Is PCR testing for Covid -19 too sensitive? NYT article Aug 29

Your Coronavirus Test Is Positive. Maybe It Shouldn’t Be.

A friend of mine gave me this article, and it appears to me that this calls into question a lot of the published numbers I have been using to talk to friends about Covid-19. I typically refer to the City of San Diego's reports as well as John Hopkins data. Does this article cast into doubt the validity of all these sources?

What numbers do you think it calls into question? It has no effect on estimates of the number of people infected with the virus, the number of people dying or having long-term health problems from it, or the rate at which people infect others. The only question it raises is whether we can do a better job of identifying who, among those who are now or have recently been infected, is actually likely to transmit the virus to someone else.

(I will note that one of my colleagues, an infectious disease doctor, described the article to me using a vomit emoji.)

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I’ve heard this from people who know this stuff much better than me, and ask for correction if I’m misunderstanding something about it.

Since no tests are ever completely perfect and so there will always be false positives or false negatives, we are stuck just trying to manage which way we prefer the sensitivity (or insensitivity) to run. Do you want a test that is so sensitive that it errs on the side of reporting false positives - but on the up-side, keeps the false negatives very low? Or do you want a test that is not easily triggered, and hence errs on the side of getting false negatives - which has the advantage of keeping false positives minimized? Sometimes this latter might be preferred … say for example if the consequences of having the malady are not severe or the required treatment for it is extreme. In that case somebody would absolutely not want a false positive! But in a pandemic where extreme contagion is an issue and where the result of a positive may mean nothing more than quarantine for a period, we have a greater interest in reducing false negatives, which necessarily means choosing a test for which we will get a few more false positives.

Have I roughly captured the essential logic here?

Not exactly. The balance between false negatives and false positives (sensitivity and specificity) you describe is a general issue in testing, but it’s not quite the issue that’s being described in the NY Times piece. There are very few real false positives with PCR testing for SARS-CoV-2 – that is, positive results for people who don’t have any virus. The question that they’re raising is how much virus (or viral RNA) should be required to call it a positive test.

I think the Times piece badly confuses separate issues (and deserves the vomit emoji). There are three distinct questions that I see about a test that finds low levels of virus:

  1. Should we call it a positive results?
  2. Should we trace contacts of that person?
  3. Should we quarantine them?

My answers are: (1) Yes. In part because we need all the information we can get about COVID-19 prevalence, and detecting virus means the person has been infected and probably pretty recently. But more importantly, because (2) yes, we should be tracing contacts of people with low viral load. The test tells us (we hope(*)) the amount of virus present when the test was done, which tells us nothing about viral load two days earlier, when the contact may have occurred. The idea that we shouldn’t trace contacts because somebody doesn’t have much virus now is just nuts. Finally, for (3)… well, we have to quarantine people immediately even if they have a low viral load, because they might just be getting sick. I think it’s a valid question whether we could let people out of quarantine earlier if they have a low load over repeated tests over a day or two – but that’s logistically complicated and would represent a refinement of quarantine, not a rethinking of testing.

(*) The entire discussion is based on the assumption that viral load as measured in a nose swab is an accurate measure of the load throughout the body, and that you can’t have a low load in the nose but a higher load in the lungs. I don’t know that we have good data on that question.

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Thanks for the clarification … (and I do admit - I haven’t read the linked article at all, being satisfied at seeing your response to it; and so was responding more to the general sensitivity issue raised.)

I think the vomit emoji is very short sighted - me and my friends will learn a lot from this.

There are useful facts in the piece but I think a poor exploration of what those facts imply.

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Understood. But it will also tell the medical establishment that they need to retain and use their PCR cycle numbers.

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