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Tracking New Coronavirus Variants In The U.S.


Throughout the pandemic, new variants of the coronavirus have appeared in the U.K., South Africa, Brazil and here in the U.S. as well. Yesterday, scientists reported preliminary evidence of seven distinct variants of the coronavirus emerging here, popping up in states all around the country. Vaughn Cooper of the University of Pittsburgh is one of the scientists doing that genetic detective work on U.S. cases. He says although the U.S. is starting to catch up to other countries, we still have a ways to go in sequencing cases of the virus.

VAUGHN COOPER: We are sequencing three per 1,000.

CHANG: Wow, that sounds like barely anything.

COOPER: Yeah, that's - we're really lagging behind other countries in the rate of genomic surveillance. The U.K. - really leading the way in terms of the numbers of genomes that they've sequenced. They've been doing quite a bit of detective work, sequencing a large fraction of cases. In fact, in Australia, nearly half of all cases have been sequenced down to the letter. In the United States, we're sort of around 40th among countries currently.

CHANG: Oh, that doesn't sound very good.

COOPER: It does not sound good.

CHANG: Why is the U.S. behind in the first place?

COOPER: Well, we really lacked a coherent national strategy to start doing this sort of work. This work is technical. It does require some specific expertise. My lab has been studying how microbes evolve for a while, and we developed the ways to sequence genomes quickly and cheaply. And others around the country have that ability as well, but there really wasn't a coherent way to incentivize all of us to get on board. There's sort of no fee for sequence - sort of bounty method or an easy grants mechanism that was going to really heavily invest in broad-scale surveillance.

CHANG: How is this kind of detective work happening in the U.S. now? Like, is it still happening in individual scientists' labs? Or is there more of an effort now to centralize all these different efforts into a central government effort?

COOPER: The answer is both. There are a few big companies being contracted to do the sequencing by the CDC, but they've also contracted with a small number - relatively small number of academic medical centers. And I understand that number of contractees (ph) is growing. We really need to do - is engage researchers at academic medical centers who have this ability to join the effort.

CHANG: And what tools do you need now from the federal government or from anywhere? What are the most important tools that you need now to better bring these different labs' findings together?

COOPER: You definitely need funding. It costs about $1- to $200 or more per virus genome. But you also need links to clinicians, really. So the most valuable data is the sequence - that it has some link, obviously protected, to clinical data because ideally, you'd want to be able to understand if the rise of a particular variant is associated with some collection of outcomes. That generally is not happening very much. And even if you don't have that ability, simply incentivizing sequencing and rapid data sharing is important. And I want to add that the United States is actually even a bit worse in the overall global rankings in our rate of data sharing.

CHANG: Well, what is the ultimate danger, in your view, of not doing enough of this genetic detective work?

COOPER: Unfortunately, many regions are still severely under-sampled. And unfortunately, the odds are that there are more lineages in our midst, sort of like a constellation of small variants. The good news is as we're paying attention to the variants that we know, they are sort of converging on a relatively few number of mutations, suggesting that these are the ways the virus is adaptively evolving to transmit and cause disease.

CHANG: Vaughn Cooper of the University of Pittsburgh, thank you very much for joining us today.

COOPER: It's been my pleasure. Thank you. Transcript provided by NPR, Copyright NPR.