Dec 16, 2021 - News

Colorado is leading in COVID detection

Percentage of recent COVID-19 cases sequenced and shared
Reproduced from GISAID; Map: Axios Visuals

It's no surprise that Colorado was one of the first states to detect the Omicron variant.

What to know: The state made genome sequencing of diseases a priority well before the novel coronavirus arrived in 2020, and public health leaders pivoted quickly to build one of the most robust systems in the country.

  • 15% of positive COVID-19 tests and wastewater samples are sequenced to determine their genetic makeup, whether at the state lab, Centers for Disease Control and Prevention or contracted commercial partners.
  • The focus enabled Colorado to be the first state to detect the Alpha (B1.1.1.7) variant that originated in the United Kingdom.

Why it matters: Colorado public health leaders say the sequencing allows the state to learn how COVID-19 changes as it moves through the population and track where variants are proliferating.

  • The information is used to deploy public resources to combat its spread, said Emily Travanty, laboratory director at the Colorado Department of Public Health and Environment.
  • But it's not a silver bullet, as Colorado saw throughout five waves of COVID.

Background: Before the pandemic, the state lab would sequence the genetic makeup of food-borne illnesses and influenza to determine sources and trajectory.

  • Those existing resources made it easy to expand the work to the coronavirus.

What they're saying: "We were an early adopter because we were able to capitalize on expertise we already had," said Travanty.

How it works: The concerted effort to screen as many COVID samples came from a desire to understand how the virus spread before and after vaccinations.

  • The process takes several days. The state can analyze 96 different positive coronavirus samples from PCR tests in a microfluidic device.
  • The lab also tripled in size and now boasts 300 people who perform diagnostic work.
  • It costs about $100 per test to analyze, officials said.

The big picture: Omicron has thrust the U.S.'s genetic surveillance capabilities back into the spotlight. The more cases sequenced, the better the chance of finding the variant before it takes off, Axios' Caitlin Owens writes.

  • The U.S. overall has vastly expanded its genetic sequencing capacity over the last several months. But looking at national numbers obscures the drastic variation between states.
  • "We have some parts of the country that are only sequencing 3% and that's not nearly enough to be able to pick up a variant in those places," Céline Gounder, an infectious disease specialist and epidemiologist at New York University and Bellevue Hospital told Axios.

This story first appeared in the Axios Denver newsletter, designed to help readers get smarter, faster on the most consequential news unfolding in their own backyard.


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