurred while searching. | 20:41 |
| LjL | %papers susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS–coronavirus 2 | 20:41 |
| Brainstorm | LjL: An error occurred while searching. | 20:41 |
| LjL | this thing doesn't work does it | 20:41 |
| de-facto | "One animal (number 776) tested positive on days 2 and 3 after inoculation with quantification cycle (Cq) values of 29.97 (day 2) and 33.79 (day 3), and another calf (number 768) on day 3 only (Cq 38.13) (Figure 1A). These animals scored positive only in the nasal swabs. Oral and rectal swabs taken simultaneously, as well as specimens collected from every other animal, remained negative throughout the study period. " | 20:42 |
| tinwhiskers | LjL: this discussion seems to suggest it has been sequenced, although I can't find the comment I saw yesterday (I think it was elsewhere). https://www.reddit.com/r/COVID19/comments/jo2muy/mink_and_covid19/ | 20:43 |
| tinwhiskers | but I've only glossed over it looking for another comment so may have misunderstood | 20:44 |
| LjL | uhm, https://www.reddit.com/r/COVID19/comments/jo2muy/mink_and_covid19/gb747en/ | 20:44 |
| de-facto | "In conclusion, our findings demonstrate that under our experimental conditions cattle show low susceptibility to SARS-CoV-2, since two out of six animals appear to be infected as demonstrated by SARS-CoV-2-genome detection in nasal swabs and specific seroconversion. However, there is no indication that cattle play any role in the human pandemic nor are there reports of naturally infected bovines. This correlates with the rather low | 20:44 |
| de-facto | genome loads we detected after experimental intranasal infection of cattle and the absence of transmission to any of the direct in-contact animals. | 20:44 |
| de-facto | " | 20:44 |
| de-facto | "Nevertheless, in regions with high numbers of cattle and high case numbers in humans, like the US or South America, close contact between livestock and infected animal owners or caretakers could lead to anthropo-zoonotic infections of cattle, as it was already described for highly susceptible animal species like mink, felids or dogs (6, 14)." | 20:44 |
| LjL | QJS39627.1;QJS39615.1;QJS39603.1;QJS39591.1;QJS39579.1;QJS39567.1;QJS39555.1;QJS39543.1;QNJ45118.1;QNJ45106.1;QNJ45142.1;QNJ45154.1;QNJ45166.1;QNJ45178.1;QNJ45190.1;QNJ45202.1;QNJ45214.1;QNJ45226.1;QNJ45238.1; if de-facto wants to play | 20:44 |
| LjL | tinwhiskers, but then this appears to be based on "Dr. Emma Hodcroft on twitter (@firefoxx66) also has a very good thread about what she was able to find, based on previous Danish papers. This mutation seems to be a few deletions that have only been found in mink populations, and then N439K which has also been found widely in humans in Europe and is already on a lot of radars." | 20:46 |
| LjL | so it's people digging for previously-published sequences that had escaped attention, which is not necessarily the sequence of the new thing that the SSI has found...? | 20:46 |
| de-facto | which mutations are those you listed above there? | 20:47 |
| LjL | she retweets "Anyway, from all we know for now the mutation that is an antibody escape mutant is at position 453. This mutation also occured in the Netherlands and seems to pop up more often. I assume at this stage full-length Spike protein vaccine platforms will have advantages" | 20:47 |
| LjL | de-facto, basically all mink-related sequences that someone on reddit has spotted, i copypasted from https://www.reddit.com/r/COVID19/comments/jo2muy/mink_and_covid19/gb747en/ | 20:48 |
| Brainstorm | Updates for US: +5308 cases (now 9.9 million), +33 deaths (now 240411) since 32 minutes ago | 20:50 |
| de-facto | also found at least on of those in this paper | 20:50 |
| de-facto | %title https://www.biorxiv.org/content/10.1101/2020.08.10.244632v2 | 20:50 |
| Brainstorm | de-facto: From www.biorxiv.org: Bioinformatic Analysis Reveals That Some Mutations May Affect On Both Spike Structure Damage and Ligand Binding Site | bioRxiv | 20:50 |
| de-facto | lol | 20:52 |
| Nov1-Vaccine | hi everyone! | 21:01 |
| Nov1-Vaccine | I hope I'm not late! | 21:01 |
| Nov1-Vaccine | I have an important mission to prevent confusion in this year's United States Presidential election | 21:02 |
| LjL | this channel is about COVID though | 21:02 |
| tinwhiskers | we've been here before | 21:03 |
| ghost_rider[m] | Nov1-Vaccine: mission ? Are you being paid ? | 21:06 |
| CoronaBot | 04/r/coronavirus: Authorities in Denmark are to ask residents in North Jutland not to leave their home municipalities due to concerns over the spread of a mutated form of coronavirus. (10016 votes) | https://www.thelocal.dk/20201105/denmark-to-restrict-north-jutland-borders-due-to-mink-coronavirus-outbreak | https://redd.it/johc48 | 21:06 |
| ghost_rider[m] | Sorry the brief oft | 21:06 |
| genera | try ##coronavirus-vox )) | 21:06 |
| tinwhiskers | wow | 21:07 |
| tinwhiskers | that seems rather futile | 21:08 |
| ghost_rider[m] | That's not new, at beginning South Korea told a cat haz it. | 21:08 |
| LjL | tinwhiskers, i can't leave my municipality either, and what i may harbor is probably not even very mutated! | 21:08 |
| LjL | ghost_rider[m], having it in the links page is new | 21:09 |
| LjL | you wanted a wiki with updated information | 21:09 |
| LjL | i am updating the information | 21:09 |
| LjL | "Anyone who tests positive for coronavirus in the affected municipalities will also be required to test for whether they have been infected with the normal strain or the variation from mink farms." ← this is kind of important | 21:10 |
| tinwhiskers | wow (again) | 21:11 |
| tinwhiskers | that is something | 21:11 |
| tinwhiskers | will they cull them if they have the mink strain? | 21:12 |
| tinwhiskers | sorry, too soon. | 21:12 |
| LjL | tinwhiskers, https://np.reddit.com/r/Coronavirus/comments/johc48/authorities_in_denmark_are_to_ask_residents_in/gb8hvxi/ hey at least we aren't the only ones noticing this | 21:13 |
| Brainstorm | New from r/WorldNews: worldnews: Vancouver man charged with breaking mandatory quarantine orders after returning from Flat Earth conference in the U.S. → https://is.gd/tNqQpw | 21:15 |
| ghost_rider[m] | LjL: sory ;p | 21:17 |
| ghost_rider[m] | LjL: I like the home page: Hi. | 21:23 |
| Jigsy | https://www.theguardian.com/education/2020/nov/05/security-fence-manchester-university-student-flats | 21:23 |
| Jigsy | %title | 21:23 |
| Brainstorm | Jigsy: From www.theguardian.com: Security fence erected around Manchester students' block of flats | Education | The Guardian | 21:23 |
| Brainstorm | New from https://covid19.specops.network : Add Denmark movement restriction news: This should really be preceded by information about the mink outbreak and its significance, but I have yet to find a satisfactory English source. → https://is.gd/z6FIDh | 21:25 |
| yuriwho | LjL de-facto https://blogs.sciencemag.org/pipeline/archives/2020/11/05/dont-make-mine-mink | 21:28 |
| yuriwho | tinwhiskers: ^ | 21:29 |
| LjL | yuriwho, thanks... i didn't have the link before although tinwhiskers cited it. then i forgot to look it up | 21:33 |
| de-facto | if Derek blogs about it then it means it really is of importance | 21:33 |
| yuriwho | yep, he wants to see the data just like I do | 21:34 |
| Brainstorm | New from Medical Xpress: Llama nanobodies could be a powerful weapon against COVID-19: Today in Science, researchers at the University of Pittsburgh School of Medicine describe a new method to extract tiny but extremely powerful SARS-CoV-2 antibody fragments from llamas, which could be fashioned into inhalable therapeutics with the potential to prevent [... want %more?] → https://is.gd/pEjHaH | 21:34 |
| yuriwho | clearly there are a lot of top scientists investigating this | 21:34 |
| Brainstorm | Updates for US: +13703 cases (now 9.9 million), +147 deaths (now 240558) since 48 minutes ago — Canada: +554 cases (now 250913), +4 deaths (now 10381) since an hour ago — Switzerland: +6 deaths (now 2628) since 2 hours ago | 21:35 |
| de-facto | hopefully they will safe some live viral samples of those strains for testing vaccines against | 21:35 |
| genera | the comments there point to another .. topic. bats living near minks. | 21:35 |
| de-facto | bats are known as natural reservoir of CoVs and when in same host they might recombine so that potentially may make it even more dangerous to have such mink farms | 21:36 |
| LjL | i think it's easy to agree at this point, for us here at least, that the mink farming should go | 21:39 |
| LjL | but there are other countries that probably think differently, and even if not, this mutation is in humans now | 21:39 |
| LjL | i don't think it can be contained if it's really in 5% of the people in those areas | 21:40 |
| LjL | Denmark hasn't shown the containment efficacy of China or anything close to it so far | 21:40 |
| de-facto | well it may be possible to contain it depending on how local it still is | 21:43 |
| de-facto | but it would require the maximum aggressive containment possible | 21:43 |
| Brainstorm | New from https://covid19.specops.network : Hyperlink Denmark news to Derek Lowe article about it: which, if nothing else, contains a number of the relevant links to the news (including ones in Danish) → https://is.gd/OEDWCm | 21:44 |
| de-facto | https://www.dr.dk/nyheder/indland/regeringen-lukker-nordjylland-ned-borgere-boer-ikke-forlade-egen-kommune | 21:44 |
| de-facto | they leave schools open, sigh | 21:47 |
| metreo | what is the reason for that? | 21:47 |
| metreo | I still don't know what they are thinking | 21:47 |
| metreo | all I can think is parents need the childcare to do their jobs | 21:48 |
| de-facto | yes probably something like that | 21:50 |
| de-facto | its a mistake in my opinion | 21:50 |
| de-facto | btw that link contains a map with infected mink farms, its not only north jutland. yet i am not sure where they found the mutant variant probably only in north jutland | 21:51 |
| de-facto | but other mutations could happen in other infected mink farms aswell, so in my opinion mink farming should be completely banned worldwide | 21:52 |
| Brainstorm | New from Medical Xpress: Telecommuting shields workers from COVID-19, says report: (HealthDay)—Working from home during the pandemic significantly reduces your risk of catching COVID-19, U.S. health officials say. → https://is.gd/b4wWXS | 21:53 |
| Brainstorm | New from PLOS ONE: Immunoproteomic analysis of Trichinella spiralis and Trichinella britovi excretory-secretory muscle larvae proteins recognized by sera from humans infected with Trichinella: by Sylwia Grzelak, Anna Stachyra, Jerzy Stefaniak, Karolina Mrówka, Bożena Moskwa, Justyna Bień-Kalinowska The present study compares the immunogenic patterns [... want %more?] → https://is.gd/V64v39 | 22:02 |
| LjL | de-facto: you convince China to ban it | 22:25 |
| de-facto | Well how about if China does not ban mink farming every trade partner still trading with China would not be considered a possible trade partner for an alliance of countries against mink farming ? | 22:27 |
| dTal | China's too big | 22:32 |
| dTal | I think in practical terms China can do what they bloody well like | 22:32 |
| de-facto | China is an export industry, i bet they care about their markets | 22:33 |
| LjL | An export industry that exports things that are essential to use and that basically only they produce by now | 22:34 |
| LjL | That's a bit of an issue | 22:34 |
| de-facto | indeed | 22:36 |
| ghost_rider[m] | China is turning to internal / consumec market. China is already one of the most developed countries in the world, they are just modest for now. | 22:43 |
| ghost_rider[m] | One thing I noticed, not all countries teach the same history. | 22:44 |
| ghost_rider[m] | China is just becoming what it was. | 22:45 |
| ghost_rider[m] | Always was. | 22:45 |
| Brainstorm | Updates for United Kingdom: +22515 cases (now 1.1 million), +378 deaths (now 48120) since 14 hours ago — US: +14814 cases (now 9.9 million), +111 deaths (now 240669) since an hour ago | 22:50 |
| de-facto | %title https://www.upmc.com/media/news/110520-shi-llama-nanobody | 22:57 |
| Brainstorm | de-facto: From www.upmc.com: Llama Nanobodies Could be a Powerful Weapon Against COVID-19 | 22:57 |
| de-facto | %title https://science.sciencemag.org/content/early/2020/11/04/science.abe4747 | 22:57 |
| Brainstorm | de-facto: From science.sciencemag.org: Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2 | Science | 22:57 |
| LjL | de-facto: are we going to have llamas spit at us | 22:58 |
| ghost_rider[m] | LjL: not sure if this days I was asking about above nano things and stuff, is that human made that uber small bots ? | 22:59 |
| de-facto | %title https://science.sciencemag.org/content/early/2020/11/04/science.abe0075 | 22:59 |
| Brainstorm | de-facto: From science.sciencemag.org: De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2 | Science | 22:59 |
| LjL | ghost_rider[m]: you mentioned something like that, but I didn't quite understand | 23:01 |
| ghost_rider[m] | Is not what I was thinking, or I never got it right | 23:01 |
| LjL | de-facto: are these intended as treatment? Prophylaxis? | 23:02 |
| ghost_rider[m] | I was thinking something more mechanical, IBM can manipulate atom by atom and I was thinking they come with "nano robots" that could "kill" the sars-cov... But it seems I was dreaming to much | 23:03 |
| de-facto | well both approaches would block the s-protein | 23:03 |
| de-facto | not sure about how stable those would be for longterm prophylaxis | 23:03 |
| LjL | de-facto: I guess they would still allow some virus to replicate since they don't block the receptors | 23:04 |
| LjL | Just much less quickly | 23:04 |
| de-facto | well if the s-protein is blocked by sticky molecules it cant dock to cells with them anymore | 23:04 |
| de-facto | its the RBD of a SARS-CoV-2 virion, so unless it uses some other docking mechanism it could not dock to its main entry receptor ACE2 to enter cells | 23:06 |
| LjL | ghost_rider[m]: nanobodies and nanobots are very different things, if you're talking about that. Nanobodies aren't robots, they are biologic and similar to antibodies but smaller | 23:06 |
| LjL | Well not smaller as in shrunk down, they kiss some parts that antibodies have | 23:06 |
| de-facto | yeah nanobodies essentially are very similar to only the sticky part of antibodies | 23:06 |
| LjL | de-facto: well what I'm saying is that most virions will dock to the decoy, but presumably by random chance some will still dock to the real ACE2 receptors instead...? | 23:07 |
| de-facto | yeah those would compete with each others i guess | 23:08 |
| de-facto | but small molecules floating around may have a higher probability to dock than a full cell | 23:08 |
| Haley[m] | think it is quite accurate | 23:08 |
| de-facto | lol | 23:09 |
| de-facto | but its true attitude is a major factor in containment | 23:10 |
| LjL | I usually delete memes and similar... I'll let it stay because I don't feel like being the ultimate party pooper today, but next time Haley[m] please just post the text without the image... I find it's ugly on Matrix when text is interspersed with things like that | 23:15 |
| Brainstorm | Updates for US: +4403 cases (now 9.9 million), +37 deaths (now 240706) since 33 minutes ago | 23:20 |
| LjL | de-facto, have you seen how many deaths we had today? i'm not sure yesterday's 350 was a fluke... | 23:20 |
| de-facto | nope havent seen, but i guess their daily average follows an exponential similar to their cause (infections) a few weeks ago | 23:35 |
| de-facto | on average around ~270 fatalities for Italy currently? | 23:36 |
| de-facto | like latest average on the exponential | 23:36 |
| de-facto | but yeah two times ~350 spikes on top of that | 23:37 |
| de-facto | hmm weird the average almost looks like linear from eyeballing it | 23:38 |
| Jigsy | https://www.theguardian.com/education/2020/nov/05/security-fence-manchester-university-student-flats | 23:39 |
| Jigsy | surprised_pikachu.jpg | 23:39 |
| Jigsy | %title | 23:39 |
| Brainstorm | Jigsy: From www.theguardian.com: Security fence erected around Manchester students' block of flats | Education | The Guardian | 23:39 |
| de-facto | more and more measures show that management seems to be somewhat helpless about what measures make sense and which just cause opposition | 23:44 |
| de-facto | though the rationale makes somewhat sense i guess "security staff will ensure that only students who live in that accommodation can access safely and help avoid the mixing of households" | 23:46 |
| Jigsy | https://i.imgur.com/5GtrTpj.png | 23:48 |
| de-facto | btw any estimates on incidence amoung students relative to average population? | 23:48 |
| Brainstorm | Updates for US: +8898 cases (now 9.9 million), +129 deaths (now 240835) since 33 minutes ago | 23:51 |
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