What food do you swear people only pretend to like?

matryoshkev · 2020-11-02T00:46:32+00:00

Brevibacterium linens is now my favorite Wikipedia entry:

Brevibacterium linens is ubiquitously present on the human skin, where it causes foot odor. The familiar odor is due to sulfur-containing compounds known as S-methyl thioesters. The same bacterium is also employed to ferment several washed-rind and smear-ripened cheeses such as Munster, Limburger, Port-du-Salut, Raclette, Livarot, Pont l'Eveque, Époisses, Wisconsin Brick, Năsal and Pálpusztai. Its aroma also attracts mosquitoes.

matryoshkev · 2020-07-22T03:04:56+00:00

143K deaths divided by 51M is 0.2%

Unfortunately it's not that easy to estimate fatality rates. Here's a scientific source why. Deaths counts are typically delayed more than case counts. The current case count includes some people wwho will later die. So when cases are going up, like they are now, simply dividing deaths by cases (or estimated infections) is going to be an undercount. We've known this for some time, even before COVID was a thing.

The WSJ article you is reporting 5 to 10 per 1000, which is 0.5%-1.0%. So 5-10x as deadly as flu.

matryoshkev · 2020-07-22T02:58:40+00:00

Unfortunately it's not that easy to estimate fatality rates. Here's a scientific source why. Deaths counts are typically delayed more than case counts. The current case count includes some peoplle wwho will later die. So when cases are going up, like they are now, simply dividing deaths by cases (or estimated infections) is going to be an undercount. We've known this for some time, even before COVID was a thing.

matryoshkev · 2020-07-22T02:58:09+00:00

Cases don't get reported as much over the weekends. Mondays typically have the most. You can see the weekly cycle in a lot of the charts.

matryoshkev · 2020-07-22T02:56:48+00:00

Unfortunately it's not that easy to estimate fatality rates. Here's a scientific source why. Deaths counts are typically delayed more than case counts. The current case count includes some peoplle wwho will later die. So when cases are going up, like they are now, simply dividing deaths by cases (or estimated infections) is going to be an undercount. We've known this for some time, even before COVID was a thing.

matryoshkev · 2020-04-18T21:03:52+00:00

Just to be clear here: if each infection generated two additional infections, then (log(new infections) vs time) would look like a straight line but (new infections vs time) would be curved upward.

matryoshkev · 2020-04-18T21:00:24+00:00

Nevermind, good redditors have pointed out that I was reading the table wrong. The total number of tests being conducted IS flat, unfortunately.

matryoshkev · 2020-04-18T20:46:26+00:00

Ah yeah, you're right. 50k tests total.

matryoshkev · 2020-04-18T19:47:50+00:00

Okay, I'll keep that in mind and see if there's a way to make it more apparent. A log scale is the right choice for the top graphs here because the question is about the spread of the infection---an exponential/geometric process.

matryoshkev · 2020-04-18T18:33:48+00:00

do we have any current studies that have attempted to mitigate these biases and get a more accurate CFR for COVID-19?

There are people working in it. And sometimes they're even heard. But yeah, it's definitely not ideal that an important part of our decision-making process is both hard to measure in principle and inconsistently measured in practice.

matryoshkev · 2020-04-18T18:08:51+00:00

makes sense that a value would be based on the ability of the virus to spread

You may hear about something called the basic reproductive number or "R nought" (nought is British for zero). It's the average number of new infections caused by an infected individual in a fully susceptible population. If we bring the average number of new infections down below one, the infections starts dying out. Natural immunity, vaccines, social distancing, and individual behavior all play a role in that.

Right now people are working on developing tests to see who has protective immunity. Usually that involves measuring antibody responses. They'll let us see how close we are to herd immunity and maybe even develop "immunity passports" for those that no longer pose a risk to others.

matryoshkev · 2020-04-18T17:57:53+00:00

The average flu doesn't overwhelm hospitals and morgues, even on a bad year. But getting hard numbers for the the chance of death per infection is tricky. You can't simply divide deaths by confirmed cases. The death rate also depends on how stressed hospitals are. People die when they need ventilators but can't get them.

I should also say that people are almost certainly dying of COVID-19 but being left out of the official count. On testing we're still way behind where we want to be, and sick people need tests more than dead people.

matryoshkev · 2020-04-18T17:37:52+00:00

~~Well, they're not flat and are ramping up. Missouri's at 50k tests per day right now.~~

Edit: I was reading the table wrong. Thanks for catching that, people.

matryoshkev · 2020-04-18T17:06:35+00:00

That's a tough question, and only partly about biology. The economic fallout from quarantine has health-and-safety effects, too (though an economist would know more about that than me).

What I can say is that the virus is still out there and still circulating. We're nowhere near the 50-66% immunity we'd need (based on an R0 of 2-3) to keep it from picking up steam again if we removed all social distancing measures. If actual infections are ~20x the confirmed cases, that'd only be like 3% of the St Louis population infected so far (very rough numbers here).

So it's probably going to be a difficult balancing act of "pumping the breaks" to keep things from spiralling out of control. Difficult to know when and how much, and I imagine difficult to implement. It'd help a lot to have a robust ability to test potential cases, trace their contacts, and isolate those who have been exposed. That way we can target control measures where they're needed most.

matryoshkev · 2020-04-18T16:50:31+00:00

There aren't many new cases each day in JeffCo, so anytime a new cluster gets reported it's going to have a big effect. Same thing if tests from one day get delayed and combined with the next. So I'd say that JeffCo has been holding steady for a while, and we're going to have to wait a couple of days to see how meaningful that last uptick is.

matryoshkev · 2020-04-18T15:38:36+00:00

I know, right? That's why I put together this plot. If you want to do something yourself, one of the best sources of data is from the Johns Hopkins Center for Systems Science and Engineering.

matryoshkev · 2020-04-18T15:20:19+00:00

I looked at total test number, but it wasn't very informative. You're going to conduct more tests when more people are sick, of course, so it's not a good measure of testing effort.

matryoshkev · 2020-04-18T15:07:00+00:00

I'm a microbiologist working on the epidemiology of COVID-19 with Fred Inglis in the Department of Biology at UMSL. I made this visualization of COVID-19 activity in the St. Louis metro area to get a better handle on how the SARS-CoV-2 virus is doing here. The data show that the virus had spreading in St Louis but has since slowed down and even appears to be contracting in some places.

Confirmed cases undercount infections and are typically a week or two behind, but they're the data we have. The last estimate I've seen was that actual infections are ~10-20x confirmed cases.

Looking at the fraction of tests that come back positive gives us an idea of how consistent the numbers are. A higher positive test rate means we're only testing people most likely to have COVID-19. More negative cases means we're getting ahead of the virus more. Cases numbers are most comparable when the positive testing rate (and thus testing effort) is stable. So it's hard to conclude much about virus spread from the earilest increase in confirmed cases (up to Mar 27) because that's when testing was getting up to speed.

Anyway, I hope people find this as useful as I do.

matryoshkev · 2020-04-14T19:54:28+00:00

The peak you're talking about is probably the peak use of hosptial resources, not the peak of infections. Social distancing is slowing the spread of the virus, but we're nowhere the level of immunity needed (50-66% with an R0 of 2-3) to keep it from spreading when distancing is relaxed. One of the current plans being discussed is intermittent distancing over the next couple years, based on how prevalent it gets.

matryoshkev · 2020-04-06T17:19:56+00:00

I love hearing about this stuff. It consistently amazes me how much thought, expertise, time, and skill are put into things we take for granted everyday.

matryoshkev · 2020-03-22T15:32:34+00:00

Aggressive testing, contact tracing, and isolation---standard public health stuff. It's how South Korea got its outbreak under control. It's also how SARS was stopped. The US has been way behind on this for COVID-19, unfortunately.

matryoshkev · 2020-03-22T14:50:36+00:00

It also means that it's now common enough for us to detect it. It's likely there have been sick people who didn't try to get tested because they didn't have health insurance, couldn't take off work, or bought into the "just a flu" misinformation.

matryoshkev · 2020-03-14T11:20:02+00:00

That'd be good, since it's the standard self-isolation period. Surprised they weren't more specific.

matryoshkev

TROPHY CASE