Gangavarapu says his team of collaborators has found plenty of B.1.1.7 in circulation. But so far, their sequencing efforts haven’t captured either of the two variants that are suspected to be the best immune evasion artists—the B.1.351 and P.1 variants, discovered in South Africa and Brazil, respectively. According to CDC data, only a handful of those have been reported in the US so far, mostly in people who recently returned from traveling. But imports aren’t the only thing to worry about. There are homegrown variants too.
Jeremy Kamil is one of the people looking for them. A virologist at Louisiana State University Health Sciences Center Shreveport, Kamil normally studies the cytomegalovirus family, but starting last spring, he combined forces with Vaughn Cooper, the director of the Center for Evolutionary Biology and Medicine at the University of Pittsburgh who runs a microbial sequencing startup, to set up genomic surveillance for SARS-CoV-2 in Louisiana. For months, they sequenced hundreds of samples from coronavirus tests randomly collected from around the state, watching for anything unusual. On January 27, Kamil noticed exactly that—a batch of samples that all contained a mutation he hadn’t seen before. When he looked closer, he saw that each of the mutant viruses were closely related—they all belonged to the same genetic lineage. And though that lineage was quite young, dating back only to the beginning of December in his data, it was growing more common every day.
Kamil uploaded the genomes to an online database called GISAID, used by researchers around the world. The next day, scientists at the University of New Mexico contacted him. They had found the same variant in their state. Meanwhile, Cooper was scouring the database looking for more viruses with the same mutation—a genetic alteration which changes the 677th amino acid in the coronavirus’s spike protein. He found more, and not just in Louisiana and New Mexico, but also North Carolina, Massachusetts, and eight other states. The researchers realized they needed a phylogenist to get their viral family tree in order, so they enlisted the help of Emma Hodcroft at the University of Bern in Switzerland. Within a week, her team had traced the emergence of seven new variants in the US, each of which had evolved the same mutation independently.
The researchers described this pattern as an example of “convergent evolution” in a preprint posted Sunday. “It’s a pretty strong indication of an adaptation, even if we don’t yet know what that adaptation is,” says Cooper, a coauthor of the study, which has not yet been peer-reviewed.
We tend to use the singular word “coronavirus” when referring to the bug that causes Covid-19. But a more accurate way to think about SARS-CoV-2 is as a population of viruses. And that population is in a state of constant flux—expanding and contracting, mutating, and evolving new lineages as it spreads from person to person. Genetic epidemiologists can track those minute changes, following them like the branches of a family tree to identify clusters of cases all linked to one another. With enough viral genomes, they can also zoom out to compare how fast different branches are growing. If one branch starts to take off, it can indicate that the genetic changes those viruses have acquired provide some kind of competitive advantage. And if a bunch of different branches independently acquire the same mutation, and they all start to take off, well, that’s convergent evolution.