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For WHOm the Bell Tolls - Covid-19 #11

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1 hour ago, Ran said:

Kal has clarified his point, but what he said was literally that we didn't know if antibodies provide immunity, and that's what I was responding to.

Yes, but then there needs to be study into why people are asymptomatic and appear to fight off the virus without their immune system adapting itself to deal with it. Here is an article from yesterday that has some interesting things to say. Could it just that a lot of people (mostly younger) have great innate immunity? Could be! But if so, then that reduces R, and herd immunity is actually probably closer, not further away.

 

One reason for the large number of asymptotic people is tha the virus, having recently crossed over into humans, is not that good at infect g humans yet. As it adapts and evolves it will be more effective and will be more widespread. We can only hope that it does not evolve to be more lethal. 

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Posted (edited)

Speaking of antibodies, Karonlinska University Hospital in Stockholm released results  (Swedish, Google Translate it) that showed at least 11% of blood donors (test with 99.5% specificity and 70-80% sensitivity, which actually means the actual number could be as high as 15-16%) are positive for antibodies as of last week; a couple of weeks earlier, the test showed about 4%. 

Notably, blood donors are generally ruled out from donating if they indicate any recent illness, so if anything a true random sampling in Stockholm could show higher numbers.  Apparently they're estimating that 20-30% have had it in Stockholm as of today, based on this.

ETA: Also, while "have you had recent illness" queries for blood donors is self-reporting, the fact that a bunch of people said "no" while having antibodies for this virus does imply that they were asymptomatic or so mild they didn't really notice.

Also, a point I forgot to note, it takes a couple of weeks from infection for these antibodies to be detected, so this is more of a snapshot of where Stockholm was  two three weeks ago. Thinking 30%+ is indeed quite possible, and would explain the plateau we've had in the region for the last two weeks without any substantial changes in policy if it's helping to push R further down below 1.

Edited by Ran

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Posted (edited)
3 hours ago, Kalbear said:

Not left to the actual reader: how many people actually have pre-existing conditions. Remember, one of the pre-existing conditions is being overweight, which over 60% of the US population is. Fuck those guys, I guess. 

I do love how it's just glossed over, like oh well, if you have any pre-existing condition time to die. 

You speak from the bottom of my heart. The virus only affects elderly people and those with pre-existing conditions. Well, we have an aging population and lots of pre-existing conditions. 18% of the population is over 65, 25% smokes, 20% is obese, 38% is a regular heavy drinker. Barely more than half of the population considers themselves healthy, chronic stress and therefore hypertension, cardiovascular diseases, cancer rates are relatively high, many people live with diabetes. I don’t have numbers but to be honest, I would be surprised if most people above 45 didn’t have any pre-existing health conditions. Old and rusty healthcare system, sixth worst mortality rate in EU, life expectancy 5 years below average.   If I take all of this into account we aren’t talking about 15 or even 20% and sickly 70+ year olds. We are talking about, what.. 50% of people? One of the reason why the “our elderly are at threat” narrative makes me sad and angry. Many more are at threat and ALL should take extra special care. 

Edited by RhaenysBee

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1 hour ago, Ran said:

Kal has clarified his point, but what he said was literally that we didn't know if antibodies provide immunity, and that's what I was responding to.

Yes, but then there needs to be study into why people are asymptomatic and appear to fight off the virus without their immune system adapting itself to deal with it. Here is an article from yesterday that has some interesting things to say. Could it just that a lot of people (mostly younger) have great innate immunity? Could be! But if so, then that reduces R, and herd immunity is actually probably closer, not further away.

 

There's certainly a significant degree of undercounting, but I remain skeptical of the claims we are starting to see, based on early antibody studies, that there are massive numbers of asymptomatic people that we are undercounting.  I don't think any country is close to herd immunity yet. 

 

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Following Mauritania a couple of days ago we now have a second country claiming to have got to zero active cases, namely Burundi. The Worldometers site says they've done a whole 80 tests, which might explain why they haven't reported many cases.

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I just saw this: 

https://www.medrxiv.org/content/10.1101/2020.04.14.20062463v1?fbclid=IwAR3yTQqS2GInnVVU_iikRQjrucsi1KYwWpV1UEEhiLTTXLvGnLfRc3tUy_g

The unadjusted prevalence of antibodies to SARS-CoV-2 in Santa Clara County was 1.5% (exact binomial 95CI 1.11-1.97%), and the population-weighted prevalence was 2.81% (95CI 2.24-3.37%). Under the three scenarios for test performance characteristics, the population prevalence of COVID-19 in Santa Clara ranged from 2.49% (95CI 1.80-3.17%) to 4.16% (2.58-5.70%). These prevalence estimates represent a range between 48,000 and 81,000 people infected in Santa Clara County by early April, 50-85-fold more than the number of confirmed cases. 

 

not peered reviewed.

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3 minutes ago, Filippa Eilhart said:

I just saw this: 

https://www.medrxiv.org/content/10.1101/2020.04.14.20062463v1?fbclid=IwAR3yTQqS2GInnVVU_iikRQjrucsi1KYwWpV1UEEhiLTTXLvGnLfRc3tUy_g

The unadjusted prevalence of antibodies to SARS-CoV-2 in Santa Clara County was 1.5% (exact binomial 95CI 1.11-1.97%), and the population-weighted prevalence was 2.81% (95CI 2.24-3.37%). Under the three scenarios for test performance characteristics, the population prevalence of COVID-19 in Santa Clara ranged from 2.49% (95CI 1.80-3.17%) to 4.16% (2.58-5.70%). These prevalence estimates represent a range between 48,000 and 81,000 people infected in Santa Clara County by early April, 50-85-fold more than the number of confirmed cases. 

not peered reviewed.

Yup, the comments are quite interesting with doctors and scientists pointing out that there are flaws in their methodology. However, there does seem to be broader agreement that an argument for 1% of the population being infected can be more strongly made, which would still be significantly more than the number of confirmed cases.

Given the lack of testing in the US, they'd also then have to factor out those people who were at home with symptoms but never went to hospital or called a health care professional, so were never entered into the statistics.

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6 minutes ago, Ran said:

Speaking of antibodies, Karonlinska University Hospital in Stockholm released results  (Swedish, Google Translate it) that showed at least 11% of blood donors (test with 99.5% specificity and 70-80% sensitivity, which actually means the actual number could be as high as 15-16%) are positive for antibodies as of last week; a couple of weeks earlier, the test showed about 4%.

Notably, blood donors are generally ruled out from donating if they indicate any recent illness, so if anything a true random sampling in Stockholm could show higher numbers.  Apparently they're estimating that 20-30% have had it in Stockholm as of today, based on this.

ETA: Also, while "have you had recent illness" queries for blood donors is self-reporting, the fact that a bunch of people said "no" while having antibodies for this virus does imply that they were asymptomatic or so mild they didn't really notice.

If true, Stockholm should be at herd immunity levels within about a month, and there should be a drastic drop in the number of new cases over the following weeks.  

NYC had similar results, with about 15% of mothers delivering babies at the hospital testing positive.  

It would be great news if these numbers were true and representative of the at large population, but I would like to see random testing of the general population with a well validated antibody assay (preferably with more than one test) before I'm convinced.

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Get ready for strong Spikes of corona virus in red states thanks to daft shit republicans. 

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1 hour ago, Ran said:

Speaking of antibodies, Karonlinska University Hospital in Stockholm released results  (Swedish, Google Translate it) that showed at least 11% of blood donors (test with 99.5% specificity and 70-80% sensitivity, which actually means the actual number could be as high as 15-16%) are positive for antibodies as of last week; a couple of weeks earlier, the test showed about 4%. 

Notably, blood donors are generally ruled out from donating if they indicate any recent illness, so if anything a true random sampling in Stockholm could show higher numbers.  Apparently they're estimating that 20-30% have had it in Stockholm as of today, based on this.

ETA: Also, while "have you had recent illness" queries for blood donors is self-reporting, the fact that a bunch of people said "no" while having antibodies for this virus does imply that they were asymptomatic or so mild they didn't really notice.

Also, a point I forgot to note, it takes a couple of weeks from infection for these antibodies to be detected, so this is more of a snapshot of where Stockholm was  two three weeks ago. Thinking 30%+ is indeed quite possible, and would explain the plateau we've had in the region for the last two weeks without any substantial changes in policy if it's helping to push R further down below 1.

According to Worldometers there have been ~1600 deaths in Sweden. You mentioned previously Stockholm is by far the most infected city in Sweden. My rule of thumb that the true infection rate is more likely to be between 100 and 200x the official death rate (CFR between 0.5% and 1%) than the reported official confirmed infection rate means infection in Sweden is somewhere around 160,000 and 320,000. With Stockholm population being 1 million-ish that 20%-30% estimate tracks. Though even if 11% is an accurate estimate of the total current and past infections it's still closer to 100x CFR than is the current official confirmed cases.

In local news, our govt has decided to extend lvl4 lock down until the 11:59PM next Monday. Not coincidentally next Monday is ANZAC day holiday (ANZAC - a WW I commemoration for Aus and NZ -  day is 25 April and when it falls on a weekend the holiday is Monday-ised). So clearly the govt didn't want to drop to lvl3 and give people a sense that they can congregate in larger groups to commemorate this day, which I'm fine with. Also interestingly an online poll conducted on a news website asking if people felt the country was ready to drop out of lvl 4 had 61% of people saying no we are not ready to drop out of lvl 4.

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41 minutes ago, Werthead said:

Yup, the comments are quite interesting with doctors and scientists pointing out that there are flaws in their methodology. However, there does seem to be broader agreement that an argument for 1% of the population being infected can be more strongly made, which would still be significantly more than the number of confirmed cases.

Given the lack of testing in the US, they'd also then have to factor out those people who were at home with symptoms but never went to hospital or called a health care professional, so were never entered into the statistics.

Yeah, I saw this study when it came out, and I decided against mentioning it here because the study was so flawed.  I don't think you can say anything with confidence based on this study.  The selection bias from recruiting subjects through Facebook ads instead of randomly selecting subjects is a major problem, as well as the limited testing of the specificity of the assay.  If the false positive rate is actually just one percent lower than claimed (98.5% v. 99.5%), false positives could account for the bulk of the positive cases they found.

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Posted (edited)
10 minutes ago, The Anti-Targ said:

According to Worldometers there have been ~1600 deaths in Sweden. You mentioned previously Stockholm is by far the most infected city in Sweden. My rule of thumb that the true infection rate is more likely to be between 100 and 200x the official death rate (CFR between 0.5% and 1%) than the reported official confirmed infection rate means infection in Sweden is somewhere around 160,000 and 320,000. With Stockholm population being 1 million-ish that 20%-30% estimate tracks. Though even if 11% is an accurate estimate of the total current and past infections it's still closer to 100x CFR than is the current official confirmed cases.

Oh, yes, CFR is terribly high here because we only test serious cases of the illness as far as reported case figures. 

I should add that a separate test of 2000 health care workers in Stockholm, reported on yesterday, showed about a third having antibodies, but I don't know the specificity or sensitivity of the test used. They are of course much likelier to have been exposed than the general population, so not too many conclusions can be drawn, other than possible supporting evidence of a low IFR.

 

Quote

In local news, our govt has decided to extend lvl4 lock down until the 11:59PM next Monday. Not coincidentally next Monday is ANZAC day holiday (ANZAC - a WW I commemoration for Aus and NZ -  day is 25 April and when it falls on a weekend the holiday is Monday-ised).

Makes sense. Norway and Denmark held off on school reopenings until after Easter, as well.

Edited by Ran

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3 minutes ago, Ran said:

Oh, yes, CFR is terribly high here because we only test serious cases of the illness as far as reported case figures. 

I should add that a separate test of 2000 health care workers in Stockholm, reported on yesterday, showed about a third having antibodies, but I don't know the specificity or sensitivity of the test used. They are of course much likelier to have been exposed than the general population, so not too many conclusions can be drawn, other than possible supporting evidence of a low IFR.

 

Makes sense. Norway and Denmark held off on school reopenings until after Easter, as well.

Only testing serious cases is consistent with a policy of not really wanting to control or limit spread to any significant extent and intending for herd immunity by infection rather than waiting for vaccination. Is it still Sweden's formal policy to let herd immunity develop by trying to have moderate community spread?

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Just now, The Anti-Targ said:

Only testing serious cases is consistent with a policy of not really wanting to control or limit spread to any significant extent and intending for herd immunity by infection rather than waiting for vaccination. Is it still Sweden's formal policy to let herd immunity develop by trying to have moderate community spread?

The stated position of FHM is that herd immunity is and never has been a goal, but it is a by product of the strategy of simply focusing at keeping the hospitals from being overwhelmed. The reason testing was so limited was simply lack of resources and capacity at the time, and wanting to focus on putting effort to building out ICU, acquiring more PPE, etc. They're working to ramp up to 100,000 a week, and are now handling over 20,000 tests a week.

All that said, I guess some of this may just be a semantic distinction. Their view, as expressed by Tegnell and Giesecke, is that "herd immunity" is the ultimate end state of this for everyone, whether it's achieved by vaccination or by natural exposure through the population. It seems pretty clear that if herd immunity's downward pressure on R is why things are plateauing, and the IFR is as low as .1 to .3 as some estimate, that there's not going to be a change of policy any time soon. In fact, Anders Tegnell (chief epidemiologist and spokesperson for FHM) said that today at the daily press conference, that the longer things go as they are, the less and less likely we're going to end up introducing more stringent measures.

BTW, here's something I wonder about:

Who holds the daily press conferences in everyone's respective countries? I know that in the US governors and the White House (and in some cases mayors) are holding these press conferences, with some experts sometimes on hand and sometimes not. In Sweden, it's representatives of the three or four agencies primarily involved in dealing with this, with nary a politician in sight (the ministers tend to do a press conference once a week, usually to announce some new measure -- the latest was reiterating that Sweden was going to extend the ban on most travellers from outside the EEA  that the EU had decided on).

 

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So interesting modeling in a Science paper:

https://science.sciencemag.org/content/early/2020/04/14/science.abb5793

Take aways: If the sars-cov-2 gives a similar protective immunity to other related corona viruses which cause the common cold (median protective antibody duration ~45 weeks), we're looking at annual outbreaks and spikes in mortality (much like the flu). So would be back and killing again early next year assuming a large portion of the population get it now.

If immunity is more like SARS (protective immunity lasts a couple years) the outbreaks shift to a 2 yearly cycle. Hopefully a vaccine would be ready by then.

If its permenent immunity you get a single large peak then it's done.

 

So if we are getting a large portion of extremely mild / asymptomatic cases which simply aren't generating a decent immune response, it looks likely we enter a situation where it becomes a yearly cycle.

 

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Posted (edited)

I must say a good indicator whether a country is able to just quarantine the vulnerable population is the experience I made today because it is just... too strange.

So two weeks ago I already mentioned how my principal asked everybody who belongs to the risk group to turn in certificates that they are so that they wouldn't be counted on with their presence at school. Note that already here there is no mention of people in the risk group belonging to your household that you could easily infect and kill, screw those people.

Today I phoned my lung specialist to ask her whether she would judge my Asthma in its current lack of severity as a risk. First thing to note is that it took me hours to get through, it appeared to me that there had been a constant onslaught the entire morning. I guess I should have seen that coming, what with the end of the Easter holidays.

In any case, the aid taking up the receiver was frustratingly pissed and hostile when I asked her whether it is possible for the doctor to make a judgement of whether I fall into the risk group. She said that I can pay 5 Euro to get a certificate that I have Asthma, but the doctor won't make any recommendation to either choice, I have to decide myself whether I'm in the risk group by looking up what the Robert Koch Institute says.

That... that certainly wasn't helpful at all. -.-

My mother's take on this is that the doctor wants to avoid any kind of responsibility by refusing to give a clear answer... which leaves me horrified at the prospect of other people with more severe preconditions not getting a clear reply either whether they could risk go to work or not.

Edited by Toth

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5 minutes ago, Toth said:

I must say a good indicator whether a country is able to just quarantine the vulnerable population is the experience I made today because it is just... too strange.

So two weeks ago I already mentioned how my principal asked everybody who belongs to the risk group to turn in certificates that they are so that they wouldn't be counted on with their presence at school. Note that already here there is no mention of people in the risk group belonging to your household that you could easily infect and kill, screw those people.

Today I phoned my lung specialist to ask her whether she would judge my Asthma in its current lack of severity as a risk. First thing to note is that it took me hours to get through, it appeared to me that there had been a constant onslaught the entire morning. I guess I should have seen that coming, what with the end of the Easter holidays.

In any case, the aid taking up the receiver was frustratingly pissed and hostile when I asked her whether it is possible for the doctor to make a judgement of whether I fall into the risk group. She said that I can pay 5 Euro to get a certificate that I have Asthma, but the doctor won't make any recommendation to either choice, I have to decide myself whether I'm in the risk group by looking up what the Robert Koch Institute says.

That... that certainly wasn't helpful at all. -.-

My mother's take on this is that the doctor wants to avoid any kind of responsibility by refusing to give a clear answer... which leaves me horrified at the prospect of other people with more severe preconditions not getting a clear reply either whether they could risk go to work or not.

Toth, if it gives you any comfort, doctors are very surprised to see how few people with asthma end up in hospital. The four big underlying factors appear to be diabetes, obesity, hyper tension and of course I can’t remember the 4th, I think it’s heart disease, but I will look it up once I get home. It is not asthma.

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Apparently Los Angeles county also did a study using the same antibody test used in the Santa Clara study.

 

Quote

Hundreds of thousands of Los Angeles County residents may have been infected with the coronavirus by early April, far outpacing the number of officially confirmed cases, according to a report released Monday.

The initial results from the first large-scale study tracking the spread of the coronavirus in the county found that 2.8% to 5.6% of adults have antibodies to the virus in their blood, an indication of past exposure.

That translates to roughly 221,000 to 442,000 adults who have recovered from an infection, according to the researchers conducting the study, even though the county had reported fewer than 8,000 cases at that time.

...

The early results from L.A. County come three days after Stanford researchers reported that the coronavirus appears to have circulated much more widely in Santa Clara County than previously thought.

The Stanford team estimated that 2.5% to 4.2% of Santa Clara County residents had antibodies to the coronavirus in their blood by early April.

...

Both counties used rapid antibody tests supplied from Premier Biotech, a Minneapolis-based company. The test has not yet been approved by the FDA, although the federal government does allow for such tests to be used for public health surveillance.

Someone needs to do a thorough validation of Premier Biotech's antibody test.  Are these results real?  Or just the result of false positives?  Can't tell yet.  Unfortunately, there are now around a hundred different antibody tests on the market, some of which are crap.  That said, even a relatively good test with 97-98% specificity would have trouble detecting low levels of infection.

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56 minutes ago, Bonnot OG said:

Get ready for strong Spikes of corona virus in red states thanks to daft shit republicans. 

Hey this is war and a good general expects to lose his troops, a lot of them, good troops all who loyally no matter what ride into that valley of death, all for the sake of their leader.

Besides, if they die, it's the fault of New York.

Their dearest infants can die with pink froth blooming out of their chests, but still they will follow their leader and blame someone else.

 

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Posted (edited)
3 minutes ago, Fragile Bird said:

Toth, if it gives you any comfort, doctors are very surprised to see how few people with asthma end up in hospital. The four big underlying factors appear to be diabetes, obesity, hyper tension and of course I can’t remember the 4th, I think it’s heart disease, but I will look it up once I get home. It is not asthma.

Well, thanks, but I had already looked all of that up two weeks ago as well. It's stated that only those Asthmatics are in the risk group who have it so severe they have to take steroid pills instead of sprays. I still would have preferred an attempt to confirm or deny stuff I read on the internet by a professional.

Edited by Toth

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