Covid-19: The T Cell Story • Hacker News Board

Re: Covid-19: The T Cell Story

#141

Post by acqq » Mon, Jun 22, 2020, 11:28 AM UTC

mlyle wrote: post #140

acqq wrote: post #139

Earlier quoted context omitted.

> if 25% infected yields expected Rt of under 1 (the threshold for herd immunity, and I think this is likely) That's what I'm missing, what are your sources to think that? I somehow haven't seen that in the links you gave.

From the very first link: > The herd immunity threshold (HIT) defines the percentage of the population that needs to be immune to reverse epidemic 15 growth and prevent future waves. Figure 3 shows the expected downward trends in the HIT for SARS-CoV-2 as the coefficients of variation of the gamma distributed susceptibility or exposure are increased between 0 and 4 (to assess robustness to changing the type of distri…

I don't think that that inferred CV from the quote says anything about the "herd immunity" in the sense which most of people would like it to be. If you have an outbreak where people start to suffer, people react, they stop behaving in a way they would do without he outbreak running. The "curve fitting" you quote, the way I see it, therefore doesn't say anything about the inherent resistance of human body or something like that, but about when different communities resort to locking themselves down or taking some other drastic action as the response to the "rising wave", even without any official ban of some activity.

Just reading, in one meat processing plant in Germany, from 3000 workers tested they have 1000 PCR positives (Rheda-Wiedenbrück meat processing plant, 1,029 cases so far (1)). It's already 30% of the tested and almost sure an "infection in one wave" (after some weeks a lot of people are PCR negative again). If it stays at 1000 (they will maybe test more: "On Friday morning, addresses of around 30% of the workers were still missing") it wouldn't mean it would have stayed at 1000 hadn't they closed the whole plant.

1) https://www.dw.com/en/coronavirus-german-slaughterhouse-outb...

Re: Covid-19: The T Cell Story

#142

Post by mlyle » Mon, Jun 22, 2020, 7:06 PM UTC

acqq wrote: post #141

mlyle wrote: post #140

Earlier quoted context omitted.

From the very first link: > The herd immunity threshold (HIT) defines the percentage of the population that needs to be immune to reverse epidemic 15 growth and prevent future waves. Figure 3 shows the expected downward trends in the HIT for SARS-CoV-2 as the coefficients of variation of the gamma distributed susceptibility or exposure are increased between 0 and 4 (to assess robustness to changing the type of distri…

I don't think that that inferred CV from the quote says anything about the "herd immunity" in the sense which most of people would like it to be. If you have an outbreak where people start to suffer, people react, they stop behaving in a way they would do without he outbreak running. The "curve fitting" you quote, the way I see it, therefore doesn't say anything about the inherent resistance of human body or somethin…

The whole point of the paper is that coefficient of variation affects the herd immunity threshold. And it obviously does, if you read the paper. The problem is, we don't know for sure what the CV is-- we can only guess based on history and observations.

> Just reading, in one meat processing plant in Germany, from 3000 workers tested they have 1000 PCR positives

This makes me think you don't understand any of the argument. A) CV includes things like contact network structure. OK, meat plants are an unfavorable contact network structure: this proves the point! If we have an observed R0 of 2.5 or 3.0, it includes (disproportionately) people who spend time in places with unfavorable conditions and contact others with unfavorable network structure. If there's a CV, what that means is that in some subgroups of contact structure and individual susceptibility (e.g. meat plants) we have an R0 much higher than 3, and in the bulk of the population we have an R0 much lower than 3.

B) Even ignoring this, there's nothing to say you won't overshoot a herd immunity threshold. The herd immunity threshold is just the threshold where each infection results in less than 1 new infection, on average: it isn't a place where infection magically stops, but instead where the number infected can be expected to naturally decrease. Obviously it's advantageous to have the infected count as low as possible when this happens, because it's only a slow decay from that point.

Re: Covid-19: The T Cell Story

#143

Post by WildParser » Tue, Jun 23, 2020, 8:00 AM UTC

mlyle wrote: post #142

acqq wrote: post #141

Earlier quoted context omitted.

I don't think that that inferred CV from the quote says anything about the "herd immunity" in the sense which most of people would like it to be. If you have an outbreak where people start to suffer, people react, they stop behaving in a way they would do without he outbreak running. The "curve fitting" you quote, the way I see it, therefore doesn't say anything about the inherent resistance of human body or somethin…

The whole point of the paper is that coefficient of variation affects the herd immunity threshold. And it obviously does, if you read the paper. The problem is, we don't know for sure what the CV is-- we can only guess based on history and observations. > Just reading, in one meat processing plant in Germany, from 3000 workers tested they have 1000 PCR positives This makes me think you don't understand any of the arg…

Have you noticed that the curves are following Gompertz-Model?

https://www.facebook.com/photo.php?fbid=10157283645163015

https://www.youtube.com/watch?v=8aHrx68IT7o

There is no constant CV>1 - it all depends on the situation.

Re: Covid-19: The T Cell Story

#144

Post by acqq » Tue, Jun 23, 2020, 10:45 AM UTC

WildParser wrote: post #143

mlyle wrote: post #142

Earlier quoted context omitted.

The whole point of the paper is that coefficient of variation affects the herd immunity threshold. And it obviously does, if you read the paper. The problem is, we don't know for sure what the CV is-- we can only guess based on history and observations. > Just reading, in one meat processing plant in Germany, from 3000 workers tested they have 1000 PCR positives This makes me think you don't understand any of the arg…

Have you noticed that the curves are following Gompertz-Model? https://www.facebook.com/photo.php?fbid=10157283645163015 https://www.youtube.com/watch?v=8aHrx68IT7o There is no constant CV>1 - it all depends on the situation.

I simply can't imagine that anybody who even basically understands the related topics could believe the facebook post you posted (I'm referring to the graph). If I'm wrong and they do exist I'm very, very sad, and even scared imagining having to deal with such people.

Also update from yesterday: in Germany's plant today's score is "more than 1500"

https://www.dailymail.co.uk/news/article-8450221/1-500-worke...

Re: Covid-19: The T Cell Story

#145

Post by WildParser » Tue, Jun 23, 2020, 12:43 PM UTC

acqq wrote: post #144

WildParser wrote: post #143

Earlier quoted context omitted.

Have you noticed that the curves are following Gompertz-Model? https://www.facebook.com/photo.php?fbid=10157283645163015 https://www.youtube.com/watch?v=8aHrx68IT7o There is no constant CV>1 - it all depends on the situation.

I simply can't imagine that anybody who even basically understands the related topics could believe the facebook post you posted (I'm referring to the graph). If I'm wrong and they do exist I'm very, very sad, and even scared imagining having to deal with such people. Also update from yesterday: in Germany's plant today's score is "more than 1500" https://www.dailymail.co.uk/news/article-8450221/1-500-worke...

Feel free to take a look at the official data yourself.

https://www.ecdc.europa.eu/en/publications-data/download-tod...

You need nothing but Excel/LibreOffice and a few simple formulas to get this picture.

Germany has a heavy 7 day rhythm, because they're doing their reporting in a very strange way. Using 7 day averages helps a lot to get rid of the reporting-noise.

You need: Daily death (averages over 7 days) Total death (Sum) (averages over 7 days)

daily/total

Just use SUM() and /

Re: Covid-19: The T Cell Story

#146

Post by acqq » Thu, Jun 25, 2020, 3:24 PM UTC

WildParser wrote: post #145

acqq wrote: post #144

Earlier quoted context omitted.

I simply can't imagine that anybody who even basically understands the related topics could believe the facebook post you posted (I'm referring to the graph). If I'm wrong and they do exist I'm very, very sad, and even scared imagining having to deal with such people. Also update from yesterday: in Germany's plant today's score is "more than 1500" https://www.dailymail.co.uk/news/article-8450221/1-500-worke...

Feel free to take a look at the official data yourself. https://www.ecdc.europa.eu/en/publications-data/download-tod... You need nothing but Excel/LibreOffice and a few simple formulas to get this picture. Germany has a heavy 7 day rhythm, because they're doing their reporting in a very strange way. Using 7 day averages helps a lot to get rid of the reporting-noise. You need: Daily death (averages over 7 days) Total…

I don't doubt that one can produce the picture. The problem is that these drawn lines over the real data don't mean anything.

https://en.wikipedia.org/wiki/Rorschach_test

Re: Covid-19: The T Cell Story

#147

Post by WildParser » Fri, Jun 26, 2020, 6:23 AM UTC

acqq wrote: post #146

WildParser wrote: post #145

Earlier quoted context omitted.

Feel free to take a look at the official data yourself. https://www.ecdc.europa.eu/en/publications-data/download-tod... You need nothing but Excel/LibreOffice and a few simple formulas to get this picture. Germany has a heavy 7 day rhythm, because they're doing their reporting in a very strange way. Using 7 day averages helps a lot to get rid of the reporting-noise. You need: Daily death (averages over 7 days) Total…

I don't doubt that one can produce the picture. The problem is that these drawn lines over the real data don't mean anything. https://en.wikipedia.org/wiki/Rorschach_test

R² > 0,995

If you subtract the trend of the first outbreak from the main trend it's R²>0,995 from the beginning down the point where old people started to wear masks and go to church. Here things get worse - as expected.

New trend is still collapsing exponentially - numbers now are so low that the curve has reporting issues (national deathcount on Sunday was -1).

Re: Covid-19: The T Cell Story

#148

Post by acqq » Sun, Jun 28, 2020, 7:44 PM UTC

WildParser wrote: post #147

acqq wrote: post #146

Earlier quoted context omitted.

I don't doubt that one can produce the picture. The problem is that these drawn lines over the real data don't mean anything. https://en.wikipedia.org/wiki/Rorschach_test

R² > 0,995 If you subtract the trend of the first outbreak from the main trend it's R²>0,995 from the beginning down the point where old people started to wear masks and go to church. Here things get worse - as expected. New trend is still collapsing exponentially - numbers now are so low that the curve has reporting issues (national deathcount on Sunday was -1).

The Saturday and Sunday are the "weird" death data in most of the countries, and not because people die less on these days, but because not all those that report the deaths do that on these days: even in hospitals in the middle of epidemics some people in administration simply don't work on weekends.

So what I see for Germany is the number of detected cases increased the last week, therefore I expect in 2-4 weeks the increase of deaths in Germany, that's how much the delay is between more cases and more deaths.

I don't see anything else that is a realistic "signal" about anything.

Re: Covid-19: The T Cell Story

#149

Post by WildParser » Mon, Jun 29, 2020, 7:45 AM UTC

acqq wrote: post #148

WildParser wrote: post #147

Earlier quoted context omitted.

R² > 0,995 If you subtract the trend of the first outbreak from the main trend it's R²>0,995 from the beginning down the point where old people started to wear masks and go to church. Here things get worse - as expected. New trend is still collapsing exponentially - numbers now are so low that the curve has reporting issues (national deathcount on Sunday was -1).

The Saturday and Sunday are the "weird" death data in most of the countries, and not because people die less on these days, but because not all those that report the deaths do that on these days: even in hospitals in the middle of epidemics some people in administration simply don't work on weekends. So what I see for Germany is the number of detected cases increased the last week, therefore I expect in 2-4 weeks the…

Currently in Germany it maybe works the other way around.

Last month around me it worked like this: Big spikes in case were caused by a test-campaign around somebody who died (or was ill). So a trend in case might in fact be an old trend of death - and the burst in case might in fact be asymptomatic or mild cases not leading to any death.

When you try to fit the spikes of death and case things are strange. In Germany maybe case and death have completely detached from each other.

Currently there are a lot of corrections going on. Bavaria had a deathcount of -3 on Saturday. Maybe they are piling up to report a big spike soon, or they stopped someone from reporting nonsense? We will see...