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Covid-19 Antibody Seroprevalence in Santa Clara County, California

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Re: Covid-19 Antibody Seroprevalence in Santa Clara County, California

#111

Earlier quoted context omitted.

It's known that the vast majority infected do not experience symptoms, or have mild symptoms. I don't think you can draw the conclusion that they had prior immunity.

Most of what I've seen suggests that at time of positive test results, 40% to 70% of people have not experienced symptoms. Have you seen numbers very different from that? [Edit: 'No symptoms experienced at time of positive test results' is intended to mean the same as 'no symptoms experienced yet at time of positive test results'.]

That can't be true for the official confirmed numbers.

Like, it was for a while impossible to get a test if you are not experiencing multiple symptoms AND can make a case that you might have been exposed via interacting with someone who has traveled. Even now I don't think they're giving the test if you don't have a fever. It's implausible that 50% of the people tested by the official pathway had no symptoms because the official pathway is not available when you have no symptoms.

But if you mean that you've seen a 50% "asymptomatic transmission" rate, in other words studies like this that purport to test a bunch of people at random and see how many of them have COVID-19, note that this definition of "asymptomatic" may include many with symptoms not severe enough to be hospitalized -- in other words they might have been feverish and coughing but not moreso than a typical cold. I myself have had a really nasty cough but it is not "dry" but "productive" and it has not come with a fever -- I would really love to be tested but right now that does not seem to be possible! Maybe I am in this above grouping of "asymptomatic" folks.

The OP article suggests that as many as 98-99% of cases might not involve hospitalization and therefore might be cases like mine (assuming I do indeed have COVID-19, maybe I don't). Now it is likely that there is some sort of selection bias in how they recruited candidates, but still it tends to push that number above your high end of 70%, suggesting maybe it's closer to 80 or 90%. On the other hand while the paper says that it did its due diligence subtracting out the test's false-positive rate, a rather small error here can have a big impact on that number because there are so few true positives right now.

In some ways the paper's claim is a bit of good news, it means that this disease has much lower mortality than we were originally told. (There may be lower bounds on mortality -- I have heard of one town in Italy where 1% of its population is gone due to COVID-19 in which case that would seem to be a good lower bound.) In other ways it is bad news, it means that this disease, still with nontrivial mortality, is going to be much less affected by quarantine countermeasures and the social distancing stuff is really the only reason it is spreading as slowly as it is, so that we need to endure the pain of isolation for much longer -- potentially until testing becomes widespread and cheap.

That may not be too much longer, as mentioned in a previous HN comment/story [1] that if you can get testing to work with the old Sanger sequencers used in the Human Genome Project you can maybe ramp up to 200,000 samples/day at first with possibilities to go up to 1M/day once you solve additional logistical problems. Before that the production of kits and sourcing of reagents may be your limit.

[1] https://news.ycombinator.com/item?id=22808208

Re: Covid-19 Antibody Seroprevalence in Santa Clara County, California

#112

There are now multiple sources of evidence pointing to a very low true infection fatality rate, as low as 0.1% in some regions. Iceland has been testing a semi-random sample using PCR since early in the epidemic, and there have been several small antibody surveys in “hot spots” showing infection rates over 15%. You can also use CDC surveillance of flu-like illnesses to estimate the total number of infected nationwide…

How do you square this with 0.14% of all of NYC and 0.25% of all of Bergamo county being dead from confirmed Coronavirus? Surely this puts a strong lower limit on IFR.

Deaths in both places can only increase and deaths will inevitably be retroactively assigned a Coronavirus cause.

Re: Covid-19 Antibody Seroprevalence in Santa Clara County, California

#113

Earlier quoted context omitted.

It's known that the vast majority infected do not experience symptoms, or have mild symptoms. I don't think you can draw the conclusion that they had prior immunity.

Most of what I've seen suggests that at time of positive test results, 40% to 70% of people have not experienced symptoms. Have you seen numbers very different from that? [Edit: 'No symptoms experienced at time of positive test results' is intended to mean the same as 'no symptoms experienced yet at time of positive test results'.]

Have not experienced symptoms yet. I haven't seen any information about testing people and then following through until a negative test, to see whether they stay asymptomatic. It's more likely that we're testing them in the window between being infected and showing symptoms.

Re: Covid-19 Antibody Seroprevalence in Santa Clara County, California

#114

"Participants were recruited using Facebook ads targeting a representative sample of the county by demographic and geographic characteristics." How is it representative when it's only Facebook users in this sample?

Unless you think FB users for some reason would be infected at significantly different rates, that shouldn't be much of a problem. I'm much more concerned about selection bias toward prior sick people; IIRC, Stanford offered to report positive results to the patient.

There would potentially be an age bias, though probably less in FB than a lot of other services you could cherrypick from. It'd also arguably bias older, since FB has been aging up in audience from what I can tell.

Without reading the study, though, possible they actually controlled that in the demographic profile for the ad.

Edit:

Going to the other thread confirmed this. From the paper,

"This study had several limitations. First, our sampling strategy selected for members of Santa Clara County with access to Facebook and a car to attend drive-through testing sites. This resulted in an over-representation of white women between the ages of 19 and 64, and an under-representation of Hispanic and Asian populations, relative to our community. Those imbalances were partly addressed by weighting our sample population by zip code, race, and sex to match the county. We did not account for age imbalance in our sample, and could not ascertain representativeness of SARS-CoV-2 antibodies in homeless populations. Other biases, such as bias favoring individuals in good health capable of attending our testing sites, or bias favoring those with prior COVID-like illnesses seeking antibody confirmation are also possible. The overall effect of such biases is hard to ascertain."

Re: Covid-19 Antibody Seroprevalence in Santa Clara County, California

#115
post #91

Earlier quoted context omitted.

Not concluding prior immunity but concluding that they now have immunity after having been infected. That is in progress towards herd immunity this number of people actually infected being revealed by these antibody studies is what is interesting. And based on my hacky heuristic described above that is currently around 2.6%. So we are still a long way off herd immunity. But at the same time closer than we thought we…

> So we are still a long way off herd immunity. But at the same time closer than we thought we were. Yes and no. A disease is endemic when R0 x S = 1 [0]. R0 for SARS-CoV-2 is estimated to be 2.5 to 3.5 and some models predicting a much higher 5.7 [1]. The herd immunity threshold is given by (1 - S)% , which implies when R0 = 2.5, 60% of the population would need to be immune; similarly 71.42% and 82.45% for R0 s, 3.…

What percentage of immunity can we expect to see a slowdown in the spread of the disease? While we may need 60% or more to achieve full herd immunity surely somewhere lower than that we can expect to see a noticeable reduction in the spread?

Re: Covid-19 Antibody Seroprevalence in Santa Clara County, California

#117
post #82

I don't see anything about sampling bias here. I would assume that people who have been ill, experienced mild symptoms, or who were exposed to confirmed cases would be more likely to respond to the facebook ads recruiting testing volunteers. I'm sure we are significantly undercounting cases but I highly doubt we are off by a magnitude of 50x.

I know. 50-85x is hard to believe. How could we be that far off?

It's impossible to believe. Currently, Santa Clara's crude CFR is 3.7%.

NYC has similar demographics (and as bad nursing home hits?) -- 0.14% of the population has died from covid. That puts an upper bound of 26x (and that's if the entire population was infected)

Re: Covid-19 Antibody Seroprevalence in Santa Clara County, California

#118
post #20

I made this comment the last time a serological testing study came out: they have 30 negative controls and claim 1.5% positives among their tests. So the number of controls is insufficient to rule out this being entirely false positives. You have to then rely on the test manufacturer's claims of false positives rates, which comes from 371 negative controls. They say: > our estimates of specificity are 99.5% (95 CI 98…

To repeat you in plainer English: the serum test isn't infallible and reports "infected", incorrectly, for uninfected patients. It does this at some rate that is very near, or perhaps larger than, the fraction of "true" infected patients they report in their results.

Teasing out data from all that noise requires that the false positive error rate be measured very accurately. And they didn't do that, so really this doesn't tell us much.

Edit: Alternatively, borrowing jargon from a more common field around here: the measured infection rate of ~3% is very close to the noise floor of the experiment. It might be that, or it might be near zero, and we can't tell the difference. This study is very good evidence that the infection fraction is not much larger, however. We can easily rule out high infection rates like the 30% numbers that seems to get thrown around.

Re: Covid-19 Antibody Seroprevalence in Santa Clara County, California

#119

Saw this comment [1] on Reddit that outlines the limitations of the study well: This is the most poorly-designed serosurvey we've seen yet, frankly. It advertised on Facebook asking for people who wanted antibody testing. This has an enormous potential effect on the sample - I'm so much more likely to take the time to get tested if I think it will benefit me, and It's most likely to benefit me if I'm more likely to h…

It’s better to have data and know its limitations, than not to have data at all.

Re: Covid-19 Antibody Seroprevalence in Santa Clara County, California

#120
post #14

There are similar high infection rates from other semi-randomized samples. https://www.nejm.org/doi/full/10.1056/NEJMc2009316 > Between March 22 and April 4, 2020, a total of 215 pregnant women delivered infants at the New York–Presbyterian Allen Hospital and Columbia University Irving Medical Center . All the women were screened on admission for symptoms of Covid-19. Four women (1.9%) had fever or other symptoms of…

NYC has 30x the per capita death rate of Santa Clara county. Santa Clara county only being 15% as infected is not consistent.

What if there are other, undiscovered factors that could explain the difference? Such as NYC populace having had exposure to some other virus that predisposed them to a greater vulnerability. Or perhaps, air pollution exposure predisposing them to greater vulnerability.
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