Utah researchers using genetic code of coronavirus to learn about spread

SALT LAKE CITY — Researchers at the Utah Department of Health and ARUP Laboratories are doing some scientific sleuthing to learn how COVID-19 has spread in Utah.

They are analyzing the genetic code of the virus to find out where it came from and potentially how to stop it.

Just as every human has a unique genetic code, each sample of coronavirus, swabbed from a patient’s nose, also has a genetic blueprint. The Utah Public Health Laboratory was one of the first public health labs to generate whole-genome sequenced data for SARS-CoV-2, the coronavirus that causes COVID-19.

“Utah was one of the early pioneers in this,” said Dr. Kelly Oakeson, the Utah Public Health Lab’s chief scientist for bioinformatics and next-generation sequencing. “Right now, we have sequenced approximately 600 or so COVID-19 genomes.”

That’s the genetic material taken from 600 Utahns who tested positive for COVID-19. Oakeson said it’s cool science that has a real public health impact.

“We try to trace it back to its source using these molecular biology gene sequencing techniques,” he said. “Our goal is to actually sequence every positive specimen in Utah. With that kind of data, then we can start pinpointing trends.”

The Utah Department of Health research team is working with ARUP Laboratories and Boston-based Ginkgo Bioworks to study the genetics of COVID-19 in Utah and analyze how the molecular makeup of the virus is evolving.

“Are we seeing all of the same variance in Utah?” Oakeson asked. “Meaning it came in once and spread through the community, one particular strain at a time? Or are we seeing multiple introductions of multiple different variants coming in from California, Washington, Texas, Nevada or wherever, and then kind of individual pockets of spread?”

Right now, Oakeson said it looks like COVID-19 came into Utah from several directions.

“It doesn’t look like it was a single point introduction,” he said. “It looks like it was kind of multiple introductions from around our neighboring states, and then also spreading back out to those neighboring states.”

Oakeson added there’s been a lot of COVID-19 transmission in and around Utah, and we are sharing it back and forth with our neighboring western states.

“We’re also trying to look at some of the hotspots,” he said.

They hope to use this tracking technique with genetic material to learn more about outbreaks in the Navajo Nation, the homeless community and long-term care facilities.

They’re compiling that genetic data to find out how the virus spreads once it gets inside one of those communities.

“Is it a single introduction that then sparks a wildfire that grows? Or is it three or four multiple introductions?”

Typically, Oakeson’s team relies on genetic sequencing and analysis to help track food-borne pathogens back to their sources — sometimes all the way back to a specific food handler or farm. They also use genetic sequencing to trace the causes of hospital-acquired infections.

“We were really hoping to apply that same type of technique and technology from the bacterial world to COVID-19,” said Oakeson.

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He hopes to analyze all COVID-19-positive samples in Utah to build a clearer picture of the spread of the virus. ARUP and the Boston-based lab have the capacity and the experience to help with that project.

As a Utah native, Oakeson enjoys working on public health solutions for his community.

“I’ve been here all my life. I love Utah. So, being able to help out the residents of Utah really warms my heart, and is what keeps me going from day to day,” he said.

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