Corona Part 2 - Testing, Opening Up, and Follow-Up

Lars Poulsen - 2020-04-15

The two kinds of tests

There are two kinds of test:

The PCR tests detect that your body (snot from your nose) contains virus. Test must be performed at a lab, using a specialized machine (which many labs have already because it works with other pathogen-specific tests) and a pathogen-specific materials kit.
Test takes at least 2 hours elapsed from the sample comes into the lab. I am guessing it uses 15 minutes of trained laboratory tech staff time.
This will by its very nature be expensive. These are the tests that the local county public health lab can now process.

The antibody tests are similar to a pregnancy test, except it uses a drop of blood instead of a squirt of urine. Test kit is self-contained, can be done in the field, response time 15 minutes (or maybe less).

These tests show if your have antibodies to the virus. If you have never been exposed, you will not have antibodies. If you have been very recently exposed, you may not yet have antibodies. If you have antibodies, you may still be infectious. If you have been sick, and recovered and been symptom free for 3-5 days, you should have antibodies and probably no longer infectious. ** This is the GOLDEN status **

How accurate are the tests, and why that matters

But tests are not perfect. The current antibody tests are about 98-99% accurate. That sounds good, .... but at this point, probably only about 1% of the population has been exposed. With 1% exposure rate and 99% accuracy, your tests will show about 1-2% positive. But ... for each positive test, there is a 50-50 chance that the test is wrong.

(For simplicity, I am assuming 1% false positives and 1% false negatives. We can disregard the false negatives because there will be so few of them.)

The 1 % that have been infected, will show up positive. But out of the 99% that have never been infected, 1% will also show positive. (50% functional accuracy.)

At this level, the test has no predictive value for individuals, but it show how widespread the infection has been.

If that number gets to 10%, to statistics get more believable.

We now get 10% true positives and 1% false positives. So a positive result has 90% chance of being correct.

With 20% penetration, 20% true positives, 1% false positive. So 95% functional correctness.

By 50% penetration, the functional accuracy is 98.5% at it is useful for predicting the status of an individual.

Opening Up - When and How?

To open up from the lockdown, we need at least one of the following:

a) the virus runs out of steam (seasonality) and becomes less infectious than the common cold or the flu.
b) population incidence gets high enough that we are protected by herd immunity (maybe 40% to 60%)
c) a vaccine is available. Probably 12 months.
d) a treatment is available so that when someone gets a bad case, we can get it under control (like we can with bacterial pneumonia). Could be 6 months if we are lucky, could be 2 years. So far, in clinical trials, the hydrochloroquine touted by the president seems to kill more people with heart attacks, than it saves from reduced lung edema.

Right now, we have none of these, but in most parts of the country, we have well below 1% incidence, and at this level, the hospitals can handle it. We might try gradually opening up in places like our local area, until we have 50% occupancy in the ICUs, then clamping down until we have headroom again. This will be tricky, because it takes 2-3 weeks from we make a change in procedures until we can see the effect. And if at this point, we have been sitting here for a month and gotten only to 1% incidence, it may take a year to get to even 20% incidence, which is not enough to give us herd immunity, and also is not enough time to get to a vaccine.

Follow-up on my previous post (2020-04-03)

Flattening the curve

I said

The "social distancing" protocols that have now been pretty uniformly adopted, aim to slow down the infection rate, so that it takes three or four days for the number of cases to double. That means that it takes a month to get from 1000 cases to a million cases, and by then, many of the early cases have healed, their hospital beds are freeing up, and an increasing percentage of the people they come in contact with have already healed and have immunity.
Under these circumstances, it may take 3 to 6 months for the infection to pass through the population, but there may be ICU beds and ventilators for most of the severely ill patients, at least in the wealthier countries, so the death toll will be much lower. Just how much lower depends on many factors that we do not yet know, but for the USA, it is projected to be between 100,000 and 250,000 - compared to 3 to 6 million without these precautions.

Two weeks further in, it appears that in the places where we shut down public life early enough, we are doing much better than expected.

Seattle area - first locus. When it hit there, we did not know much yet. But once the local governments figured it out, they clamped down, and got it under control
New York City - second locus. They were not prepared, but as soon as they saw the ramp-up they realized that they were on the track that had already been disastrous in Italy, and clamped down. The result has been mixed: By the time they clamped down (similar stage as Seattle area), the epidemic had gained momentum. The higher population density in NYC meant it had a LOT of momentum by then, and the hospital systems have been at about 200% of capacity since, but I do think the curve has peaked.
New York edges: New Jersey and Long Island - repeating the story with 10 days delay. But the heroic resources that New York had marshaled (Javits convention center, Navy Hospital ship etc), may be available to help with hospital capacity.
New Orleans - total shipwreck. Mardi Gras swamped the city with tourists from everywhere mingling in crowded streats and bars, then going home after sharing germs for a week. Two weeks later, it seems to be as bad as the worst of New York without the heroic leadership.
California - Saw New York and clamped down before the ramp-up got going. Looks like succesful flattening of the curve.

Most places where local leadership has clamped down, it appears that we have low incidence of infections, and plenty of room in the hospitals.

Many conservativ midwestern states - and rural ares everywhere - the low population density has afforded the luxury of a late and slow ramp-up, but in those places where local leadership has taken that as a good enough reason to do nothing, we should expect a delayed but overwhelming infection rate.

What went wrong in the USA ?

So many things went wrong in the U.S.:

The warehouses full of supplies (face masks, disposable gowns,
ventilators, portable hospital units, etc) had stopped being maintained. Some supplies had been dispersed, building leases discontinued etc. Equipment such as ventilators had not been maintained (batteries replaced, periodic functional checks etc).

Some of these problems turned out to be predating the Trump administration. Such as warehouses full of facemasks with dry rot and 2010 expiration dates.

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