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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

#11

Post by jandrese »

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.…

Everybody knows this, but the US healthcare system was so unprepared for this that there simply weren't (aren't) enough test kits around to do a proper study. Even people who have the symptoms struggle to find a place that will test them in some cities.

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

#12

Post by drtillberg »

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…

There are several variables here but it's also important to keep in mind that the 36% positive rate in this cohort presumably does not include people who had the virus and recovered.

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

#13

Post by goatsi »

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…

Or the majority were presymptomatic. They don't give a timeline of how long after the first cases in the cluster were detected that the testing took place, so these individuals might have been in the first week of the infection.

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

#14

Post by jlmorton »

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 only those with severe symptoms. Even limiting our sample to people presenting with severe matching symptoms of COVID-19, we're finding ~20% PCR-positive for SARS-CoV-2.

Beyond that, we also have good evidence that the Basic Reproduction Number is somewhere between 2-3. Given a seeding of cases in mid-to-late January, even without social distancing measures, it would be unlikely to have 10% of the population infected yet.

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

#15

Post by raincom »

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.…

In the developing countries without universal health care, there are government health workers, who are into vaccination, prevention, etc. In situations like this, these workers are mobilized for random testing. However, in the states, I don't see such a workforce. It is mostly done by volunteers, such as that Stanford drive in testing.

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

#16

Post by gnulinux »

drtillberg wrote: post #12
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…

There are several variables here but it's also important to keep in mind that the 36% positive rate in this cohort presumably does not include people who had the virus and recovered.

A Diamond Princess ex-passenger died as late as March 24. The first patient was tested positive on February 1, and the ship was quarantined on Feb 4, and everyone left the ship on March 1. It doesn't seem unlikely you can die from this virus a month (or even two months?) after testing positive. Or maybe I'm missing something?

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

#17

Post by smallgovt »

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 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 that 10 were positive -- a 2% infection rate. The standard error (binomial approximation) for this sample is 0.6%. So, by doing a mere 500 randomized tests, we have a 95% confidence interval of 0.8%-3.2%.

Given that overall population infection rate is so important in planning for re-opening, why are we not doing randomized testing in hotspots like NY on a regular basis? Am I missing something?

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

#18

Post by raphlinus »

gnulinux wrote: post #8
easytiger wrote: post #5

Earlier quoted context omitted.

Yup. And for far longer.

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.

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

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

#19

Post by sjg007 »

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.…

It's probably low prevalence in the population based on our understanding of when covid-19 first appeared.

The UK has some randomized seriological surveillance and it's about 13% prevalence. That matches with the pregnancy study of 15% prevalence (which may be enriched due to hospital visits).

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

#20

Post by Retric »

gnulinux wrote: post #8
easytiger wrote: post #5

Earlier quoted context omitted.

Yup. And for far longer.

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 top of that it’s spread rapidly across every country outside of China and there uncontrolled growth rate showed a similar doubling every few days.

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