How Scientists Trace New Coronavirus Variants

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NPR's Ailsa Chang talks with biologists Pardis Sabeti and Sharon Peacock about how genomic sequencing was used in the U.K. to trace a new coronavirus variant and what the U.S. can learn from it.

Transcript

AILSA CHANG, HOST:

A new variant of the coronavirus has now been found in at least 10 states. The strain, known as B117, is thought to be more contagious. And U.K. scientists first alerted the world about it in December. In the meantime, we have heard reports of other additional variants found in South Africa and in Japan. So what does this say about the coronavirus' ability to evolve and our ability to fight it?

Well, I have a couple of virus detectives with me now. Pardis Sabeti is a computational biologist at the Broad Institute in Massachusetts, and Sharon Peacock is the director of the COVID-19 Genomics U.K. Consortium. Welcome to both of you.

PARDIS SABETI: It's a pleasure to be here.

SHARON PEACOCK: Thank you very much.

CHANG: So Dr. Peacock, let's just start with you. You know, it was your team that helped track down this new COVID variant. Can you just explain - how did you first figure out that you found something new?

PEACOCK: Well, there are many, many mutations in the viral population. And what you need to do is look for a signal in people for some different viral behavior. And so in December, what we noticed was that there were numbers of cases of COVID-19 in people in the south of England.

Now, they were under lockdown restrictions. And strangely, in other parts of the country, that same lockdown was controlling the disease very well. But in the south of England, it wasn't managing to control spread of the infection. And so at that point during the investigation - the outbreak investigation - it became very apparent this was associated with this new variant, which contained a large number of mutations, which we hadn't seen before. And that's what really set it off.

CHANG: OK. And how different, exactly, is this strain - B117 - from the initial strain sequenced in China at the very beginning of the pandemic? Like, how different both genetically and how different in the way the two viruses interact with us as human hosts?

PEACOCK: This virus is actually strikingly different, and it has 23 different mutations. And what concerns us is that some of those mutations are in part of the virus called the spike protein, which is the protein that interacts with humans and attaches to human cells and is part of the entry process into the body. And so this is actually very unusual. But in particular, it has mutations that could change the biology - the way that the virus interacts with humans.

CHANG: Well, OK. Dr. Sabeti, along with the U.K. variant, scientists have found other significant variants in South Africa and in Japan. Is that all that surprising to you or were scientists expecting this to happen as we got deeper and deeper into the pandemic?

SABETI: You know, these are viruses, and like everything on Earth, they change over time. But viruses, in particular, they're replicating and spreading quickly, and they have high mutation rates compared to us. Just the way that their biological machinery works is they're making more changes each time they replicate. So this is expected. We saw during the Ebola outbreak, during the previous SARS outbreaks, during every outbreak, you know, that happens, viruses are mutating all the time. That's what we expect.

CHANG: So can tracking these sorts of variants help us curb the spread of the virus in some way?

SABETI: It can. And, you know, I think it's very important to do - as the U.K. did - is to be able to scan at high resolution in real time, or near real time. Because if you do identify something like the B117 mutation, and you notice, hey, there's something going on in this part of the country and oh, there's this new variant to pay attention to, we can scan for where that variant is occurring and try to then move our public health resources, which are inherently limited, but to take all the resources we can to stop that variant from going anywhere.

CHANG: Well, given that this U.K. strain appears to be more contagious, let me ask both of you this question. Does our current public health guidance around social distancing and mask wearing, does that need to change?

PEACOCK: There's no reason to think that standard advice about infection prevention and control needs to change. So we still need to wash our hands, wear masks and distant - socially distance. And so it is more contagious, but there's every reason to think that if we follow the guidance, that disease transmission can be reduced and prevented.

CHANG: And Dr. Sabeti?

SABETI: Yeah. I think that the guidelines that we have in place are very good. And they work for most viruses - you know, washing hands and social distancing, wearing masks. The more contagious a virus, the more it means we have to be really regimented about that. And any breaches at all, and you could have mass containment failure. And so it just makes us have to really ante up on those.

CHANG: So, you know, this strain, as we keep saying, was first detected in the U.K. So let me ask you, Dr. Sabeti - how equipped do you think the U.S. is to detect these kinds of genetic changes in the virus moving forward?

SABETI: The U.S. is very equipped to detect these kinds of mutations, and they have been doing across the board. The difference between the U.K. and the U.S. in this instance is the U.K., on a national level, really put down a lot of funds and support and made this a priority whereas - I'll say that my colleagues and I here in the U.S., most of this work is done on our discretionary funds, on very limited budgets. And so we're very poised and doing a lot of great and exciting sequencing across the U.S., but not at the level and the scale that's needed. And so we've been calling for some time - for many, many years - to have national funding to scale this up. We're poised and able to do it. Literally, it's just about getting more sequences through the pipeline, which is more funding and support and prioritization of the need.

CHANG: So as this pandemic continues to drag on, what else will you be watching for? Like, are you going to be expecting more strains to emerge?

PEACOCK: I think it's very likely that we'll see new variants emerge. And what we're really watching for are variants that actually are transmissible, but that actually have the ability to escape immunity. So that's either the immunity that's acquired naturally if you have COVID-19 once or immunity that's developed through vaccination. So in particular, looking for combinations of mutations that could allow a virus to be very fit and spread amongst the population, but that could also threaten the efficacy of vaccines.

The other thing we worry about is mutations that could affect the way that diagnostic tests can work. So some mutations can affect the ability of a diagnostic test to detect the virus. So also looking out for those types of mutations.

CHANG: That is Sharon Peacock, director of the COVID-19 Genomics U.K. Consortium, and Pardis Sabeti of the Broad Institute. Thank you to both of you.

PEACOCK: Thank you.

SABETI: Thank you.

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