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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

#121

Post by [deleted] »

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.

[deleted]

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

#122

Post by casefields »

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.)

"I am realizing more and more how unusual, unscientific, unmedical, and counterproductive it is for WHO to select the name #COVID19 and reject SARS2. In fact it would be most consistent with medical practice to just call it SARS. Here's why..."

https://threadreaderapp.com/thread/1245791851342229504.html

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

#123

Post by gridlockd »

gns24 wrote: post #68
gridlockd wrote: post #51

Earlier quoted context omitted.

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.

It's worth noting that the German study in Gangelt was done because it was considered a hot-spot - this wasn't an attempt to estimate the infection rate across the country. It does however demonstrate that even in places where lots of people have had it, herd immunity still looks a long way off.

It is worth noting indeed.

However, if we apply the estimated mortality rate (0.37%) based on that to 11500 deaths in hot-spot New York, it would amount to over 3 million cases, again roughly 15% of the population.

Now perhaps Germans are so much healthier and their healthcare is so much better, making their real mortality rate so much lower. It's all speculation at this point, either way.

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

#124

Post by LatteLazy »

nkohari wrote: post #120
LatteLazy wrote: post #115

Earlier quoted context omitted.

I'm never clear what asymptomatic means in this context. Does it mean the period for which a patient is infectious before they become symptomatic? Or do some people never become symptomatic? And if it's the second, do they cease to be infectious like symptomatic individuals after a time? Or are they infectious long term (aka carriers)?

Asymptomatic means the person had no symptoms at the time of the test, and possibly never developed symptoms. They could also have been presymptomatic , in which case they subsequently developed symptoms after the test. This study didn't do any follow-ups to differentiate.

>presymptomatic

That makes sense and that's a useful word, thanks!

I've heard it takes about a week before you get symptoms and then they last for 2 days on average. So even if everyone developed symptoms only 22% of people with the disease would have symptoms on a given day...

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

#125

Post by MaulingMonkey »

pm_me_ur_fullz wrote: post #79
sjg007 wrote: post #24

Earlier quoted context omitted.

Because it's not true.

Why is that the most preposterous hypothesis that doesn't warrant any review? We have no reliable antibody tests, and then won't give the unreliable ones people because they are so rare. So where does the confidence come from that we can rule out this possibility? What if this is already the "second wave". Something with lower symptoms wouldn't have warranted checking for a new strain, complications and deaths would…

> Why is that the most preposterous hypothesis that doesn't warrant any review?

It's not. What is preposterous is advancing the hypothesis without any meaningful evidence, to the detrement of more useful topics, or even useful discussion of the same topic.

It's one thing to be an epidemiologist saying "hey, let's see how we can double check the exact origins of this", which is a potentially useful line of inquery. It's another to take some hypochondriac's third hand retelling of someone else's flu symptoms back in December and jump to the same untested unproven unscientific fear-driven conclusions they did on little more than their wild speculation. Even if they do somehow end up being right, they'll be right in the "broken clock is right twice a day" sense rather than a bringing anything useful to the table sense.

So far, alternative suggestions as to the virus's origins have looked more similar to the latter - with perhaps some undertones of (completely understandable and expected) attempted political diversion (I sure wouldn't want fault for this mess hanging on my neck!) If you have some epidemiologist's proposed study that you're trying to drive funding towards - something that even remotely looks like the former - it'd be a welcome breath of fresh air on the topic, and I'd suggest sharing that as a far more useful and constructive way of advancing the hypothesis.

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

#126

Post by gridlockd »

jsnell wrote: post #65
gridlockd wrote: post #51

Earlier quoted context omitted.

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.

It wasn't a study of representative German households, but just those in a Gangelt. A small town that was basically the ground zero for the epidemic in Germany. Those numbers do not generalize to Germany as a whole, let alone other countries. Also, the particular antibody tests they used appears to have a much higher FP rate than they claimed. Another study found 4% FPs rather than <1% like the press release for the…

It does generalize to my point, because we're talking about the basic reproduction number of the virus. It is not supposed to vary dramatically across populations.

If COVID-19 can spread to 15% of that particular population within that timeframe, and the estimate of a basic reproduction number of 2-3 predicts that this is not possible, then the estimate must be wrong.

> Also, the particular antibody tests they used appears to have a much higher FP rate than they claimed. Another study found 4% FPs rather than Perhaps, but that doesn't put much of a dent into the results.

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

#127

Post by usaar333 »

zzzzzzzza wrote: post #118
usaar333 wrote: post #112

Earlier quoted context omitted.

An average age of 59 on the Diamond Princess (1.8% CFR) is not representative of the general population. This is a substantially more at-risk group. Germany and Singapore are also missing many infections. A recent serological study in Germany actually argued for 0.4%. You are correct that IFR is skewed by who the population is and what interventions are done. But then again, so is the often cited flu benchmark (where…

https://www.reddit.com/r/medicine/comments/fyf0yh/megathread... you mean this serological study? And taiwan is at 1.5% CFR as well? And still 60 or so unresolved diamond princess cases with ~7 in critical condition?

Yes, I agree it is preliminary and not too much should be drawn off it.

Every country is missing large numbers of cases, so CFR doesn't mean much - randomized testing is what is needed.

Imperial College's paper (linked above which gives a 0.7% population IFR) uses Diamond Princess as an input. The relative risk ratio they give for someone age 70 (mean age on Diamond Princess) is something like 4.5x (IFR ~3%), so you'd natively guess about 80 deaths from the 2,666 passengers.

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

#128

Post by _euac »

wutbrodo wrote: post #119
sauwan wrote: post #48

Earlier quoted context omitted.

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…

> The Diamond Princess likely had a very atypical (older) population than the general population though. This would dovetail with the fact that places like sub-Saharan Africa and India haven't been hit very hard yet; they also happen to be _very_ young compared to Western countries.

I don't know if people are aware of this, but there's an increasing suspicion that countries still using the BCG vaccine for tuberculosis might be seeing [1]way lower infection rates.

If that's the case, it'd explain why developed countries are bearing the brunt of the pandemic. A very interesting example of similarly developed countries with comparable (but not equal) populations and population density, but different vaccination regimes are Portugal and Spain. Looking at their [2]respective [3]charts, the differences are stark. A similar difference can be seen between Ecuador and Argentina, even though the Greater Buenos Aires area is very population dense.

If this pans out, following the trends and [4] this map would validate that hypothesis.

[1]https://nypost.com/2020/04/14/coronavirus-death-rates-lower-...

[2]https://www.worldometers.info/coronavirus/country/portugal/

[3]https://www.worldometers.info/coronavirus/country/spain/

[4]http://www.bcgatlas.org/

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

#129

Post by Retric »

yters wrote: post #91
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…

what do you think about iceland?

Iceland’s peak was significantly more recent than China or South Korea which continued to have regular deaths over a month after their peak. So, my expectation is their deaths will likely double in the next three weeks. Which would be consist with ~1/2 their ICU cases dying. That said it’s a small sample size so significant variability is possible.

Just compare new cases vs new deaths here: https://en.wikipedia.org/wiki/2020_coronavirus_pandemic_in_S... vs new cases here: https://en.wikipedia.org/wiki/2020_coronavirus_pandemic_in_I...

On the positive side, they seem to have contained the virus extremely successfully which was likely aided by a low population density, early reaction, and good testing.

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

#130

Post by jimrandomh »

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…

It is very important to distinguish asymptomatic (does not have symptoms and will never develop them) from presymptomatic (does not have symptoms yet, because the test caught the infection sufficiently early). The people in this study are mostly presymptomatic, and will develop symptoms later.
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