One of the bizarre subplots of President Donald Trump’s illness has been the White House’s unwillingness to explore exactly how he contracted Covid-19. Offers by the Centers for Disease Control and Prevention to investigate the outbreak have been rebuffed, leaving open pressing questions. Who gave the virus to the president, and where did that happen? To whom did he give it, and in what circumstances? Is the disease now sweeping through the White House all from a single source, and if so, who is the source? Twenty years ago it would have been all but impossible to answer those questions, but they can now be answered quickly and cheaply — so quickly and cheaply that I can’t help but wonder why we don’t already have the answers. I sat down with microbiologist Joe DeRisi, a co-president of the Chan Zuckerberg Biohub, who is a pioneer of the use of genomic sequencing both to identify and to track infectious diseases. He has a few thoughts on the subject. Here is a lightly edited transcript of our discussion.
Michael Lewis: When a person is tested for Covid, and their test turns out positive, that’s one piece of information you get — positive or not positive. But there’s other information there. What is that information?
Joe DeRisi: Besides knowing whether you have the virus or not, when you test positive you can also extract the actual sequence of the virus. And what that means is the genetic information that composes all the proteins of that virus.
ML: And what’s the use of that information?
JD: The genetic program of the virus — you might think is set in stone. But it isn’t. The virus is made of RNA, and when it replicates itself, it tends to make errors. From generation to generation, the virus introduces small mutations, errors in its own genetic code. And it does this at about a rate of a new mutation every two to three transmission events.
ML: So you can see it changing as it moves through the population?
JD: That’s right. When a second mutation or error is introduced in that same virus as it’s passed from one person to another, it inherits all those previous mutations. You have a breadcrumb trail that links all those viruses together throughout their history.
ML: And with this information, then, you might be able to detect who gave it to whom in a population?
JD: Knowing the sequence of mutations links it to all its past infections. If you have sequences of a bunch of people that were positive, let’s say in an outbreak in a fish packing plant or something like that, you would then be able to know whether those individuals who were sick had the same virus or a different virus. If it was the same virus, then that would imply that they likely transmitted it to each other. If they had a different set of mutations, then you could conclude that there’s no way they could have gotten it from each other at the workplace.
ML: You might be able to keep the fish packing plant open because you could see that it wasn’t inside the place; the thing was being transmitted by people bringing it in from outside.
JD: Correct. This idea of using genomic epidemiology — that is, mapping the mutations inside the genome and using it for public health purposes — is often used to rule out possibilities: We can rule out that this person gave it to that person. Now if it’s an identical genome, the most likely scenario is that they were closely linked in the transmission chain.
ML: The sequencing enables you to see social relationships in the community you might not otherwise see.
For instance, if you see that a woman has it and a guy four doors down the hall from her has it and it’s the same virus, and those two claim to have no relationship, then you might dig further, because the virus is telling you that they came in contact in some way. And it makes me wonder how it might be used in the case of the president right now. If you had the positives from in and around the White House, what do you think you might be able to deduce from them?
JD: If we had all the positive cases from the White House and from members of Congress who were in contact with the White House, and their friends and family, and we sequenced the viral genome from those — not the people, just the viral genome — we could probably create a linkage map that indicates who likely gave it to whom.