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Estimating unobserved SARS-CoV-2 infections in the United States

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Re: Estimating unobserved SARS-CoV-2 infections in the United States

#41

Post by sacred_numbers »

IAmGraydon wrote: post #33
dehrmann wrote: post #31

I've been looking at the infection rates in the US falling over the past few weeks, and I'm wondering if it's because we achieved herd immunity for the current r0, people changed their behavior when they saw cases rising, or fewer people are getting tested because with the lag in processing time, a positive result isn't actionable.

The way that the areas that are now most resilient are the same areas with high population density which were hit very hard early on (NY, NJ, for example) tells me that we have somehow hit herd immunity. There is some evidence coming out that other coronaviruses (which cause the common cold) could have causes immunity in some unknown percentage of the population, meaning the percentage of SARS-CoV-2 infection require…

The herd immunity threshold depends on behavior. It may be at 30% infected when the population is wearing masks and social distancing, but could be 70% if restrictions are removed. I agree that parts of New York City have probably reached herd immunity for current behavior patterns, so restrictions can probably be slightly relaxed, but 70% of the population is still vulnerable to infection, so you can't throw caution to the wind.

Re: Estimating unobserved SARS-CoV-2 infections in the United States

#42

Post by ohmaigad »

robbintt wrote: post #40
IAmGraydon wrote: post #33

Earlier quoted context omitted.

The way that the areas that are now most resilient are the same areas with high population density which were hit very hard early on (NY, NJ, for example) tells me that we have somehow hit herd immunity. There is some evidence coming out that other coronaviruses (which cause the common cold) could have causes immunity in some unknown percentage of the population, meaning the percentage of SARS-CoV-2 infection require…

Share the evidence or delete the comment as misinformation.

https://www.nih.gov/news-events/nih-research-matters/immune-...

Can't comment on the other stuff.

Re: Estimating unobserved SARS-CoV-2 infections in the United States

#43

Post by hodgesrm »

robbintt wrote: post #40
IAmGraydon wrote: post #33

Earlier quoted context omitted.

The way that the areas that are now most resilient are the same areas with high population density which were hit very hard early on (NY, NJ, for example) tells me that we have somehow hit herd immunity. There is some evidence coming out that other coronaviruses (which cause the common cold) could have causes immunity in some unknown percentage of the population, meaning the percentage of SARS-CoV-2 infection require…

Share the evidence or delete the comment as misinformation.

The evidence is not hard to find. [1] Took me about 60 seconds.

I would suggest in future supplying this to the conversation yourself as it makes for a more productive discussion.

[1] https://www.nih.gov/news-events/nih-research-matters/immune-...

Re: Estimating unobserved SARS-CoV-2 infections in the United States

#44

Post by fullshark »

ouid wrote: post #12
SpicyLemonZest wrote: post #2

Interesting. An estimate that infections were multiple orders of magnitude higher than detected in mid-March is higher than I'd heard before, although I suppose it's probably implied by the "basically everyone in New York caught it" theory.

It's not that hard to work backward from the observed fatality rate and the death curve to the infection curve two weeks ago. That's basically all they're doing in this paper. It does not suggest that everyone in new york caught the virus. Just that in the early days of the pandemic, when schools were open and no one knew about the virus, the model for growth was exponential with about a 25% increase in cases per day…

Not 2000 cases, 200 cases (1 / 0.53%). If it were 2000 cases then 40 million new yorkers got COVID (which is larger than the population of NYC).

Back of the envelope based on this

* https://www.cdc.gov/nchs/nvss/vsrr/COVID19/

* https://science.sciencemag.org/content/368/6498/eabd4246

* https://worldpopulationreview.com/us-cities/new-york-city-ny...

-> about half of NYC has been infected.

Re: Estimating unobserved SARS-CoV-2 infections in the United States

#45

Post by 0xFFC »

jandrewrogers wrote: post #14
MengerSponge wrote: post #8

Earlier quoted context omitted.

As nice as it would be, seroprevalence studies have ruled out the "basically everyone in New York caught it" theory.

A substantial percentage of infections are believed to not show up in seroprevalence studies. One of the major areas of research right now is determining how large this population is.

> A substantial percentage of infections are believed to not show up in seroprevalence studies

What is the reason behind this?

Re: Estimating unobserved SARS-CoV-2 infections in the United States

#46

Post by kspacewalk2 »

jliptzin wrote: post #39
lettergram wrote: post #37

It seems cases and pandemic related deaths are likely dramatically under reported and detected: https://austingwalters.com/u-s-covid19-less-tests-more-death... Real deaths seem to be closer to 250-300k at this point (whereas officially it’s 170k-180k). Also testing is down for those curious... about 25% down from a month ago. edit : added “pandemic related deaths” - not all deaths are necessarily covid, but could be…

I know for a fact deaths are dramatically under reported (at least in FL) because I have relatives that died of COVID and the nursing homes put congestive heart failure and respiratory failure as cause of death and not COVID. After receiving positive COVID test results...

It's much less clear cut than that. In fact death with COVID ≠ death from COVID every single time, even for elderly people.

Re: Estimating unobserved SARS-CoV-2 infections in the United States

#47

Post by hodgesrm »

air7 wrote: post #26
SpicyLemonZest wrote: post #11

Earlier quoted context omitted.

The core result is > Simulating from 1 January, we obtained 108,689 (95% PPI: 1,023 to 14,182,310) local infections cumulatively in the United States by 12 March (Fig. 1A). What that means is that they don't really know - that confidence interval is absurd - but they have reason to think there could have been 100k Americans with the coronavirus on March 12.

Results with such confidence intervals should not be allowed to be published. As if we don't have enough fake news/hype going around.

I don't understand the comments on this thread that seem to want to suppress preliminary data about COVID.

Sure, the confidence interval is ridiculously large but the paper is open about its methods and conclusions. It's definitely in the "more work is needed" category, but I don't see how this information should not be published.

Re: Estimating unobserved SARS-CoV-2 infections in the United States

#48

Post by _Gyan_ »

Delhi, at least, appears to have around a 5% detection rate over the past month.

There was a population-wide serosurvey conducted from Aug 1st to 7th, which resulted in a 29.1% prevalence estimate, and an earlier one from June 27th to July 10th, which resulted in a 22.8% estimate. Assuming a 2 week period for IgG to be detected after infection, these surveys correspond to prevalence as of 20th July and 20th June roughly. With a population of 20M, that's around 1.25M new infections in that period. The confirmed cases by PCR testing increased by ~60000, yielding (roughly) a detection rate of 5%.

Re: Estimating unobserved SARS-CoV-2 infections in the United States

#49

Post by tripletao »

robbintt wrote: post #40
IAmGraydon wrote: post #33

Earlier quoted context omitted.

The way that the areas that are now most resilient are the same areas with high population density which were hit very hard early on (NY, NJ, for example) tells me that we have somehow hit herd immunity. There is some evidence coming out that other coronaviruses (which cause the common cold) could have causes immunity in some unknown percentage of the population, meaning the percentage of SARS-CoV-2 infection require…

Share the evidence or delete the comment as misinformation.

Multiple papers (including one in Nature[1]) have reported T-cell immunity to SARS-CoV-2 in something between a third and half the samples collected before the pandemic. That doesn't mean the virus won't replicate in people with that pre-existing immunity, and there's evidence from homeless shelters and such of almost everyone testing positive (both by PCR and later for IgG in their blood); but people with that T cell immunity very likely get less sick, and might be less infectious (though near-certainly still infectious, and that's more speculative).

And it seems from the hostility of your response ("delete the comment as misinformation") that you find it incredible that herd immunity could exist with less than 1 - 1/R0 of the population infected? But even ignoring any pre-existing immunity, that calculation assumes a homogeneous and well-mixed population. That's clearly not the case, since some people (a nurse in a crowded ER, a police officer, a store clerk, a nightlife enthusiast, etc.) have far more contacts than others (a remote worker who gets stuff delivered). People with more contacts will get infected first, with disproportionate harm, and then become immune first, with disproportionate benefit. Many papers have modeled[2] this; though no one's found a great way to measure that heterogeneity yet, so for now, it's hard to say much beyond that the effect exists, and is potentially big.

And finally, herd immunity isn't a binary threshold, especially in a heterogeneous population. As others have noted, even places without enough immunity for R 1. https://www.nature.com/articles/s41586-020-2550-z

2. https://www.medrxiv.org/content/10.1101/2020.02.10.20021725v...

Re: Estimating unobserved SARS-CoV-2 infections in the United States

#50

Post by tomarr »

kspacewalk2 wrote: post #46
jliptzin wrote: post #39

Earlier quoted context omitted.

I know for a fact deaths are dramatically under reported (at least in FL) because I have relatives that died of COVID and the nursing homes put congestive heart failure and respiratory failure as cause of death and not COVID. After receiving positive COVID test results...

It's much less clear cut than that. In fact death with COVID ≠ death from COVID every single time, even for elderly people.

Well sure, and that is a perfectly valid comment at the micro level. However, we can relatively clearly see that the COVID-linked death reporting is under-reported from mortality baselines.

Therefore it's highly likely that for a given death it is more likely to be incorrectly categorise as non-COVID when COVID was responsible, than to be incorrectly designated COVID.

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