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Covid-19: The T Cell Story

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Re: Covid-19: The T Cell Story

#51

Post by dehrmann »

jlmorton wrote: post #47
redis_mlc wrote: post #45

Earlier quoted context omitted.

> In Massachusetts (where we have been hit pretty hard by C19) we're trending downwards in a significant way and have been for a few weeks now. Same in California - corona is a health care non-issue here, aside from our governor running for President soon, so it's a political issue. So we'll be the last to leave lockdown, and it's looking like Jan. 2022 now. By non-issue, I mean hospitalizations and deaths according…

I'm not sure if you're talking about daily deaths, or in total, but California has had 5,286 deaths as of today, not 58. We also had 81 deaths today specifically. In a perfect world, the point of a lockdown is to arrest the spread of a disease entirely. Unfortunately, we're well past that point in the US. Having failed at that, the goal is not just to keep health care utilization below capacity, but also to buy time…

They probably meant per day. I think "flat" is a fair characterization of the metric:

https://i.imgur.com/zZ7UGVW.png

Deaths has a few problems. One is that once SARS-CoV-2 finds a nursing home, it's a lot of at-risk people in once place, so it gets hit hard. If deaths is the metric you care about, it's best to put a lot of effort into testing workers at care facilities and putting those facilities strict lockdowns. Once we learned this, we started "gaming" the metric a bit. The other problem is it's a lagging indicator.

Positive tests are problematic because early on, there was a shortage, presumed positive people weren't being tested because it wouldn't change anything, people without symptoms aren't being tested, etc. It's the flakier metric, for sure.

For how many tests are coming back negative, I wish we were doing random testing and random antibody testing. If we're not doing those, we're still being reactive.

Re: Covid-19: The T Cell Story

#52

Post by acqq »

lsllc wrote: post #36
nodamage wrote: post #9

> And wherever we look, infections level off before 10%-20% of the population is infected. This is somewhat mysterious. This is not really true. Bergamo had a 58% infection rate as of last month: https://bergamo.corriere.it/notizie/cronaca/20_maggio_22/ber... Several prisons have seen infection rates in the 70-80% range: https://www.npr.org/sections/coronavirus-live-updates/2020/0... The USS Theodore Roosevelt had an…

In Massachusetts (where we have been hit pretty hard by C19) we're trending downwards in a significant way and have been for a few weeks now. But I see more human activity out and about than ever (at least compared to March/April and mask wearing / social distancing is has been pretty obviously in decline for a number weeks now). The state is now well into it's re-opening phase 2 and even with the recent protests, th…

> Maybe the R0 curve just flattens more quickly than we thought?

I think that's a confusion of R0 with Rt, Rt is what is influencing what we observe and simply not a constant, and additionally not the same in different settings or states:

https://rt.live/

More importantly, for the Rt == 1 (and being constant) the number of cases would be constantly growing linearly. Only for Rt > 1 the growth is exponential.

As long as the Rt is around 1 it is not surprising that we don't see long lasting exponential growth.

But also note that the values calculated there are more an "illustration" of how the past partial data can be fit to some model than a certainty of the present. The model is helpful to allow us to have a possibility to talk about some concept (Rt and the differences in growth), but is not the current truth, especially for the situation where the data isn't complete and there is a delay in obtaining the updates versus what is actually happening at the moment at every place during the ongoing pandemics. Those who aren't in statistics now can be already infected and die in some weeks, or infect others, and we are never sure how much of those there are at the moment, given the constant changes of the behavior and the movements of the people.

Re: Covid-19: The T Cell Story

#53

Post by dehrmann »

xmichael0 wrote: post #37

So... Does this mean that we can "self" vaccinate by going maskless and running around the city and in and out of grocery stores every few days? I am mostly joking here, but I am also serious, the post implies that we can develop immunity by getting minor exposures over a period of time. I read the article twice and probably need it twice more to fully understand it, but please enlighten me.

That's essentially how live-attenuated vaccines work. You'd have the same benefits and drawbacks, but a dosing issue.

Re: Covid-19: The T Cell Story

#54

Post by redis_mlc »

dehrmann wrote: post #51
jlmorton wrote: post #47

Earlier quoted context omitted.

I'm not sure if you're talking about daily deaths, or in total, but California has had 5,286 deaths as of today, not 58. We also had 81 deaths today specifically. In a perfect world, the point of a lockdown is to arrest the spread of a disease entirely. Unfortunately, we're well past that point in the US. Having failed at that, the goal is not just to keep health care utilization below capacity, but also to buy time…

They probably meant per day. I think "flat" is a fair characterization of the metric: https://i.imgur.com/zZ7UGVW.png Deaths has a few problems. One is that once SARS-CoV-2 finds a nursing home, it's a lot of at-risk people in once place, so it gets hit hard. If deaths is the metric you care about, it's best to put a lot of effort into testing workers at care facilities and putting those facilities strict lockdowns.…

58 total deaths for the SF Bay Area in 2020, out of about 4 million people.

The positive rate for 2020 of all tests is 3%, but it really appears that whatever tests they're using are just wrong - California had daily flights from Wuhan.

The one logical conclusion from this thread is that if ships, hospitals and nursing homes have high rates of infection, and California homes don't, turn off your central AC and heating in NY, etc.

Re: Covid-19: The T Cell Story

#55

Post by WildParser »

lsllc wrote: post #36
nodamage wrote: post #9

> And wherever we look, infections level off before 10%-20% of the population is infected. This is somewhat mysterious. This is not really true. Bergamo had a 58% infection rate as of last month: https://bergamo.corriere.it/notizie/cronaca/20_maggio_22/ber... Several prisons have seen infection rates in the 70-80% range: https://www.npr.org/sections/coronavirus-live-updates/2020/0... The USS Theodore Roosevelt had an…

In Massachusetts (where we have been hit pretty hard by C19) we're trending downwards in a significant way and have been for a few weeks now. But I see more human activity out and about than ever (at least compared to March/April and mask wearing / social distancing is has been pretty obviously in decline for a number weeks now). The state is now well into it's re-opening phase 2 and even with the recent protests, th…

Exactly. Things with R0 a) Take the number of deaths per day, divide it by the total number of deaths. f'/f.

b) Take a look at this in a log-chart. Use 7 day averages for f' and f to get a cleaner picture.

You will see that f'/f falls down exponentially since pretty much the beginning.

c) determine the exponent by estimating the derivative ln(f'/f)'.

d) Now use that to calculate the function f.

e) Calculate an enddate when it will fizzle.

Re: Covid-19: The T Cell Story

#56

Post by Judgmentality »

dehrmann wrote: post #51
jlmorton wrote: post #47

Earlier quoted context omitted.

I'm not sure if you're talking about daily deaths, or in total, but California has had 5,286 deaths as of today, not 58. We also had 81 deaths today specifically. In a perfect world, the point of a lockdown is to arrest the spread of a disease entirely. Unfortunately, we're well past that point in the US. Having failed at that, the goal is not just to keep health care utilization below capacity, but also to buy time…

They probably meant per day. I think "flat" is a fair characterization of the metric: https://i.imgur.com/zZ7UGVW.png Deaths has a few problems. One is that once SARS-CoV-2 finds a nursing home, it's a lot of at-risk people in once place, so it gets hit hard. If deaths is the metric you care about, it's best to put a lot of effort into testing workers at care facilities and putting those facilities strict lockdowns.…

> https://i.imgur.com/zZ7UGVW.png

I'm assuming the peaks and valleys correspond to weeks, but why are deaths correlating so strongly with the day of the week?

Re: Covid-19: The T Cell Story

#57

Post by phreeza »

WildParser wrote: post #55
lsllc wrote: post #36

Earlier quoted context omitted.

In Massachusetts (where we have been hit pretty hard by C19) we're trending downwards in a significant way and have been for a few weeks now. But I see more human activity out and about than ever (at least compared to March/April and mask wearing / social distancing is has been pretty obviously in decline for a number weeks now). The state is now well into it's re-opening phase 2 and even with the recent protests, th…

Exactly. Things with R0 a) Take the number of deaths per day, divide it by the total number of deaths. f'/f. b) Take a look at this in a log-chart. Use 7 day averages for f' and f to get a cleaner picture. You will see that f'/f falls down exponentially since pretty much the beginning. c) determine the exponent by estimating the derivative ln(f'/f)'. d) Now use that to calculate the function f. e) Calculate an enddat…

If people are infectious for some finite number of days, f'/f will always tend to zero, even if f' stays constant.

Re: Covid-19: The T Cell Story

#58

Post by WildParser »

phreeza wrote: post #57
WildParser wrote: post #55

Earlier quoted context omitted.

Exactly. Things with R0 a) Take the number of deaths per day, divide it by the total number of deaths. f'/f. b) Take a look at this in a log-chart. Use 7 day averages for f' and f to get a cleaner picture. You will see that f'/f falls down exponentially since pretty much the beginning. c) determine the exponent by estimating the derivative ln(f'/f)'. d) Now use that to calculate the function f. e) Calculate an enddat…

If people are infectious for some finite number of days, f'/f will always tend to zero, even if f' stays constant.

It falls down exponentially! Just look at it. If you do a bit of math you will see that f will just converge.

Re: Covid-19: The T Cell Story

#59

Post by acqq »

mlyle wrote: post #32
MiguelVieira wrote: post #10

Earlier quoted context omitted.

Also this Washington choir where over 80% of the attendants were infected https://www.livescience.com/covid-19-superspreader-singing.h... This article is just wishful thinking.

"This phenomenon is called overdispersion, and it means that while on average a patient infects 2 or 3 new people, this average consists of many people infecting nobody, and then some mass spreading events infecting many more. "

> then some mass spreading events infecting many more

The point is however that it is impossible that the choir selected their members based on the criteria of "members can be only these who will be easily infected with the at the moment still unknown disease." There the existence of the superspreading event to "80% of some random selection" disproves the hypothesis that "on average much less than 80% of the population can be infected at once". That's obviously not true.

Re: Covid-19: The T Cell Story

#60

Post by jacobush »

lsllc wrote: post #36
nodamage wrote: post #9

> And wherever we look, infections level off before 10%-20% of the population is infected. This is somewhat mysterious. This is not really true. Bergamo had a 58% infection rate as of last month: https://bergamo.corriere.it/notizie/cronaca/20_maggio_22/ber... Several prisons have seen infection rates in the 70-80% range: https://www.npr.org/sections/coronavirus-live-updates/2020/0... The USS Theodore Roosevelt had an…

In Massachusetts (where we have been hit pretty hard by C19) we're trending downwards in a significant way and have been for a few weeks now. But I see more human activity out and about than ever (at least compared to March/April and mask wearing / social distancing is has been pretty obviously in decline for a number weeks now). The state is now well into it's re-opening phase 2 and even with the recent protests, th…

That's what bertheb says, R0 depends on the other variables, like density, climate etc etc.
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