Genetic Analysis Of Coronavirus Helps Researchers Track Spread

May 3, 2020

Analyzing the genetic code of the new coronavirus is giving researchers a new way to track the virus, as it spreads and mutates over time. The approach can help fill in the gaps of traditional “boots on the ground” epidemiology, which relies on case investigation and contact tracing.

Scientists can now analyze the genome of the coronavirus so quickly, they’re tracking its spread around the world, almost in real time. It’s a relatively recent technological development, and the tools have become even more powerful and accessible in the years since the West African Ebola outbreak, when researchers’ use of genetic analysis represented “a watershed moment."

Paraic Kenny, who directs the Kabara Cancer Research Institute at Gunderson Medical Foundation, is doing this work in Wisconsin, Minnesota and Iowa. By analyzing the genetic code of different strains of the virus that patients contract, he’s able to track the subtle mutations in the virus over time. Based on those mutations, he’s able to follow the virus through patients, as they carry it from New York City to Postville to LaCrosse, and who else contracted it along the way.

“When a virus infects a person, it needs to make many, many copies of itself in order to infect somebody else. And these copies are not always made faithfully,” Kenny explained.

Sometimes a “spelling mistake” is introduced into the “instruction manual” to build the virus as it replicates. Every subsequent person who is infected with the virus will have the same spelling mistake in the same position, allowing researchers to track the mutations across people and across time, Kenny said.

“It makes it challenging to say that an exact individual gave this disease to another exact individual. But we can be really, really confident that if individuals have very closely related viruses, that they share a very common infection history in the recent past,” Kenny said.

This approach can help fill in the gaps of contact tracing, which relies on patients’ relationship and memories. The specificity of genomic analysis can link cases that might not seem connected otherwise.

Of the cases he’s analyzed, Kenny says an outbreak at a meat processing plant in Postville stands out for how fast it spread, even crossing state lines.

“What we’re seeing with this outbreak in Postville really underlines the infectious nature of this virus and its ability to spread quickly in situations where that is not being mitigated,” he said.

He says it’s “highly likely” that outbreaks are spilling over at other industrial facilities as well, infecting not only workers but their families and others in the broader community.

“In the next weeks we will be seeing, I’m sure in all of those cases if we are not seeing it already, spill over into other populations in those regions that are not directly working in those plants, or households members of individuals who work in those plants,” Kenny said.