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VSthe oronavirus variants are here. Now what?
A new report from infectious disease experts provides policy recommendations on how the United States can mitigate the impact of 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 may emerge as the SARS-CoV-2 coronavirus continues to evolve.
Suggestions include maintaining policies that have been shown to reduce viral transmission, prioritizing contact tracing and investigation of cases of infections deemed to be caused by one of the variants of concern, and building a national strategy. larger-scale and better-coordinated genomic sequencing. The Covid-19 package Congress is putting together will likely include an influx of funds for genomic surveillance, so researchers are trying to imagine what such a national system should look like.
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Already, three variants have emerged which in different ways present challenges for the U.S. Variant B.1.1.7, which was first seen in the UK, is more transmissible than earlier forms of virus and, increasingly, more deadly, research indicates. 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 re-infecting people who have recovered from a first bout of Covid-19. Some vaccines have also been shown to be less effective against B.1.351, and given that it shares some of its mutations with P.1., Experts fear the same may be true with the latter.
STAT spoke with Caitlin Rivers, an infectious disease epidemiologist at the Johns Hopkins Center for Health Security and co-author of the report, about their recommendations. Snippets of the conversation are below, edited slightly for clarity.
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Your first recommendation for dealing with current variations is to maintain policies that slow down transmission. But the governors or the mayors are looking at the pretty big drop in cases right now and saying to themselves, okay, there are some things we can alleviate. Some have ended mask mandates and some allow more activities like indoor dining or easing capacity limits for businesses. Why is this not the time for you?
Two reasons. First, although we are down a lot from the peak of the outbreak in early January, we are still well ahead of the previous two hikes. So things are better, but they are not good. So for that reason alone, I would recommend continuing to keep the restrictions in place until we get a countdown to a much more reasonable level.
And the second reason is the variations. Right now they are circulating at a fairly low level in the United States – it varies from place to place – but low on average. But we have seen in places where the B.1.1.7 variants take hold, it causes resurgences. And the lower we can be at the starting point if B.1.1.7 starts to settle, the better our long term position will be. We are now preparing for a better future.
What are some of the limitations of the US genomic surveillance system? Where are the bottlenecks?
We have a great capacity in this country to do this work. We have a great capacity for sequencing, we have a great scientific capacity for characterization. What we really lack is coordination – how to bring it all together and make sure that all of that effort and information is pulled together into a system that helps support our response.
The scale is also a bottleneck. There are many elements that we need for an effective genomic surveillance system. The CDC is doing this work, private sequencing companies are doing this work, university labs are involved in the characterization, but it hasn’t been on the scale needed to support the scale of response we need. And it’s not coordinated enough to make the most of these existing elements.
How quickly can the genomic surveillance system in the country be strengthened? Is this something that would take a long time or could some things be done faster?
We could do a lot more with what we have, because there is a lot of sequencing capacity in the United States. There is still a lot of things on the table that we could make better use of.
The other motivation is that there is substantial funds for this in the US bailout, and so he looks to the future to see how we might use those funds and how could they go to building a functional system.
Based on the data available, which is limited, how do you see what is currently happening with the variants in the United States?
Variant B.1.1.7 is certainly at a higher prevalence than the other two. We have seen that in the UK this precipitated a strong resurgence which caused a lockdown. That is the concern here – that it would become established and reverse some of the progress that we are seeing.
The other two are circulating, as far as we can judge, at much lower levels, although we don’t look too hard. The biggest concern with these is immune leakage [when the virus mutates in such a way that immune protection from an earlier infection or a vaccine isn’t as robust]. So in particular, as we look to the future, it will be very important to have a good system that can monitor these and other variants and adapt our countermeasures accordingly.
Another point: there is a lot of talk now about genomic surveillance, but what I don’t hear as much about is characterization. Just because you’ve identified a new variant doesn’t mean you know what to do with it. It is really important to see how you turn these sequencing results into something meaningful for public health.
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 a new variant to determining what does this mean, if any? Does characterization mean?
Yes that’s exactly it.
Can you explain what you envision what the next few months might look like with the variants and cases?
The variants are a bit curved. I could see a scenario where B.1.1.7 could slow down our progress and perhaps precipitate resurgences in some communities – maybe not nationwide, as some communities have fairly high levels of population immunity. , but some places could go up. But as we go through summer and into next winter, that’s where we want this monitoring system to come in. If there are any variants that show immune leakage, what we don’t want is to not be prepared and go through another wave because this hypothetical variant no longer fits vaccines.
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