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Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by xyhopguy on Monday May 11, 2020 @03:43PM (#23146128)
people say that because .25% of the population in NYC are dead from covid. we dont see those numbers here -- if it was widespread in feb, what caused the discrepancy?
Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by 013a on Monday May 11, 2020 @06:19PM (#23147799)
While it's harsh to say: People die every day. The CDC officially states that, on average, ~880 people per 100,000 die every year in the United States (in 2017). Extrapolating that to NYC, this means that the city can expect to loose about 0.1% of its population every year (possibly even more; I imagine some forms of death are more prevalent in large cities. Possibly less; healthcare is better).

Yes, losing 2x+ the annual number in one quarter should be noticed. But, maybe the virus evolved additional transmissibility over time, or maybe it evolved to be a little more deadly.

It simply seems less likely that this virus was first noticed in November, by China, yet it didn't hit major urban areas in the rest of the world for another four months. We're too interconnected as a species; nearly half a million people came to the US from China alone, after COVID-19 was classified there [1]. It feels more likely that people have been getting it, and dying from it, well before March; these cases were just simply miscategorized as the flu.

[1] https://www.nytimes.com/2020/04/04/us/coronavirus-china-trav...

Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by jrockway on Monday May 11, 2020 @04:26PM (#23146601)
I guess we need to know the total number of cases to figure out what the deaths mean, and until everyone has gotten an antibody test, we can't know that total number.

To make the numbers work for the "weird cold" in early February case, I guess we have to work backwards. Assume that when we went into lockdown was the actual peak, 8 million people in New York City had COVID-19. That means that there is one death for every 500 cases. Then we have to pick a reproduction rate, which I have no idea how to pick, so I'll say that it increases by 1.5x every day (so on day one you have x cases, then on day 2 you have x + 1.5x, then on day 3 you have x + 1.5x + (1.5)^2x, etc. Going back a month from March 20 (which is approximately 30 days, and when a lot of people report their "weird cold"), that would mean we'd expect around 8 million / 383500 = 20 cases on Feb. 20. With 1 death per 500 cases, you'd have 0 deaths at that level.

I know I've pulled these numbers out of my nether region and so they are likely very wrong. But with some back-of-the-envelope math, I think we can have some sick people in February without a lot of deaths.

Obviously my 8 million total cases in NYC number is too high, and the 20 cases on 2/20 is too low for me and my friends to be those cases. But that exponential can be tweaked to make something plausible. If we make it 1.2 instead of 1.5, then we should have had about 7000 cases on 2/20, and that means around 14 deaths. That seems quite plausible to me. So I dunno. There was a weird cold. It's weird. It could mean anything.

I signed up to get an antibody test. 1 test is not data, but it will be very interesting to see the results.

Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by Izkata on Tuesday May 12, 2020 @10:49PM (#23162930)
> Then we have to pick a reproduction rate, which I have no idea how to pick, so I'll say that it increases by 1.5x every day (so on day one you have x cases, then on day 2 you have x + 1.5x, then on day 3 you have x + 1.5x + (1.5)^2x, etc

> I know I've pulled these numbers out of my nether region and so they are likely very wrong. But with some back-of-the-envelope math, I think we can have some sick people in February without a lot of deaths.

Yeah, in two ways: That's not how the growth rate math works, but if we went by your math instead of the number, that's about 4-5x faster than what we were seeing in March.

A growth rate of 1.5 means if we had X cases on day 1, we'd have X(1.5^1) on day 2, and X(1.5^2) on day 3. This virus's growth rate at the beginning of the pandemic stage was around 1.4 (or to use your math, 0.4? I'm not sure what you meant by "(1.5)^2x", is that a typo of "(1.5^2)x" or did you mean 1.5^(2x)"? The second one is straight wrong).

Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by not2b on Monday May 11, 2020 @06:33PM (#23147950)
1 out of 421 NYC residents have died, based on today's numbers, and recent serological tests estimated that 20% of residents were exposed. If that's right, then the death rate would be about 1/84, or about 1.2%. But I've seen other claims that the exposure rate in NYC is higher, which would give a lower fatality rate.
Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by taeric on Monday May 11, 2020 @09:49PM (#23149706)
Don't forget to factor this breaking through to long term care facilities. From the last I looked at this, if it had not hit long term care, the number of deaths would have been low enough that it may have gone undetected longer. (In WA, 92% of the deaths are still folks over sixty! I don't know the numbers for how many of them were in long term care.)

Which is to say, you can't just look at the population death rate and really appreciate just how dangerous this is for older populations. The CFR for over sixty is a staggering 15% in WA. That is ridiculously high and completely masked if you look at all cases.

Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by postingawayonhn on Tuesday May 12, 2020 @02:09AM (#23151001)
> Don't forget to factor this breaking through to long term care facilities.

If they're not taking any precautions (because there's no knowledge of the virus in the community) then it can spread to those types of facilities very easily. In New Zealand where only 1,500 people have have COVID-19 (likely to be very accurate, 200,000 tests have been conducted) there's already been two outbreaks in nursing homes.

Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by taeric on Tuesday May 12, 2020 @09:22AM (#23153677)
Certainly. I am not implying that we should just let it run its course. Just as I would not let any disease we have a vaccine for loose in a nursing home without the vaccine.

I just think the total IFR actually undersells how dangerous this is.

Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by raducu on Tuesday May 12, 2020 @02:56AM (#23151204)
A friend of a friend got released from the hospital, she had covid-19 and was searching for an oxygen concentrator for her (permanent?) lung damage.

She's 29 and otherwise healthy. I'm sure we would have noticed this disease without the high mortality rate among the elderly.

Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by taeric on Tuesday May 12, 2020 @09:20AM (#23153661)
I'm sure we would have noticed. I'm not sure we would have noticed as quickly. We certainly would not have tested to find that nearly a quarter of NYC could have it.

Yes, it can do damage and is very dangerous for an at risk group. No, we don't know who that is, yet. Age clearly proxies for a risk factor. But which one?

Unless you are wanting to claim that no children have gotten this. Which, seems highly unlikely. (Or is the risk whether it will provoke an immune response?)

Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by nitrogen on Monday May 11, 2020 @08:40PM (#23149282)
If I'm interpreting this[0] right, it looks like the normal death rate is 3.51 per 421 people per year. 1/421 in NYC (is that just COVID cases or all excess deaths?) is over much less than a year, so it seems fairly serious.

But I also had a truly "weird cold" go through my workplace early this year in SFBA, so I still have to wonder what that was.

[0] https://www.wolframalpha.com/input/?i=us+death+rate+*+421+pe...

Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by drran on Tuesday May 12, 2020 @02:31AM (#23151086)
Average death rate is 1/65-1/80 per year, or 1.5-1.2%, depending on country life expectancy.
Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by xyhopguy on Monday May 11, 2020 @05:56PM (#23147580)
That's a great point although obviously its very hard to estimate something that has a horizon of atleast a month. the bay area did shut down quite a bit earlier, it could be that the lack of deaths is simply due to a better response.
Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by MarkusQ on Monday May 11, 2020 @05:19PM (#23147213)
> people say that because .25% of the population in NYC are dead from covid

Source? I can only get a rate that high by taking the highest death count I can find (which involves extrapolations to attribute deaths to Covid-19) for New York State and dividing it by the population of New York City (which is clearly invalid).

Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by not2b on Monday May 11, 2020 @06:29PM (#23147900)
From https://www1.nyc.gov/site/doh/covid/covid-19-data.page I compute 0.23% of NYC's population has died of Covid-19, counting confirmed + probable deaths and dividing by 8.399 million people. That's 1 out of every 421 people.
Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by xyhopguy on Monday May 11, 2020 @05:53PM (#23147546)
hm, care to explain more? that's exactly how I think about it. Total deaths in NYC attributable to covid (~20k) over the total population (8.5M) = ~.25%. In my mind this is a very easy lower bound to estimate, what am I missing here?

In anycase, even a rate of ~.1% would be absurd given ~20% of people are testing positive by antibody tests.

Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by MarkusQ on Monday May 11, 2020 @06:32PM (#23147931)
Actually, I was asking <i>you</i> to explain, or at least give your source.

I subsequently found what I believe you are working from here: https://www1.nyc.gov/site/doh/covid/covid-19-data.page which does specify New York City (as opposed to New York State) so both the numerator and denominator refer to the same thing.

Interestingly, they appear to be using a larger denominator than your 8.5 million (NYC metro vs. NYC proper perhaps?) and get a rate of 0.175% = 175.66/100,000, eg in the "citywide total" line of https://github.com/nychealth/coronavirus-data/blob/master/by...).

But this is at least closer to your figure than I was able to get previously.

Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by xyhopguy on Monday May 11, 2020 @09:37PM (#23149640)
whoops, I presumed you were asking about the math. My source is nytimes which pulls from the dataset you linked.

https://www1.nyc.gov/assets/doh/downloads/pdf/imm/covid-19-d...

Specifically has numbers for NYC. You can sum the boroughs or use the total listed below. Using confirmed by pcr cases you get ~15k/8.6 = ~.175% as you said.

Using probable excess deaths adds an extra 5k deaths, hence ~.25%

Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by weaksauce on Monday May 11, 2020 @04:16PM (#23146506)
different strains?
Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by xyhopguy on Monday May 11, 2020 @05:51PM (#23147527)
afaik there havent we havent observed major functional mutations in the virus
Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by sanxiyn on Monday May 11, 2020 @07:07PM (#23148327)
We haven't confirmed functional mutations. One of currently known mutations (D614G being a prime suspect) can be functional and we can't rule out the possibility.
Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by weaksauce on Monday May 11, 2020 @06:08PM (#23147700)
The Strain that was seen in ny was more deadly than the strain seen on the west coast. And I’m not sure how many others are out there.
Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by xyhopguy on Monday May 11, 2020 @06:13PM (#23147748)
they have a different lineage, but as I stated previously, no major functional mutations were observed.
Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by arcticbull on Monday May 11, 2020 @07:53PM (#23148869)
We don't yet know why (or even if) more people died in New York than on the west coast, per capita. We certainly cannot yet attribute it to a different strain.
Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by christkv on Tuesday May 12, 2020 @02:14AM (#23151021)
You want to use the word isolate. The SARS2 virus is a strain of the original SARS virus I think
Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by elorant on Monday May 11, 2020 @04:41PM (#23146796)
Viruses tend to become less lethal as time passes, not more.
Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by risaacs99 on Monday May 11, 2020 @05:05PM (#23147070)
I keep reading people asserting this, and I assume it's because we believe that a virus that becomes less lethal would have an evolutionary advantage.

But, wouldn't lengthening the incubation period also be a successful evolutionary strategy regardless of lethality?

It seems to me that there are many possible strategies that a mutating virus might gain an advantage and we shouldn't just assume that the only one that they would use would be to become more mild.

Luckily, sars-cov-2 seems relatively stable.

Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by guscost on Tuesday May 12, 2020 @10:58AM (#23154689)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4873896/

> Trade-offs between different components of parasite fitness provide the dominant conceptual framework for understanding the adaptive evolution of virulence (Alizon et al. 2009).

...

> By far, the most widely studied trade-off involves transmission and virulence (Anderson and May, 1982; Frank, 1996; Alizon et al. 2009). Transmission and virulence are linked by within-host replication: increasing parasite abundance increases the likelihood of transmission, but also increases the likelihood of host death; mathematically, this assumption can be formalized by making transmission rate β an increasing function of parasite-induced mortality rate ν. Nearly all of the literature we summarize below assumes this trade-off. However, another potential trade-off suggested by an examination of R0 involves virulence and recovery rate (Anderson and May, 1982; Frank, 1996). This trade-off is also mediated by replication rate, with high abundance increasing the likelihood of host death, but also decreasing the likelihood of the host clearing the infection (Antia et al. 1994); mathematically, this assumption makes recovery rate γ a decreasing function of parasite-induced mortality rate ν.

Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by saiya-jin on Monday May 11, 2020 @05:39PM (#23147418)
'Tend to' doesn't mean some conscious, directed effort. On large enough scale, this is generally the more probable direction, and that's about it. Its truly random by nature.

It can very well go the other way as with 1918 'spanish' flu. Or it can change in ways that won't affect overall mortality much.

Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by Filligree on Monday May 11, 2020 @10:32PM (#23149990)
It's interesting you should mention the 1918 flu. That one had two waves, the first one less lethal... Evolution is random, add you say, but that's not quite what happened.

It was in the middle of world war 1. Soldiers were infected, and the ones that became the most ill were sent home to recuperate, or die. Either way they spread the virus better than the ones who weren't as ill, and who stayed in the field.

So the usual evolutionary pressure was upside down here.

Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by arcticbull on Monday May 11, 2020 @07:54PM (#23148880)
> On large enough scale, this is generally the more probable direction, and that's about it. Its truly random by nature.

If it's truly random it wouldn't be directional, yeah?

Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by jjjensen90 on Tuesday May 12, 2020 @02:51AM (#23151181)
The genetic mutations are random, the survival of a lineage based on pressures and fitness can be "directional" by the human definition.
Re:New Abbott SARS-CoV-2 antibody test has 99.90% specificit... by Natsu on Monday May 11, 2020 @06:38PM (#23147979)
You're neglecting the other side of things in that analysis. The more successful deadly viruses tend to eliminate their victims, so the surviving population has a higher concentration of people who are resistant or immune to it, including those who acquire immunity after being exposed to the virus.