Coronavirus variants are here. Now what?

A new report from infectious disease experts provides policy recommendations for how the United States can blunt the impact of the variants that have already emerged, as well as build a genomic surveillance system so the country can better identify, track, and assess other variants that might emerge as the SARS-CoV-2 coronavirus continues to evolve.

The suggestions include maintaining the policies that have been shown to drive down viral transmission, prioritizing contact tracing and case investigation of infections found to be caused by one of the variants of concern, and building a scaled-up and more coordinated national genomic sequencing strategy. The Covid-19 package that Congress is assembling now will likely include an influx of funding for genomic surveillance, so the researchers are trying to envision what such a national system should look like. 

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Already, three variants have emerged that, in different ways, present challenges for the U.S. The B.1.1.7 variant, which was first seen in the United Kingdom, is more transmissible than earlier forms of the virus, and, research increasingly indicates, more lethal. Then there are P.1 and B.1.351, which were first seen in Brazil and South Africa, respectively. They appear to be better at reinfecting people who’ve recovered from an initial bout of Covid-19. Some vaccines have also been found to be less effective against B.1.351, and given that it shares some of its mutations with P.1., experts fear the same could be true with the latter.

STAT spoke with Caitlin Rivers, an infectious disease epidemiologist at the Johns Hopkins Center for Health Security and a co-author of the report, about its recommendations. Excerpts from the conversation are below, lightly edited for clarity. 

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Your first recommendation to deal with the current variants is to maintain policies that slow transmission. But governors or mayors are looking at the pretty steep decline in cases right now and being like, great, we can ease some stuff. Some have ended mask mandates, and some are allowing more activities like indoor dining, or easing capacity limits at businesses. Why is this not the time for that in your eyes?

Two reasons. One, although we have come down a lot from the peak of the surge in early January, we’re still well ahead of the two previous surges. So things are better, but they’re not good. So for that reason alone, I would recommend continuing to keep restrictions in place until we get case counts down until a much more reasonable level.

And the second reason is the variants. Right now they are circulating at a pretty low level in the United States — it varies from place to place — but low on average. But we’ve seen in places where the B.1.1.7 variants gets a toehold, it causes resurgences. And the lower we can be at the starting point if B.1.1.7 does start to become established, the better position we’ll be in in the longer term. We’re setting ourselves up now to have a better future. 

What are some of the limits of the U.S. genomic surveillance system? Where are the bottlenecks?

We have great capacity in this country to do this work. We have a lot of sequencing capacity, we have a lot of science capacity for the characterization. What we’re really missing is the coordination — how to bring it all together and make sure that all of this effort and information is coming together into a system that helps to support our response. 

Scale is also a bottleneck. There are a lot of the building blocks that we need for a successful genomic surveillance system. CDC is doing this work, private sequencing companies are doing this work, academic labs are involved in characterization, but it hasn’t been at the scale that’s required to support the magnitude of the response that we need. And it’s not coordinated enough to make the most out of those existing elements.

How quickly can the genomic surveillance system in the country be strengthened? Is it something that would take a long time or could some things be done more quickly?

We could be doing a lot more with what we have, because there is a lot of sequencing capacity in the United States. There is a lot left on the table that we could be making better use of.

The other motivation is that there are substantial funds for this in the American rescue package, and so it’s looking ahead to see how could we use those funds and how could they go to building a functional system.

Based on the available data, which are limited, how do you view what’s happening with the variants in the U.S. right now?

The B.1.1.7 variant is definitely at higher prevalence than the other two. We have seen that in the U.K., it precipitated a severe resurgence that prompted a lockdown. That is the concern here — that it would become established and would reverse some of the progress we’re seeing. 

The other two are circulating, as far as we can tell, at much lower levels, although we’re not looking all that hard. The bigger concern with those is immune escape [when the virus mutates in such a way that immune protection from an earlier infection or a vaccine isn’t as robust]. So particularly, as we look forward, having a good system in place that is able to watch out for those and other variants and adapt our countermeasures accordingly is going to be really important.

Another point: There’s a lot of talk right now about genomic surveillance, but what I don’t hear as much conversation about is characterization. Just because you’ve identified a new variant doesn’t mean you know what to make of it. Envisioning how you turn those sequencing results into something meaningful for public health is really important.

So you’re saying if you identify a new variant that you think has some sort of impact on transmission or immunity, for example, how do you go from identifying you have a new variant to figuring out what, if anything, it means? Is that what characterization means?

Yes, that’s exactly it. 

Can you explain what you’re envisioning what the next few months might look like with the variants and cases? 

The variants are a bit of a curveball. I could see a scenario where B.1.1.7 could slow down our progress and maybe precipitate resurgences in some communities — maybe not nationwide, because some communities have fairly substantial levels of population immunity, but some places could go back up again. But as we pass through the summer and into next winter, this is where we want this surveillance system to come into place. If there are variants that are showing immune escape, what we don’t want is to become unprepared and suffer another wave because this hypothetical variant is no longer a good match for the vaccines.