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

Re: Covid-19: The T Cell Story

#111

Post by salmon30salmon » Thu, Jun 18, 2020, 4:44 PM UTC

raducu wrote: post #70

guscost wrote: post #48

Earlier quoted context omitted.

So those people in one town did not have enough cell-mediated immunity to clear the viral dose from spending all day in an enclosed space with dozens of coworkers shedding the virus. This does not in any way suggest that 50% of the general population cannot have enough cell-mediated immunity (or even immunity from a cross-reactive adaptive/antibody response to another coronavirus) to clear e.g. the viral dose from ea…

Surely it could be true that all population is immune to exposure to exactly half a virion well cooked with sauce, but such an information is pretty useless in any practical way, isn't it? Half immunity in only certain circumstances is useless for all practical purposes.

No, it is incredibly useful. That means a subset of the population, or a population certain environments, can be exposed and not get infected. AFAIU, every exposure has the chance of the immune system creating antibodies as it does for foreign cells.

Furthermore, if we know that shared living spaces, farm work communes, jails etc are the main source of serious infection, we can hyper-focus on those scenarios and allow the economy to somewhat recover.

We all need to get off our relative high horses, by the way. What is an opportunity to work from home for a lot of us, is a recipe for financial disaster and bankruptcy for many, many others.

Re: Covid-19: The T Cell Story

#112

Post by salmon30salmon » Thu, Jun 18, 2020, 4:47 PM UTC

nodamage wrote: post #27

thewarrior wrote: post #21

Earlier quoted context omitted.

I think you’re being too negative here. I’m not an expert. My understanding is given that there is a pre existing T cell response that doesn’t mean that you will not be infected or that you will not have antibodies if infected. However it could totally be possible that when infected you are much less likely to show symptoms,die or spread it to others. It’s a tough hypothesis to completely verify but the dip in deaths…

I'm not sure what exactly you think is negative? The claim that infections top out at 10-20% is clearly not true. Even if it were true, we don't really know enough yet to conclude that T-cells would be the reason why. > It’s a tough hypothesis to completely verify but the dip in deaths and infections in many places in spite of lifting lockdowns lends some support to this theory. This sounds like a pretty weak correla…

It isn't true _everywhere_. It might be true in some places. For example, towns with young residents and lots of children. Or suburbia where there isn't much incidental contact with others for long periods of time.

The goal here, in my opinion, is to _never_ return to the sort of broad stroke lockdown where society stops completely. That is an entirely untenable solution, and any new evidence we have to mitigate the virus without that sort of action is welcome news. We should be cheering these researches on, not vilifying them. They are doing science. It is an imperfect art, it is a series of terrible mistakes that eventually lead to a revelatory moment.

Re: Covid-19: The T Cell Story

#113

Post by hcknwscommenter » Thu, Jun 18, 2020, 5:23 PM UTC

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'm not sure if your sources really say what you imply that they do. Bergamo had a 58% COVID exposure rate as of last month, as determined by serology studies.

How many of those had a full blown infection? I suppose detectable antibodies suggests there was at least some level of infection, but a very mild infection plus rapid clearance in a plurality of the population fits with the sentence you quote. The other cites you provide basically show the same thing. Of course social distancing/lockdowns also help. Why not both? The reality is that there are two mysteries here: i) a lot of people are relatively unaffected by the virus and serology shows they were exposed; ii) a lot of people, even under very crowded conditions (USS Teddy R; prisons) just don't get COVID at all. 40% of those on the carrier simply never got it. How is that possible? The prison data is high if we take your the 80% upper level of your range, but you will expect to see those sorts of outliers in small datasets. This is particularly true where the early antibody tests were not very specific (i.e., relatively high false positive rate).

Re: Covid-19: The T Cell Story

#114

Post by hcknwscommenter » Thu, Jun 18, 2020, 5:26 PM UTC

redis_mlc wrote: post #45

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…

> 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…

Are you ignoring LA county? It's rising rapidly there and starting to spread to the surrounding areas. The wealthy So. Cal. residents who haven't fled yet will move North and then the North will get hit, kind of like what happened to Connecticut via MA and NY.

Re: Covid-19: The T Cell Story

#115

Post by mlyle » Thu, Jun 18, 2020, 5:50 PM UTC

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…

We obviously have a huge variation in spread. Indeed, the choir is evidence of superspreaders who produce many cases, and we have an average R0 of 2-3. Singing loudly in enclosed spaces with many people is an example of a contact network structure that causes greatly increased susceptibility and contagion. Indeed, it proves the whole point!

But, the belief that herd immunity = 1 - (1 / R) is based on the assumption that those infected have equal susceptibility and equal probability of spread. This is a fair assumption when it comes to a vaccination program which will administer doses not correlated to susceptibility and contact network structure. It is not a fair assumption when it comes to actual spread of disease in the wild, which will preferentially spread in the more susceptible networks.

Reality is certainly better than this; the question is how much better. There's been some quality analysis of time-series data that implies the threshold may be 20-30%.

I believe that New York City's quick decline in death rates compared to jurisdictions with similar or stricter controls but lower seropositivity may imply that ~20% exposure is enough to significantly attenuate spread.

Re: Covid-19: The T Cell Story

#116

Post by hcknwscommenter » Thu, Jun 18, 2020, 6:25 PM UTC

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…

That is a fundamental misunderstanding of how probabilities work. There is always bunching, streaking, things that look like patterns but are not, and the like.

Re: Covid-19: The T Cell Story

#117

Post by jlmorton » Thu, Jun 18, 2020, 7:30 PM UTC

redis_mlc wrote: post #54

dehrmann wrote: post #51

Earlier quoted context omitted.

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 heatin…

The number of deaths for the SF Bay Area is not 58, either. It is:

San Francisco: 47 Alameda: 116 Santa Clara: 152 San Mateo: 99 Contra Costa: 50 Marin: 18 Solano: 23

In other words, about ~500 deaths. If you had 60% of the population infected, you might expect 20x that figure.

Why would it matter that California had daily flights from Wuhan? It changes the math almost by nothing. Whenever an initial seeding occurs, domestic cases rapidly and overwhelmingly takeover in spread.

Wuhan has, as of early June testing, a SARS-CoV-2 seropositive rate of approximately ~3%. There were very few infected people coming on those daily flights in January, and by February domestic spread was many orders of magnitude larger than any seeding event.

California also shutdown earlier than other states, especially in the Bay Area, where essentially all major employers implemented work from policies 7-10 days before the official Shelter-in-Place notice.

California may have had an earlier seeding, but we know for sure it was spreading domestically by mid-January in several cities around the country.

Re: Covid-19: The T Cell Story

#118

Post by hcknwscommenter » Thu, Jun 18, 2020, 7:51 PM UTC

ajsnigrutin wrote: post #85

not2b wrote: post #20

Earlier quoted context omitted.

But the article claims it will discuss "How around 50% of us appear to have (some?) Cell Mediated Immunity against COVID-19". If we're seeing farms where every single person falls ill, that suggests that 50% of us aren't immune, though I suppose "(some?)" is a cop out.

Why would that be an XOR situation? They're all tested positive, but 50% of them might have some form of immunity, and are fighting it off like that would a normal cold (or even with zero symptoms). The virus is still in their system, but their bodies are disposing of it without issues.

Boom. That's totally correct. Plus, these articles showing "every single worker" infected or 60% of carrier passengers/prisoners etc. don't do a good job of reporting how may actually sick people there are. Immunity is not all or nothing. It's a relative amount of resistant. Many (likely all) of these "naturally immune" folks (if they exist, and I think the evidence is pretty compelling personally) would get COVID if injected with a sufficient dose of purified virus. Many (likely all) would get COVID if an infected person sneezed into their face. Many (maybe? probably?) would be fine sharing a grocery store with a pre-symptomatic carrier. That's huge if true. Time will tell.

Re: Covid-19: The T Cell Story

#119

Post by hcknwscommenter » Thu, Jun 18, 2020, 7:53 PM UTC

dalore wrote: post #96

tomp wrote: post #90

Earlier quoted context omitted.

Why do you think "northern hemisphere summer" would have any (positive) impact? I mean, just look at Brazil, an "eternal summer" country, they're not doing that well... Except if it's the combination of heat+low humidity, there might be counterexamples to that as well though (Iran?).

It's not the heat but the UV exposure and people's ability to create vitamin D from it. People in countries that have "eternal summer" tend not to go out in the sun as it's hot. Also skin pigmentation is a big factor.

"tend not to go out in the sun as it's hot"

Is that really true? Most of these "hot" LATAM and asian countries do not have wide-spread central air conditioning. In those countries, staying inside is horrible in the hot months.

Re: Covid-19: The T Cell Story

#120

Post by hcknwscommenter » Thu, Jun 18, 2020, 7:55 PM UTC

GreenHeuristics wrote: post #93

newmana wrote: post #84

Earlier quoted context omitted.

Sweden has achieved about 15% infection rate and has showed no signs of slowing. https://www.smh.com.au/world/asia/new-beijing-outbreak-raise... https://www.worldometers.info/coronavirus/country/sweden/

No, the 14% figure is for people that self-requested testing. You can see it as an upper boundary, but it won't be the actual figure, which is likely around 8% or so.

Exactly. In other words 86% of Swedes who had reason to suspect an infection and wherewithal to request testing and provide sample did not have COVID.