Samples From Idaho Help Scientists Chart The Path Of Novel Coronavirus

May 4, 2020

When people test positive for COVID-19, public health officials ask about their recent movements and with whom they've interacted. This process is called contact tracing, and its purpose is to learn about how the disease has spread in an area to prevent further transmission.

 

At the same time, scientists at research institutions are trying to answer these same questions about the outbreak by looking more closely at the virus itself. 


The novel coronavirus’ genetic material has a 29,000-letter code. As the virus passes from person to person that code largely stays the same, but sometimes the virus mutates, and certain letters in the code are different. 

Pavitra Roychoudhury, a researcher at the University of Washington's Virology Lab, is comparing patterns of the virus' letters in different samples, a process called genomic sequencing.

"If you have two people that have positive tests, how similar is the virus in those people?”

 

The mutations give Roychoudhury and her fellow researchers clues about how the virus has moved around the world

 

Many hospitals and medical providers from across the country have been sending samples from nasal swabs to the University of Washington to run through coronavirus tests. When a positive sample is identified, it's sent to the sequencing team to take a closer look. The lab is analyzing samples from many states, including Idaho.

 

Roychoudhury wasn't able to say exactly where the Idaho samples originated, but so far the team has looked at at least 40 from Ada, Twin Falls and Kootenai counties.

 

By examining the positive samples from Idaho, Roychoudhury said the virus' genomic patterns look similar to clusters from Utah and Washington. That means the virus likely came into Idaho from multiple places, including those states.

 

And then, there are some samples that look pretty Idaho-specific, an indication of community transmission.

 

“When you see a cluster of sequences that are highly similar to each other from the same location, that tells you that it's very likely that there was transmission occurring within that population," Roychoudhury said.

Public health officials say community spread, by definition, is when they can't determine how or where an individual became infected. So far, it's been identified in 17 Idaho counties. And according to Roychoudhury, scientists can see evidence of community transmission in Idaho at the level of virus' genome. 

Roychoudhury said research like this relies on robust testing. The more samples that are sent to labs like hers, the more equipped scientists are to chart the novel coronavirus' history and to inform public health leaders about its transmission.

Find reporter Rachel Cohen on Twitter @racheld_cohen

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