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Covid-19 at a homeless shelter in Boston: Implications for universal testing

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Re: Covid-19 at a homeless shelter in Boston: Implications for universal testing

#91

Post by yters »

Retric wrote: post #20
gnulinux wrote: post #8

Earlier quoted context omitted.

It seems to indicate this disease infected a lot more than what we see, and maybe mortality rate is lower than what we currently assume. Maybe it's around 0.1% to 0.5%. So is it possible this disease appeared in China way before December, maybe a few months back. Then in December it reached a saturation point (i.e. infected hundreds of thousands of people, so deaths started to get noticed by respiratory specialists).…

No for several reasons. The Dimond Princess had over 100 crew of young healthy adults test positive and only 25% where asymptotic long term. Additionally South Korea has a massive effort into contact traction which demonstrated just how rapidly the disease spread. Their mortality numbers looked to be about 0.6% early on, but eventually hit 2% a month after the peak with people spending weeks in critical condition. On…

what do you think about iceland?

Re: Covid-19 at a homeless shelter in Boston: Implications for universal testing

#92

Post by FrojoS »

autokad wrote: post #39
raphlinus wrote: post #18

Earlier quoted context omitted.

No. We know from genomic analysis [1] that "The common ancestor of circulating viruses appears to have emerged in Wuhan, China, in late Nov or early Dec 2019." It's fun to speculate about other possibilities, but I personally like to stick to what the science tells us. [1]: https://twitter.com/nextstrain/status/1248707010750640128

well, google coronavirus searches in China, specifically Hubei province, spiked in September of 2019. Science is a term being twisted out of its original context. if people keep doing that, its going to be a pejorative.

Source?

Re: Covid-19 at a homeless shelter in Boston: Implications for universal testing

#93

Post by smallgovt »

DenisM wrote: post #28
smallgovt wrote: post #17

Earlier quoted context omitted.

> We need more studies to gather data on these asymptomatic cases if we want to reopen the economy soon. I don't understand what's so hard about measuring population infection rate. Assuming the population infection rate is between 1-10%, we would only need to do around ~500 randomized tests to achieve a 95% confidence interval of +/- 1%. For example, let's say we tested 500 random NYC residents for COVID and found t…

False positive rate of some antibody tests is 9%, which makes any effect size below that invisible.

Ah, I see. Is it true that these tests are a work in progress and the false positive rate will drop in the coming weeks/months? If so, it seems like we should start doing random sampling and saving the samples for future testing (so we can see how infection rate trended). This could be invaluable data that we're losing.

Re: Covid-19 at a homeless shelter in Boston: Implications for universal testing

#94

Post by DenisM »

duxup wrote: post #43
DenisM wrote: post #28

Earlier quoted context omitted.

False positive rate of some antibody tests is 9%, which makes any effect size below that invisible.

Jebus, 9% false positive ... is that even useful?

Great question, and the one I struggled with a lot. When I finally saw the light it was like find the glasses I have misplaced three days ago. Here:

1. Efficacy of a test can only be judged against specific priors, not any possible circumstance.

2. Likewise, the goal of a test is to assist in making a particular decision, not all possible decisions.

Specifically 9% false positive rate is not useful for testing general population where effect size is expected to be on the order of 1-10%. However it is very useful in testing groups where expected effect size is much larger for example "all symptomatic people who came to hospital" at 50% or "all contacts of a known case" at 20%. The numbers are made up to illustrate the math.

Importantly our goal is not to detect all infected people ending the epidemic in XYZ days flat, it is to reduce the viral spread factor below 0.5, halving the epidemic every XYZ days. Thinking in absolutes is counter-productive.

Bearing all this in mind, the test can be useful. For example let's take a pool of people who are symptomatic, and say we expect 50% were in fact infected. The false positives (9% of the healthy 50% == 4.5%) will be outnumbered by true positives (* 99% of the infected 50% == 49%). So now you're looking at 49% vs 4.5%, a respectable 11:1 accuracy under the given priors. Not bad, for some applications.

And here's one good application: test a group of people from the pool of the currently symptomatic, quarantine them for two weeks, then release them into the wild without self-isolation rules. They will all be healthy due to quarantine, and 10/11 will be immune. If we keep releasing 91% immune groups of people into the general population the virus will die off.

* the antibody test I was referring to has 99% true positive and 9% false positive rates.

Re: Covid-19 at a homeless shelter in Boston: Implications for universal testing

#95

Post by rocha »

usaar333 wrote: post #75
MiguelVieira wrote: post #55

Earlier quoted context omitted.

Likewise, South Korea reports a fatality rate of about 2% https://www.worldometers.info/coronavirus/country/south-kore... Since they have coronavirus relatively under control and have been doing extensive testing and contact tracing for months, it's plausible that they've caught most cases. It's wishful thinking to believe the infection fatality rate is an order of magnitude lower.

It is not plausible they caught most cases. Here's the result of randomized testing in Iceland, which also has the virus under control and has done even more testing per capita ( https://www.nejm.org/doi/full/10.1056/NEJMoa2006100?query=fe... ) Randomized testing was still finding 0.6% of the population (outside those otherwise quarantined already) actively infected. This means even in Iceland, less than half of infe…

The comparison between the two countries is so difficult. The population of Iceland is around 360K, while South Korea is over 51 million (~140x). The population density is in the same order, 3 per Km^2 to 500 per Km^2 respectively (~160x).

Re: Covid-19 at a homeless shelter in Boston: Implications for universal testing

#96

Post by throwaway_pdp09 »

jlmorton wrote: post #14
jcp2fa wrote: post #6

> Cough (7.5%), shortness of breath (1.4%), and fever (0.7%) were all uncommon among COVID-positive individuals It seems the more important point here is that the majority of the COVID-positive individuals were asymptomatic, putting another datapoint towards the conclusion that there are orders of magnitude more people that have this disease than have tested positive. We need more studies to gather data on these asym…

We already have lots of data that says this is not true. For instance, on the Diamond Princess, widespread testing of a confined group initially found many asymptomatic infections, but the majority of those turned out to be pre-symptomatic, not asymptomatic. Longer term follow-up found ~25% of infections were asymptomatic. In the US, we're now doing significant amounts of testing, but we're still primarily testing on…

> good evidence that the Basic Reproduction Number is somewhere between 2-3.

May be about double that. Per wiki article, I noticed this a few days ago (https://en.wikipedia.org/wiki/2019%E2%80%9320_outbreak_of_no...)

"Initial estimates of the basic reproduction number (R0) for COVID-19 in January were between 1.4 and 2.5,[381] but a subsequent statistical analysis has concluded that it may be much higher.[382]"

From that link wiki provided (https://wwwnc.cdc.gov/eid/article/26/7/20-0282_article) (edit: and note this is published on the CDC website)

"...we calculated a median R0 value of 5.7 (95% CI 3.8–8.9)"

So this sucks harder then.

Re: Covid-19 at a homeless shelter in Boston: Implications for universal testing

#97

Post by raphlinus »

bb2018 wrote: post #82
autokad wrote: post #39

Earlier quoted context omitted.

well, google coronavirus searches in China, specifically Hubei province, spiked in September of 2019. Science is a term being twisted out of its original context. if people keep doing that, its going to be a pejorative.

Do you have a link to that? I'd love to know more about why this would be the case.

Here's my attempt to validate the claim: https://trends.google.com/trends/explore?date=2019-01-01%202...

I'll leave it for readers to determine whether it holds up.

Re: Covid-19 at a homeless shelter in Boston: Implications for universal testing

#98

Post by Retric »

w0utert wrote: post #81
Retric wrote: post #20

Earlier quoted context omitted.

No for several reasons. The Dimond Princess had over 100 crew of young healthy adults test positive and only 25% where asymptotic long term. Additionally South Korea has a massive effort into contact traction which demonstrated just how rapidly the disease spread. Their mortality numbers looked to be about 0.6% early on, but eventually hit 2% a month after the peak with people spending weeks in critical condition. On…

>> Their mortality numbers looked to be about 0.6% early on, but eventually hit 2% a month after the peak with people spending weeks in critical condition. I see this repeated often but this is a misrepresentation of the statistics. Case fatality rate (CFR) is not the same as mortality rate. The CFR is the ratio between deaths and confirmed cases, mortality rate is the ratio between deaths and total number of people…

Mortality rate is population and cause specific. So CFR is a mortality rate, though different than the overall diseases mortality rate.

That said, your definition is also in common usage and less ambiguous.

Re: Covid-19 at a homeless shelter in Boston: Implications for universal testing

#99

Post by thehappypm »

rb808 wrote: post #4

Also 15% of pregnant Moms in NYC had the virus. This could already be much more widely spread that people think. https://www.nbcnewyork.com/news/local/nyc-hospital-finds-hig...

That is mind-boggling. You don't test positive if you've cleared the virus, either, so that 14% is actually a lower limit because some portion of them might have had it long enough ago to clear. I don't know what pregnancy does to the immune system -- but we do know that these women were all young enough to give birth (likely <40 years old).

Re: Covid-19 at a homeless shelter in Boston: Implications for universal testing

#100

Post by halfdan »

usaar333 wrote: post #75
MiguelVieira wrote: post #55

Earlier quoted context omitted.

Likewise, South Korea reports a fatality rate of about 2% https://www.worldometers.info/coronavirus/country/south-kore... Since they have coronavirus relatively under control and have been doing extensive testing and contact tracing for months, it's plausible that they've caught most cases. It's wishful thinking to believe the infection fatality rate is an order of magnitude lower.

It is not plausible they caught most cases. Here's the result of randomized testing in Iceland, which also has the virus under control and has done even more testing per capita ( https://www.nejm.org/doi/full/10.1056/NEJMoa2006100?query=fe... ) Randomized testing was still finding 0.6% of the population (outside those otherwise quarantined already) actively infected. This means even in Iceland, less than half of infe…

Half of Iceland's population lives in the Reykjavik area. The rest are thinly spread out over the country - which of which is still inaccessible due to ice (usually until April/May). Comparing this to a densely populated South Korea is incredibly difficult.
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