Coronavirus Case Counts Are Meaningless* *Unless you know something about testing. And even then, it gets complicated.

fivethirtyeight.com ^ | Apr. 4, 2020 | Nate Silver

[daniel1212]

If you’re a regular reader of FiveThirtyEight, you’re probably used to looking at data in sports — where basically everything that happens on a basketball court or a baseball diamond is recorded — or in electoral politics, when polls (in theory, anyway) survey a random sample of the population. COVID-19 statistics, especially the number of reported cases, are not at all like that. The data, at best, is highly incomplete, and often the tip of the iceberg for much larger problems. And data on tests and the number of reported cases is highly nonrandom....

if you’re not accounting for testing patterns, it can throw your conclusions entirely out of whack. You don’t just run the risk of being a little bit wrong: Your analysis could be off by an order of magnitude. Or even worse, you might be led in the opposite direction of what is actually happening...

According to two recent epidemiological studies, which tried to infer the true number of infected people from the reported number of deaths, there is roughly a 20-fold difference in case detection rates between the countries that are doing the best job of it, such as Norway and the worst job, such as the United Kingdom. (The United States is probably somewhere in the middle of the pack by this standard.) That means, for example, that in one country that reports 1,000 COVID-19 cases, there could actually be 5,000 infected people, and in another country that reports 1,000 cases, there might be 100,000!..

According to an expert survey published by FiveThirtyEight, the number of detected cases in the United States could underestimate the true number of infected people by anywhere from a multiple of two times to 100 times. The same holds in other countries....

The not-so-simple math behind coronavirus testing...

The most important number in any epidemiological model is R, or the reproduction ratio...Assumptions about the R of COVID-19 vary ,...epidemiologists make a distinction between R0 (pronounced R-zero or R-naught), which is called the basic reproduction ratio, or how fast the disease spreads in the absence of any interventions or any immunity whatsoever, and the effective reproduction ratio, called R-effective or simply R.3...

There’s a lot of disagreement about these values — both how fast COVID-19 was spreading initially and how effective various interventions have been at lowering R. So you are welcome to download the spreadsheet at the end of this article and tweak those assumptions....

Another real-world problem is that the tests aren’t perfect. In fact, according to reporting by The Wall Street Journal on Thursday, around 30 percent of people who actually have COVID-19 test negative for it — which is what we’d call a false negative. Other estimates of false negatives aren’t quite so high , so I assume a 20 percent false negative rate in the scenarios.

Then, of course, there’s also the question of false positives, i.e., when a test reports that someone has COVID-19 but they actually don’t....

Even if false positives are rare, false positives may swamp true positives if the underlying incidence of a disease is low. Say, for instance, that in the early stages of an outbreak in a town of 100,000 people, 100 people or 0.1 percent of the population actually has the disease. If everyone gets tested, then there will be roughly 200 false positives (0.2 percent of the population) — larger than the number of people who are actually sick! This is why some of the discourse around false positive tests is confusing .

[daniel1212]

Excerpts of a very long and substantive article .

Another post to ponder: WITHDRAWN: Potential false-positive rate among the 'asymptomatic infected individuals' in close contacts of COVID-19 patients [discuss]

[daniel1212]

There are quite a few things to look at here. The most obvious and probably the most important one is simply that a 15-day delay between when someone gets infected and when their case shows up in the data as a positive test makes a huge difference.

Next, even with relatively good testing, you’re still likely to miss many cases.

There’s also a third issue: If testing is increasing, the rate of growth of a disease can be overestimated. Alternatively, if testing is stagnant or decreasing, the rate of growth can be underestimated.

More graphs: https://fivethirtyeight.com/wp-content/uploads/2020/04/silver.COVID-TESTING.0403-2.png?w=575 https://fivethirtyeight.com/wp-content/uploads/2020/04/silver.COVID-TESTING.0403-3.png?w=575

[RetiredTexasVet]

Probably the same geniuses that brought you the Climate Change Conspiracy model.

[daniel1212]

Probably the same geniuses that brought you the Climate Change Conspiracy model.

I think the author is showing deficiencies that should be readily acknowledged, and note "Meaningless" is with asterisks.

[neverevergiveup]

I think we are going to find that the false negative rate for the PCR-based testing are going to be at least 30%, and possibly more like 40%.

First, there is sampling error, because you are depending upon the virus being present in the nasopharynx or throat. It may not be, in some infected patients, AND even if it is, the technique used to obtain samples from these sites is likely to be of variable effectiveness (different people collecting the samples, different techniques, etc.).

Then, you have the vagaries of the reverse transcription and PCR amplification steps, and the possibility for patient specific sample conditions to alter their efficiency.

Yes, PCR is also susceptible to false positives, but that's a separate concern.

The bottom line is that we are really NOT tracking this very precisely - but that's the nature of dealing with a new viral threat.

[proxy_user]

There is one major flaw in the article. If everyone is self-isolating, there are likely to be many fewer cases of regular flu and colds, so the rate of false negatives may be higher than suspected. If you have only mild symptoms, you may be nearly recovered by the time you can have the test.

It would be interesting to take the people who got sick, but tested negative, and give them the CV antibody test when it becomes available.

[daniel1212]

It would be interesting to take the people who got sick, but tested negative, and give them the CV antibody test when it becomes available.

Yes, and there there is New research raises questions about coronavirus immunity: 6% of recovered patients in one study didn't develop antibodies at all . Figure that out.

[daniel1212]

The bottom line is that we are really NOT tracking this very precisely - .

Or reporting it comprehensively. What would be useful would be the percentages of tests per population, and the rate of of positive infections per tests per state, and per capita of total pop. and of deaths per infections and per capita of total pop.

[Paladin2]

Just shows that it pays to ramp up testing as quickly as possible and don’t stop ramping up.

No discussion of the second wave, but having the high volume testing in place for that event can only help to adjust the societal response to control the rate more appropriately.

[Paladin2]

Modeling the models can be instructive.

[Hieronymus]

Good for you for posting Silver. He does good work at tiimes, and I think this is some of it.

[Texas Eagle]

The books are cooked, I tell you.

I'm sure you all are getting tired of me pointing out that I work at a small rural hospital in Northern California (aka The State of Jefferson)in a little town called Colusa. Roughly 60 miles north of Sacramento.

We opened up an entire wing of our hospital (about 30 beds) to accomodate non-corona overflow from Sacramento and surrounding cities.

The only other hospitals in this area of any size are in Marysville (about 45 miles north of Sacramento on Hwy 99), Chico (about 45 miles north of Marysville on 99)Red Bluff is another 45 miles north of Chico and then Redding is another 45 miles north of Red Bluff. Willows is about 70 miles north of Sacramento on I-5.

Dixon and Davis to the west of Sac and Roseville to the east have sizeable hospitals but as for Northern California, it's like we are dead center. We expected a huge influx.

We have had meeting after meeting on how we were going to deal with the deluge. Everybody has been very professional but you could feel the tension in the air.

As of now, we haven't had to use a single bed in the wing we opened. We've had to cut hours in our ER, EVS (where I work) and nursing staff.

There has been one confirmed case in Colusa County and three or four "suspected" cases that came back negative.

As of yesterday, we had 11 patients. Three of those are "Skilled Nursing" patients that have been there when I started back in December. Not to be morose, but there is only one way they will be leaving unless God intervenes.

At the risk of sounding like I am heaping praise upon myself, one of them had a DNR directive that has since changed since I have been there. I pray with him every time I clean his room and he has since changed his outlook on life and has changed his DNR. He now wants to live and has mended fences with his sister and mom whom he hasn't spoken to in years.

I apologize for rambling but I am finishing off a bottle of wine and this stuff is just pouring out of me.

Bottom line is, I'm glad things have not been as apocalyptic as we were led to believe it was going to be but it angers me that so many people have lost their jobs and businesses as a result of all this. And now we have to rely on a bunch of people who have never owned a business or treated a single patient to guide us through this? Lunacy. Sheer lunacy.

Anyway, thanks for being there my fine feathered FRiends.

Keep calm, stay positive and FReep on.

[_Jim]

re: “Another real-world problem is that the tests aren’t perfect. In fact, according to reporting by The Wall Street Journal on Thursday, around 30 percent of people who actually have COVID-19 test negative for it — which is what we’d call a false negative. Other estimates of false negatives aren’t quite so high , so I assume a 20 percent false negative rate in the scenarios.”

What’s being tested for in most cases, is the effect that SARS-Cov-2 virus has in a special test environment, and, it looks like other factors can ‘show’ or develop into a false positive.

The virus itself is small, quite small, and requires an electron microscope to actually “see”. A ‘regular’ microscope won’t do.

The size is about 120 nm (120 nanometers.) Not even microns (micrometers) but nano-meters. 1 times ten to the minus ninth. (1*10^-9)

https://www.ncbi.nlm.nih.gov/books/NBK554776/

“T hus, SARS-CoV-2 belongs to the betaCoVs category. It has round or elliptic and often pleomorphic form, and a diameter of approximately 60–140 nm. “

[daniel1212]

Good for you for posting Silver. He does good work at tiimes, and I think this is some of it.

He certainly gets into it, by the grace of God.

[daniel1212]

Good for you for posting Silver. He does good work at times, and I think this is some of it.

So if we could only test people via licking a stamp. You mail it in and get your results in a week. Saves the postal office.

[daniel1212]

I'm sure you all are getting tired of me pointing out that I work at a small rural hospital in Northern California (aka The State of Jefferson)in a little town called Colusa. Roughly 60 miles north of Sacramento. We opened up an entire wing of our hospital (about 30 beds) to accomodate non-corona overflow from Sacramento and surrounding cities. The only other hospitals in this area of any size are in Marysville (about 45 miles north of Sacramento on Hwy 99), Chico (about 45 miles north of Marysville on 99)Red Bluff is another 45 miles north of Chico and then Redding is another 45 miles north of Red Bluff. Willows is about 70 miles north of Sacramento on I-5.

Sound like a place you would see in a movie.

We have had meeting after meeting on how we were going to deal with the deluge. Everybody has been very professional but you could feel the tension in the air. As of now, we haven't had to use a single bed in the wing we opened. We've had to cut hours in our ER, EVS (where I work) and nursing staff. There has been one confirmed case in Colusa County and three or four "suspected" cases that came back negative.

Build it and they will come. More will, but not as NYC.

As of yesterday, we had 11 patients. Three of those are "Skilled Nursing" patients that have been there when I started back in December. Not to be morose, but there is only one way they will be leaving unless God intervenes. At the risk of sounding like I am heaping praise upon myself, one of them had a DNR directive that has since changed since I have been there. I pray with him every time I clean his room and he has since changed his outlook on life and has changed his DNR. He now wants to live and has mended fences with his sister and mom whom he hasn't spoken to in years.

That is a positive result, by the grace of God.

Bottom line is, I'm glad things have not been as apocalyptic as we were led to believe it was going to be but it angers me that so many people have lost their jobs and businesses as a result of all this. And now we have to rely on a bunch of people who have never owned a business or treated a single patient to guide us through this? Lunacy. Sheer lunacy

The lesson is that people should not be so reliant upon the government, while as a nation,

Let us search and try our ways, and turn again to the Lord. Let us lift up our heart with our hands unto God in the heavens. (Lamentations 3:40-41)

[daniel1212]

The virus itself is small, quite small, and requires an electron microscope to actually “see”. A ‘regular’ microscope won’t do. The size is about 120 nm (120 nanometers.) Not even microns (micrometers) but nano-meters. 1 times ten to the minus ninth. (1*10^-9) https://www.ncbi.nlm.nih.gov/books/NBK554776/ “T hus, SARS-CoV-2 belongs to the betaCoVs category. It has round or elliptic and often pleomorphic form, and a diameter of approximately 60–140 nm. “

And thus something so small can fell massive men, and massively effect massive nations. In one hour so to speak, judgment can come via even the smallest sources.

[Yardstick]

A virus is almost just a tiny packet of information.

[_Jim]

re: “A virus is almost just a tiny packet of information.”

ANd ppl would be shocked, SHOCKED! I tell you IF they knew how many viruses were just ‘floating around out there’!!

Introductory lecture - and just how prevalent viruses are around us -

Virology Lectures 2020 #1: What is a Virus?
Vincent Racaniello
https://www.youtube.com/watch?v=lj3NhPgOoX4

[SueRae]

That was a great post to read as my last one for the night. GOod for you and good for your patient. You ended my day on a high note.