Washington State Department of Health provides next-generation genome sequencing to identify new COVID strains

The State Public Health Lab is in Shoreline on 15th NE
Photo by Steven H. Robinson

OLYMPIA -- The Washington State Department of Health (DOH) has increased its capacity to identify new strains of COVID-19 using next-generation genome sequencing equipment.

The goal is to test several thousand specimens a month at the Public Health Lab in Shoreline,.

Sequencing has been used since the beginning of the COVID-19 outbreak to analyze the RNA structure of the virus and determine how it is mutating. 

Like all viruses, COVID-19 constantly mutates as it spreads. By combining sequencing data with data from case and contact investigations, we can better detect outbreaks, identify and track new and emerging variants, and determine the effectiveness of public health control measures.

Both the B.1.1.7. and B.1.351 variants identified in Washington state were detected during routine genome sequencing.

DOH also contracts with virology labs at the University of Washington and Fred Hutchinson Cancer Research Center to conduct genome sequencing of COVID-19 specimens. Other regional labs in Washington also conduct these tests. Sequencing data results are shared with the Centers for Disease and Prevention (CDC).

The new equipment will process samples of specimens from people who have tested positive for COVID-19. These specimens are sent to virology labs when a person is tested. The process does not require a second test or contact with the person who tested positive. Personal identifiers are removed to protect privacy.

The equipment DOH has purchased includes next-generation genome sequencing tools. 

“This is a whole different technology,” said DOH Deputy Director of Microbiology Philip Dykema, PhD. “This equipment uses nano technology to sequence molecules at a much higher rate of speed, while sequencing the whole strand from end-to-end.” Dykema said.  

This capability will be invaluable even after the pandemic ends.

Sequencing will continue to be an important part of DOH’s COVID-19 surveillance, says Scott Lindquist, MD, MPH., Acting State Health Officer and State Epidemiologist for Communicable Diseases: 

“This is a vital tool in quickly identifying virus mutations so that important public health decisions can be made to protect the health and safety of all those in Washington state.”

Currently, Washington state labs conduct sequencing on approximately two percent of SARS-CoV-2 specimens. According to Science Magazine, that places Washington third among all states based on the number of specimens sequenced per capita. “Our goal is to increase that rate to five percent,” said Lindquist.

The Department of Health publishes a weekly SARS-CoV-2 sequencing and variant report on the agency’s web site that summarizes genome sequencing from multiple laboratories to provide a statewide view of sequencing capacity and data.

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