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How Genetic Mapping Is Allowing Scientists To Track The Spread Of Coronavirus


Scientists are tracking the coronavirus with technology that was unavailable just a few years ago. The approach looks for genetic changes in the virus. And as NPR's Jon Hamilton reports, it's helping to answer questions about where and how the virus is spreading.

JON HAMILTON, BYLINE: When a man in the Seattle area tested positive for coronavirus back in January, government scientists sequenced the entire genome of the virus in his body. That turned out to be critical five weeks later, when tests revealed a second infected person. Trevor Bedford is a computational biologist at the Fred Hutchinson Cancer Research Center.

TREVOR BEDFORD: That virus basically looked identical to the virus from five weeks previously. And this is consistent with taking that virus and just letting it evolve kind of in place for five weeks.

HAMILTON: It looked like the first man who'd been infected in China had passed the virus to at least one other person in Washington. Bedford says disease models suggested that by the time the second case appeared, the outbreak was already getting big.

BEDFORD: You get around $600, maybe a thousand infections.

HAMILTON: Recent testing supports that early prediction. So far, the state has found more than 1,200 infected people. And new sequences suggest two other versions of the coronavirus are now circulating in western Washington. Scientists say they may have come from Europe and Iran. All of this information comes from a field known as genomic epidemiology. Jesse Bloom at Fred Hutchinson says it's changing how public health officials handle epidemics like coronavirus.

JESSE BLOOM: The ability to sequence these viruses really rapidly has really had a profound impact on our ability to understand what's happening and understand the epidemiology of the virus.

HAMILTON: Bloom says the approach is based on the way viruses change over time.

BLOOM: Because coronaviruses have a fairly high mutation rate, as the virus transmits from person to person, every couple of transmission events it will get a mutation.

HAMILTON: These mutations act like a ticking clock, showing how long it's been since an outbreak began. They also show whether viruses found in different people are likely to have come from the same source. But to be really useful, sequencing has to be done fast, and that's only been possible in the past few years. Kristian Andersen studies infectious disease at the Scripps Research Institute in La Hoya, Calif. He was part of a team that studied the Ebola outbreak in West Africa, which ended in 2016.

KRISTIAN ANDERSEN: And we managed to sequence about a hundred genomes back then, which we thought was pretty fast because it took us only about three months.

HAMILTON: Now sequences can be done in days. And scientists have already shared more than 700 coronavirus genomes from around the world. Andersen says genomic information was especially important early on. For example, the first thing doctors in China needed to know was what was making people sick.

ANDERSEN: And the sequencing answered that immediately, saying, like, this is a novel coronavirus.

HAMILTON: The next question - where did it come from?

ANDERSEN: And turns out that that's bats because there are very similar viruses circulating in bats.

HAMILTON: As the infection spread to other countries, scientists were able to pinpoint when it arrived and to make educated guesses about where it came from. Andersen says now that there are so many sequences available, it should also be possible to study local factors that help or hurt the virus.

ANDERSEN: What is the effect of temperature? What is the effect of rainfall? What is the effect of human movement and things like that? So understanding the factors driving the spread.

HAMILTON: Andersen says there are limits, though.

ANDERSEN: As you are starting to work with a lot of sequences available, analyzing them becomes very difficult just in terms of compute time.

HAMILTON: Also, he says, there's still no way to sequence virus from every person infected in a large outbreak, so it's important to keep using other tools like testing, surveillance and contact tracing.

Jon Hamilton, NPR News. Transcript provided by NPR, Copyright NPR.

Jon Hamilton is a correspondent for NPR's Science Desk. Currently he focuses on neuroscience and health risks.