If only we knew the viral load

A new study shows that knowing the viral load of infected people can help chart the pandemic

Welcome to Plugging the Gap (my email newsletter about Covid-19 and its economics). In case you don’t know me, I’m an economist and professor at the University of Toronto. I have written lots of books including, most recently, on Covid-19. You can follow me on twitter (@joshgans) or subscribe to this email newsletter here.

One of the most frustrating things about current testing practices is that we throw away key information that could help us understand someone’s infection. The PCR test that is most widely used gives an outcome as to whether someone is infected or not with SARS-CoV-2. But it also gives a strong indication as to the viral load of a person. This is because the PCR test operates in cycles. It starts with a sample from a person and extracts the genetic material. It then looks for the marker of the coronavirus. If it doesn’t find it, it replicates the genetic material and then, in that cycle, looks again for the viral marker. It keeps replicating the material each cycle at an exponential rate until either it finds the viral marker or it reaches 40 or so cycles in which case it stops and pronounces the person ‘negative.’ The number of cycles can be measured and is called the Ct score. The lower the Ct score, the more of the virus there is in the sample as it took ‘less time’ to find it.

The following graph (from the New York Times) shows the typical path of the virus from exposure to recovery. It is somewhat understated as the unshown Y-axis is in log units — indicating that the peak of the viral load is many orders of magnitude more than what might happen a few days around it. This graph is the reason the President Trump’s doctor cleared him as non-infectious even though it is likely he would have tested positive under a PCR test. They had tested him continually and so knew that he had likely passed the infectious viral load and that load was well on the way down.

Would that everyone had the frequency of testing that the President has. If you have that frequency and you record the Ct score, you can pinpoint where in the cycle you are with respect to the virus. This is important as you want to receive treatment just before symptoms have appeared as the symptoms are evidence that the virus has become the Covid-19 disease with all of its bad consequences. But not only do people not get frequent tests, even when they do, the Ct score is not kept. The reasons for this remain mysterious to me but many have confirmed that it is often regulators who prevent that number being reported or even kept.

A new paper shows that this is even a bigger lost opportunity than what we are losing at the individual level. The authors postulate that they could use just one day of PCR test data across those infected in a population to precisely map the dynamics of the virus. At present, this has to be guessed from total numbers who are infected which, at the very least, requires us to measure the number of infected each day. We are not great at doing that.

If you had the Ct score for all of those tests, then if the virus is steady — not expanding or contracting — it is likely that the aggregate pattern of scores will look like a blown-up version of the above graph. By contrast, if the virus is spreading, the aggregate pattern will be skewed to the left as relatively more people are in the early stages of the virus. If the pattern is skewed right, the opposite is true.

They run simulations and then compare the result with hospital data that includes the Ct score. The two match up.

Think of it. We can get data that properly identifies the most significant population-level number, the reproduction number, for the coronavirus without widespread testing and right at the moment rather than waiting for a time series pattern to emerge.

In a world in which we have the most testing ever done on populations, it is extremely frustrating that the test results are crimped in ways that really harm our ability to see what is happening. This has to end. Governments need to act now to mandate the recording of Ct scores with every positive test result.

What did I miss?