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

https://www.pnas.org/content/early/2020/08/20/2005476117

by krjachkov • 6 years ago

60 71 6 years ago

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.

sushshshsh2• 6 years ago

I don't know a single person in NY who wasn't coughing for a week at some point between january and march.

Jenk• 6 years ago

The problem with this is that people have many reasons to cough. You could say that same statement for any year and it would be accurate.

ryanworl• 6 years ago

In the last few days of January and two weeks in early February in Manhattan, I (26M) got quite sick. The first few days were pretty bad and I had 102F fever. I had lots of difficulty breathing and a dry cough for around 2 weeks after. A friend/co-worker who sits next to me at work had essentially identical symptoms 12 hours before me lasting for similar amount of time. I think his breathing problems were less bad than mine.

The worst hit me on the weekend and I returned to work on Monday with the cough.

Around 1 week prior I attended a company holiday party at a large museum with (probably?) one thousand attendees from all over the world. They mostly came from the EU, but at least some from APAC as well.

I have no evidence that this was COVID-19, but in retrospect the symptoms matched reasonably well and I haven't been sick since.

DoofusOfDeath• 6 years ago

Is it possible that your NY social network at the time was part of a fairly insular clique?

That might explain why your sample is (potentially) not representative of the overall city or state.

tyingq2• 6 years ago

I had wondered how the current new cases / day in NY were so low as compared to other areas. This seems likely to be at least part of it.

What's the theory on why other places that were hit hard early are still quite high...like California? Lower density?

SpicyLemonZest6• 6 years ago

California wasn't hit very hard early. In terms of total reported cases, they're only just now starting to catch up with New York (21 per thousand for the state vs 17 per thousand for California) - and as we catch up we've had a pretty sharp improvement from the peak in July.

The theory is that California flattened the curve in the original sense, delaying the peak in order to ensure it's moderately lower and protect the capacity of the healthcare system.

MengerSponge• 6 years ago

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

jandrewrogers• 6 years ago

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.

SpicyLemonZest6• 6 years ago

T-cell immunity is known to be a relevant factor, though. It'd be unreasonable to assume it fully plugs the gap, but I think there's gotta be some explanation for why only areas hit hard in April were able to keep cases low over the last few months.

zaroth2• 6 years ago

It’s statistically impossible for literally everyone in NY to catch COVID.

What recent studies have shown is that while the naive herd immunity threshold is perhaps around 60% (working backwards from R0 estimates), after you factor in clustering of populations, baseline hygienic improvements, and moderate social distancing, that NY did reach an effective level of herd immunity.

ouid2• 6 years ago

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, the best estimate for the number of infections was 2^(14/3)*(1/1.5%)x deaths. Each death corresponded to about 2000 cases.

SpicyLemonZest6• 6 years ago

I haven't exhaustively evaluated it, but they claim to be actually simulating the transmission, not just tracing the death curve.

fullshark2• 6 years ago

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.

icedchai• 6 years ago

People have been saying 10x for months: https://www.washingtonpost.com/health/2020/06/25/coronavirus...

I would not be surprised if it were much higher.

cma2• 6 years ago

Seems unlikely. This is showing a 10:1 estimate, where New Yorkks, based on zero positivity, was 6:1 or so. Using 10:1 it would be around 25% infected in New York State.

kgin• 6 years ago

I seem to be hitting trying to read this. Can someone help summarize the results of this analysis?

SpicyLemonZest6• 6 years ago

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.

air7• 6 years ago

Results with such confidence intervals should not be allowed to be published.

As if we don't have enough fake news/hype going around.

m3kw9• 6 years ago

100k was estimated to be infected by early March.

dehrmann3• 6 years ago

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.

IAmGraydon• 6 years ago

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 required to reach herd immunity is much lower than thought.

robbintt• 6 years ago

Share the evidence or delete the comment as misinformation.

sacred_numbers• 6 years ago

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.

sokoloff• 6 years ago

In my area, the lag in testing results is only 24-36 hours (that’s for free city-provided testing without a requirement to suspect you have it or have been exposed [so utterly routine processing])

segmondy• 6 years ago

You're looking at garbage data. The data has never been accurate or consistent.

dehrmann3• 6 years ago

Citation needed. I agree that it's not perfect, and it can actually be hard to count, but the aggregate numbers for the US tell a very consistent story, and it doesn't scream "garbage data."

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

dankle• 6 years ago

108,689 (95% posterior predictive interval [95% PPI]: 1,023 to 14,182,310)

So between 1000 and 14 million. Got it.

jhfdbkofdcho• 6 years ago

Not all of those numbers are equally likely though.

lettergram• 6 years ago

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 from lack of healthcare availability, etc.

sxp• 6 years ago

https://www.cdc.gov/nchs/nvss/vsrr/covid19/excess_deaths.htm... has a similar graph as your link, but you can mouseover to get weekly numbers.

jliptzin• 6 years ago

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...

kspacewalk2• 6 years ago

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

dm319• 6 years ago

You would expect those deaths to show a signal in the all-cause, excess mortality. When I last checked, somehow, US still had lower excess mortality than the UK per capita. Although numbers are very low in the UK, whereas they are still pretty high in the US.

_Gyan_• 6 years ago

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%.

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

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