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Oregon’s COVID-19 story emerges from gene sequencing

16 genomes from OHSU show great diversity
This electron microscope image shows SARS-CoV-2, orange, the virus that causes COVID-19. Researchers at OHSU are sequencing COVID-19-positive samples and comparing genomes to characterize how COVID-19 is spreading around the country and world — and how it entered and is spreading in Oregon. (Flickr/NIAID-RML) CC license

One or two individuals did not spawn the outbreak of COVID-19 in Portland, Oregon — in fact, the state’s outbreak may have one of the most diverse origin stories discovered to date in the U.S.

Researchers at the Oregon SARS-CoV-2 Genome Sequencing Center at Oregon Health & Science University began sequencing the novel coronavirus the week of April 13, and released the initial 16 SARS-CoV-2 genomes sequenced at OHSU to the viral sequence database GISAID on May 11. The MJ Murdock Charitable Trust has provided funding to support the group’s work sequencing COVID-19-positive samples from across the state.

In the weeks after the first COVID-19 case was identified in Oregon, researchers from across OHSU began discussing the importance of sequencing Oregon viral genomes and how to make that happen. By sequencing and comparing genomes, investigators can characterize how COVID-19 is spreading around the country and world — and how it entered and is spreading in Oregon.

This first release more than doubles the available data on Oregon SARS-CoV-2 genomes. Before May 11, only 11 Oregon SARS-CoV-2 genomes had been sequenced. By comparing data, investigators can characterize how COVID-19 is spreading around the country and world, and how it entered and is spreading in Oregon.

The first findings

Brian O'Roak, Ph.D.
Brian J. O'Roak, Ph.D.

“These first sequences reveal that, unlike some other outbreaks in the U.S., the introduction of the virus to the Portland metro area in Oregon is very diverse,” said Brian O’Roak, Ph.D., associate professor of molecular and medical genetics in the OHSU School of Medicine. “The current early data suggest there were 13 introductions of SARS-CoV-2 over the past two months.” 

Sequencing so far reveals two major branches of the novel coronavirus in Oregon.

“Most of the samples are descended from the A2a lineage, which you might have heard about in the news,” said O’Roak. “This is the strain that spread across Europe and New York. We have multiple independent introductions of this strain to Oregon, including one that makes up 20% of the samples.”

woman working at a laboratory bench with goggles on and inspecting a container
Ruth O'Connell, Ph.D., is inspecting samples going through cDNA synthesis, which converts the single stranded viral RNA into double stranded molecule that then can be sequenced. (OHSU)

The second major branch — again, about 20% of the samples — likely traveled down I-5 from British Columbia, through Washington and then into Oregon early in the outbreak. Other branches identified in the sequencing traveled through Europe to Canada in early March and then down to Oregon right before Gov. Kate Brown issued the Stay Home, Save Lives executive order.

Somewhat surprisingly to the team, there was no evidence that the first reported case in Oregon continued to spread. Either descendants of that case will be found when more samples are processed, or that the initial introduction to Oregon was successfully contained by testing, tracing, isolation and Oregon’s Stay Home, Save Lives initiative.

What’s next?

More samples will tell more of Oregon’s COVID-19 story, but we have an introduction to the COVID-19 outbreak in Oregon.

The team is rapidly ramping up, and will be sequencing at least 50 genomes a week. Their intention is to partner with clinical labs throughout the state with positive samples. All data are being made immediately publicly available to aid in the scientific community’s understanding of COVID-19 in Oregon.

Want more information on the Oregon SARS-Cov-2 Genome Sequencing Center? Contact:

The Oregon SARS-Cov-2 Genome Sequencing Center is co-led by principal investigators O’Roak; Ben Bimber, Ph.D., research assistant professor, OHSU Oregon National Primate Research Center; and Andrew Adey, Ph.D., assistant professor of molecular and medical genetics, OHSU School of Medicine. Brendan O'Connell, Ph.D., and Ruth O’Connell, Ph.D., are leading the viral molecular biology and sequence generation. OHSU School of Medicine collaborators include William Messer, M.D., Ph.D., assistant professor of molecular microbiology and Immunology; and Guang Fan, M.D., Ph.D., professor of pathology. OHSU Vaccine and Gene Therapy Institute contributors include Daniel Streblow, Ph.D., associate professor, and Alec Hirsch, Ph.D., assistant professor.

The current data release is freely viewable at,map&f_division=Oregon&l=radial




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