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Covid-19: The T Cell Story

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Re: Covid-19: The T Cell Story

#71

Post by redis_mlc »

ziga wrote: post #12
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…

Imperial College report showing mobility trends explain over 80% of observed variations in transmission: https://www.imperial.ac.uk/media/imperial-college/medicine/m...

> Imperial College report

Imperial College is always wrong.

Re: Covid-19: The T Cell Story

#72

Post by raducu »

xorfish wrote: post #68
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…

I have seen that "infection level off after 10-20%" multiple times. It is simply not true. Some areas level off at 1-2%, some at 5%, 10, 20% or whatever else. It all depends on when strong social distancing measures were taken. There were only a few places such as NYC or Bergamo, where measures were taken too late and infections went over 20%.

I know hn doesn't like sarcasm, but saying that infection level off after 10-20% "naturally" after the world experienced the biggest lockdown since the spanish flu, is like saying the fire I saw on the news was extinguished because I took a pee at the same time.

Nevermind resurgences post lockdown in shithole places where people don't follow distancing and don't wear masks -- like India or my belloved Romania -- surely, this fact cannot be explained by this bullshit theory.

Re: Covid-19: The T Cell Story

#73

Post by redis_mlc »

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.

It's essentially what we've done in SF:

1) Allow a million passengers from China to disembark in Calif.

2) Everybody goes to the grocery store twice a week and mingles in a leisurely fashion.

For us, it's worked out great. Probably the lowest measured infection and documented mortality rates in the world for an area that doesn't do testing and tracing.

Seen any apocalyptic news stories about SF hospitals like NY? Nope, me neither.

I'm much more worried about the negative cardiac effects of no exercise than corona deaths.

Re: Covid-19: The T Cell Story

#74

Post by rightbyte »

acqq wrote: post #59
mlyle wrote: post #32

Earlier quoted context omitted.

"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 populati…

No.

If it is true that say 50% have a harder time catching covid then given that there is a superspreading event at a choir to 80% you need to take into account the others choirs at the other end of the tail.

I.e. given 100 choirs there will be a distribution of "not easiely infected" individuals with choirs with few off them.

I am not saying anything of the validty of the claim, just that the choir doesnt disprove it.

Re: Covid-19: The T Cell Story

#75

Post by neuronic »

christkv wrote: post #5

Kind of shows how little we know about the human immune system. Hopefully this pans out and we won’t see massive new waves. I have an anecdotal example of that this might be something. A friend and his wife got tested before delivering their baby and she was positive for antibodies and he was negative. He might have just beaten the virus before the body even started creating antibodies.

For my master thesis, I wrote a small tool that would take and analyze raw genomic high throughput data of various T-cells (chip-seq + rna-seq of th17 to be precise) and create a regulatory network in Cytoscape. The basis was a paper relating to The Th17 Project [1].

What I learned is that we are sort of in the very beginnings of understanding how immune cells work (together), how their plasticity works in terms of gene expression at any given point in time. For example, environmental circumstances such as cytokine presence can lead to T-cell types "transforming" to other types which have other effects etc. but it's not well understood how this occurs. A very large amount of genes regulate each other, you get a complicated network of up- and downregulations and it's hard to reproduce and understand what needs to be done to generate a certain type of T-cell with certain characteristics and behavior.

And then you haven't even tried doing that in-vivo where you could try to push the immune system to express genes such that many T-cells of type X are generated to enhance or fight inflammation. Because then you just disturbed a complex interacting system with zero idea what the total effect is and whether "the network" is resilient enough to not crash and burn somewhere somehow.

It's very very complicated with a huge amount of combinatorics involved so Complex Systems Theory helps to build models helps a bit.

[1] http://th17.bio.nyu.edu/pages/index.html

Re: Covid-19: The T Cell Story

#76

Post by DyslexicAtheist »

raducu wrote: post #72
xorfish wrote: post #68

Earlier quoted context omitted.

I have seen that "infection level off after 10-20%" multiple times. It is simply not true. Some areas level off at 1-2%, some at 5%, 10, 20% or whatever else. It all depends on when strong social distancing measures were taken. There were only a few places such as NYC or Bergamo, where measures were taken too late and infections went over 20%.

I know hn doesn't like sarcasm, but saying that infection level off after 10-20% "naturally" after the world experienced the biggest lockdown since the spanish flu, is like saying the fire I saw on the news was extinguished because I took a pee at the same time. Nevermind resurgences post lockdown in shithole places where people don't follow distancing and don't wear masks -- like India or my belloved Romania -- sure…

> the biggest lockdown since the spanish flu

what lockdown has there been in place during the Spanish flu? afaik[1] it was a big cover up in most of the world:

> "the reason why it was even called Spanish flu was because Spain was not involved in the war, having remained neutral, and had not imposed wartime censorship."

--> hence I assumed Spain was not affected by the propaganda/cover-up efforts and reason for it's spread was precisely the lack of social distancing and lockdowns throughout the world as war ravaged on.

[1] https://en.wikipedia.org/wiki/Spanish_flu#Etymology

Re: Covid-19: The T Cell Story

#77

Post by phreeza »

WildParser wrote: post #58
phreeza wrote: post #57

Earlier quoted context omitted.

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.

I think it really depends on your underlying dynamics, but I just want to point out that f'/f going to zero does really not imply that f will converge.

If for example you are in a still strongly growing (but no longer exponential) regime where you can approximate the currently infected number of persons as proportional to t^2 , and there is some constant IFR, then f'(t) is also proportional to t^2. f(t) will then be growing as t^3, so f/f' will go as t^-1, which will look quite similar to an exponential decay at the timescale of the process.

Re: Covid-19: The T Cell Story

#78

Post by mr_toad »

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.

Innate immunity is more like a built-in mask. It’s pretty much the opposite of building up an immunity.

Re: Covid-19: The T Cell Story

#79

Post by acqq »

rightbyte wrote: post #74
acqq wrote: post #59

Earlier quoted context omitted.

> 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 populati…

No. If it is true that say 50% have a harder time catching covid then given that there is a superspreading event at a choir to 80% you need to take into account the others choirs at the other end of the tail. I.e. given 100 choirs there will be a distribution of "not easiely infected" individuals with choirs with few off them. I am not saying anything of the validty of the claim, just that the choir doesnt disprove i…

> I.e. given 100 choirs there will be a distribution of "not easily infected" individuals with choirs with few off them.

That's a valid point -- one choir alone would not be enough to be the proof, it could still be an accident that such individuals happened to be in one particular choir, but it's not the only such "random sample." Given that we have more "random samples" of different sizes, they can be observed as contributing to the evidence, the logic of the proof is there, and the evidence accumulates, especially as it can be observed that no specific "traits" of the infected could be recognized to bring "the difference" between "less" and "more" easy infections.

One of the arguments supporting the significance in the choir is -- the earlier in the spread of infection we observe such choirs, there's less chance that "100 choirs" from your example were even exposed to the virus, and less chance that that specific choir was exceptional. Similar spreads early in epidemics would also point in non-exceptionality of that one.

Re: Covid-19: The T Cell Story

#80

Post by acqq »

jacobush wrote: post #62
acqq wrote: post #44

> Does this mean that if you recently had a Coronavirus that caused a head cold that you have a measure of protection? Apparently, no , as there are no observed differences in the percentages of infected when the people who have children or work with children are compared with those who don't. If the stated assumption were true, those that were more exposed to other coronaviruses (which would be expected among those…

These cold viruses circle the globe too, and just because some children had colds and transferred them to adults, does not mean that they had exactly the strain that could potentially give partial Covid19 immunity. So while I agree with your general advice about sources, I don't find your "apparently" to be apparent at all.

> while I agree with your general advice about sources, I don't find your "apparently" to be apparent at all.

"Apparently" was used in the sense "I haven't seen and verified the sources myself" (i.e. the specific scientific material that supports the conclusion of an expert) but at least I took the effort to get the claim about that conclusion from a recognized expert directly." That is, I can't give you the ultimate source that the said expert used for that conclusion, but according to my understanding from reading a transcript of his podcast he concluded that and I have chosen to believe him. Experts spend their whole life to achieve expertise. There are a lot of "preprints" and even fast-approved published scientific papers floating around, which eventually (even extremely fast) are recognized to be flawed by the experts, but only after the false claims are repeated across the media. In such a situation, unless we are the experts ourselves, and unless we have infinite time available, our best bet is to trust the experts who are less prone to present or accept false claims. I consider Christian Drosten one of these.

Being curious, I do check some source scientific works myself, I'm just admitting that for that particular claim I haven't checked the sources myself but decided to trust Drosten. I also claim that I at least spent enough energy to read the exact transcript of his talk and avoided to read "journalistic interpretations" -- the expert's statements are very often totally deformed by retelling. If that's not enough for you and you believe that you can catch him in an error, I'd really like to know why you even believe to be able to achieve that. And if you believe that I'm claiming something he hasn't said, you can check the transcripts of his last two podcasts yourself and write here if I made an error, I'll be happy to learn more.

At some level every one of us has to trust some experts, the question is just if we can also recognize these who just claim some expertise but are actually promoting false claims. I believe that Ioannidis, for example, is an example of such, and I also see that other experts agree.

For "as close to the experts as possible" sources I also recommend everything from https://www.microbe.tv They also admit that they do make errors sometimes, because they didn't recognize early enough how serious this virus is going to affect everybody. But getting the coverage from the experts directly allows one to remain much saner than when reading media who regularly completely distort what experts actually say. And even when media accurately quote some single paper, media often falsely reflect what the whole body of knowledge actually is, as in xkcd "Significant" comics.

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