UO genome sequencing detects variant strain of coronavirus

Lab worker holding DNA samples

A University of Oregon genomics lab has detected a coronavirus variant, B. 1.429, that was first found in California, in samples taken from Lane County tests.

The UO’s Genomics and Cell Characterization Core Facility conducted whole genome sequencing of the coronavirus samples, also known as SARS-CoV-2, as part of a pilot study. The lab conducted genomic sequencing on a number samples stripped of identifying information that had been collected through the UO’s COVID-19 response efforts, including the Monitoring and Assessment Program. Lane County Public Health announced the detection March 2.

According to the Centers for Disease Control and Prevention, the B.1.429 variant appears to spread more easily and quickly, but currently there is no evidence that it is a more dangerous strain. Unlike variants first discovered in the United Kingdom and South Africa, which have not been detected through the UO’s sequencing, the CDC does not consider B.1.429 variant a “variant of concern.”

The CDC has also advised that that the two main vaccines currently available — Pfizer-BioNTech and Moderna — should be effective against it.

“The mutations which produce virus strain variants are inevitable so long as the virus has the opportunity to replicate. We see this happen in every virus strain we are aware of from measles to influenza,” said Lane County Senior Public Health Officer Dr. Patrick Luedtke. “Reducing the opportunities COVID has to replicate, or spread, is our greatest tool at fighting the impact new variants have on our community’s health. We do that by masking, distancing, reducing contact with others, and getting as many people vaccinated as possible.”

The B.1.429 variant strain has also been detected in 49 states, including Oregon, and is believed to have been circulating in the U.S. since last July. It has recently been associated with significant outbreaks in California.

In January of this year, genomic testing by Oregon State University through wastewater sampling detected a mutant strain of COVID-19 in multiple locations across Oregon including in Corvallis and in Albany, Forest Grove, Klamath Falls, Lincoln City and Silverton. This variant includes the L452R mutation also found in the B.1.429 variant identified by the UO from positive samples.

“Because of the next-generation sequencing capabilities available through the Genomics and Cell Characterization Core Facility at the University of Oregon, we may now be able to augment genomic sequencing capabilities across the state,” said Brian Fox, executive director of the COVID-19 Monitoring and Assessment Program. “Having confirmed this capability using samples collected through MAP’s testing effort, we stand ready to provide this service to support public health efforts as resources are made available. Though the presence of the variant does not change our proactive testing and tracing strategy, it provides critical information for the public health community to understand the evolution of the virus and which variants are in circulation.”

To date, the UO has processed nearly 56,000 COVID-19 tests from Lane County and, increasingly, from around the state. Those who test through the UO surveillance testing program include UO students living on and off campus, UO employees, and other Lane County and Oregon residents. Individuals must be age 3 or older and be free of COVID-19 symptoms at the time their sample is taken.

Following an increase in positive cases with the start of winter term in January, positive COVID-19 cases have declined steadily over the last five weeks both in the residence halls and the overall UO community, thanks in part to the UO’s proactive testing and tracing efforts.

“While detection of the variant in Lane County is not unexpected, it is a reminder of the importance for each of us not letting our guard down in our own COVID-19 prevention efforts at this time,” said Andre Le Duc, the UO’s chief resilience officer. “With UO case numbers declining and more people becoming vaccinated, it would be easy to become complacent. We’re all tired. We’re all so ready for the end of this new normal. But we must remain strong for each other. The COVID-19 prevention basics of wearing a mask, washing your hands and watching your distance all help control the spread of the virus, including the variants.”

The university is also urging members of the UO community not to travel at this time or over spring break. Those who do travel should take additional precautions. The CDC recommends obtaining a test 3-5 days after return and self-isolating until a negative test result is received.