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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

#51

Post by gridlockd »

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…

If you already have severe symptoms the PCR test from a throat sample is likely to give a false negative.

The BPR is estimated from the known cases, so it cannot tell you anything about a hypothetical large number of unknown cases.

Antibody tests in a recent German study of households gave 15% infection rate.

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

#52

Post by cgb223 »

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…

> In the US, we're now doing significant amounts of testing, but we're still primarily testing only those with severe symptoms

Its not a significant amount of testing if we're only testing those with severe symptoms

Here in SF at least there are scores of people I know who all were sick with a "weird flu" at some point from February to now who would all kill for a test to show that they have COVID immunity. These are people who could potentially go back into society and do more work / enjoy their lives instead of being shuttered inside with anxiety

It is currently _IMPOSSIBLE_ to get any kind of test to prove that

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

#53

Post by malpighien »

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.

It would be the test using QPCR to amplify the virus genomic material from samples collection. That test is a lot more specific though there can be issues with how the samples were obtained.

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

#54

Post by ksaun »

sauwan wrote: post #48
jlmorton wrote: post #14

Earlier quoted context omitted.

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…

The Diamond Princess likely had a very atypical (older) population than the general population though. The CDC is currently estimating an R0 of 5.7, which has likely been repressed by shelter in place orders. But even if it was only 4 before any interventions, there's still a chance there there are closer to 20M cases in the US rather than the 660,000 now. My point is just that there's still a lot we don't know, and…

Here is a reference for the R0 = 5.7 estimate: https://wwwnc.cdc.gov/eid/article/26/7/20-0282_article

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

#55

Post by MiguelVieira »

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…

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.

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

#56

Post by jlack »

drtillberg wrote: post #7
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...

The Boston Globe this morning ran an op-ed advocating testing a random sample of residents to get a better sense of community-wide infection rates.[1] It's amazing that this needed to be stated in a major market newspaper four weeks after most business and school was stopped due to the virus. Goverent is doing some interesting things, random sampling apparently isn't one of them, for reasons it's hard to understand.…

Random testing was performed in Johnson County(KS) over the weekend.

https://www.kansascity.com/news/local/article242010356.html

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

#57

Post by viklove »

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's really not that much, I would expect the infection rate in NYC to be anywhere between 10-20%, that makes sense given the numbers we're seeing in hospitals.

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

#58

Post by gowld »

kens wrote: post #34

Regarding the title "Covid+", it seems that most people (even on the news) don't care about the difference between SARS-CoV-2 (the virus) and COVID-19 (the disease). Is this distinction being abandoned? (I'm not trying to be pedantic here; I'm just curious about the common usage.)

"Covid+" was a tweet, not the research article.

As always, the distinction between two tightly bound things is not important when you talking about features common to both, such as which people have them.

Humans tend to migrate toward shorter more pronouncable, easier to type terms. Language evolves like a virus ;-)

https://www.merriam-webster.com/words-at-play/synecdoche-met...

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

#59

Post by throwaway_USD »

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…

>We already have lots of data that says this is not true... Longer term follow-up found ~25% of infections were asymptomatic.

Based on other available data the severity of the Covid symptoms are dependent on both the length of exposure and total exposure to the virus. A cruise ship with recirculated air likely means prolonged exposure to high concentrations of the virus that won't fit most other patients exposure.

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

#60

Post by raphlinus »

gowld wrote: post #47
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

That report appears to based on genomic analysis, which obviously only includes cases that were tested, not undocumented transmissions before the discovery. The article you cite says: "The common ancestor of circulating viruses appears to have emerged in Wuhan, China, in late Nov or early Dec 2019. Accordingly, the majority of sampled and inferred ancestral cases were located in Asia during this early period. "

It samples cases that are detected after the fact, from which they are able to reconstruct the phylogeny with impressive clarity. If you are not familiar with the work of nextstrain.org, I highly recommend it, they are brilliant.
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