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Another variant of the virus, of less concern, found in Corvallis, in other towns in Oregon
CORVALLIS, Ore. (KTVZ) – Genetic sequencing of COVID-19 samples performed by the Center for Genome Research and Biocomputing at Oregon State University has detected several variants of the SARS-CoV-2 virus that causes COVID-19 in samples from across the state, including the highly contagious British strain in a sample from Bend.
Bend’s wastewater sample was obtained on December 22, and sequencing performed by OSU revealed the British strain on January 21, the school said on Friday.
Bend is one of many places in the state where OSU’s TRACE Community Project conducts wastewater testing, which is funded in part by the Oregon Health Authority.
“The OHA is working quickly with the Centers for Disease Control and Prevention and partners statewide to implement COVID-19 sequencing surveillance to track changes in viral mutations over time. All viruses mutate and these variations are not unexpected, ”said Dr. Melissa Sutton, OHA Medical Director of Respiratory Viral Pathogens.
“We will see COVID-19 variants increase and decrease in abundance in our population over time, and the rise of a new variant is not necessarily a source of warning,” added Sutton. “However, variant surveillance is essential to our understanding of disease transmission. , disease severity, ability to avoid testing, vaccine effectiveness and resistance to treatment. ”
As a partner of OSU’s TRACE project, since last spring, the university’s Center for Genome Research and Biocomputing has been performing genetic sequencing on all positive COVID-19 samples obtained from TRACE tests of individuals and wastewater from OSU campuses and Oregon communities.
In recent weeks, researchers at the center have been particularly attentive to identifying any evidence of variants of SARS-CoV-2, including the British, South African and Brazilian variants which have been found to be more contagious than common variants of the virus. . All three of these variants have a mutation in the virus spike protein that can allow individual particles of the virus to attach to a person’s cells more efficiently.
“With the arrival of new variants, it becomes increasingly important to understand which variants are circulating between communities,” said Brett Tyler, director of the Genome Center.
The Centers for Disease Control and Prevention has stepped up surveillance for mutant spots across the country, as agency experts fear the mutant strains could possibly escape the vaccine being distributed, especially if there are delays in getting the second dose of vaccine needed by people. strong immunity.
And since the current mutants in the UK, South Africa and Brazil are much more contagious and therefore spread faster, contact tracing for any case of mutant COVID-19 will need to be swift to avoid further spread.
On Monday, the OSU lab completed genetic sequencing of more than 1,100 samples – 936 wastewater samples and 174 individual samples from the TRACE OSU and TRACE Community surveys statewide. In Oregon, only OSU and OHSU in Portland are currently performing genetic sequencing on viral samples.
Five individuals tested at OSU’s Corvallis campus were positive for the “L452R” mutant strain of COVID-19. The strain was also present in the campus wastewater samples.
“This strain is not the most worrying, like the other three (variants from UK, South Africa and Brazil), but it has spread widely in southern California and has been associated with recent major epidemics in Santa Clara County, ”Tyler said.
The L452R variant first appeared last March. It does not have the mutation in the spike protein that makes the other variants so worrying, but lab tests have shown that its mutation can reduce antibody binding, which could affect the effectiveness of the COVID-19 vaccine. although it is not known how well the lab tests will mimic real world infections.
“Normally when you vaccinate people they generate a lot of different antibodies against the spike protein. The fact that a particular antibody might not bind as well – we’re somewhat concerned about this strain, but it’s not as concerning as the British, South African and Brazilian strains, ”Tyler said. “But we want to keep an eye on it.”
There are two subtypes of the L452R strain, and both have been detected in samples analyzed by OSU, he said. The strains have also been detected in wastewater from Albany, Forest Grove, Klamath Falls, Lincoln City and Silverton.
“It’s no surprise that we detected this strain,” Tyler said. “Since the L452R has been around for a long time and is currently prevalent in California, it stands to reason that it would likely find its way here. But it does indicate the importance of sequencing to ensure follow-up. ”
As the country enters the vaccination phase of the pandemic, it will become more important to know exactly which viral strains are circulating, as they could impact the effectiveness of the vaccine, said Tyler Radniecki, associate professor of engineering at OSU and responsible for the wastewater sampling of TRACE.
“The more the pandemic gets, the more genetic variation we see in the virus, and some variations in this phase of the pandemic may well matter,” Radniecki said.
“Wastewater sampling is particularly powerful, because of its broad scope,” Tyler said. “Each sample represents a survey of an entire community, or sub-section of a community, which is much more cost effective than testing people one by one.”
OHA will partner with OSU to expand its wastewater monitoring to all counties in the state, Radniecki said. All samples from these sites will be sequenced weekly.
The three laboratory staff at the Center for Genomic Research and Biocomputing, plus a bioinformatician, are working on the sequencing of COVID-19. The lab has the equipment capacity to double or triple its sequencing results, but would require more staff.
Collection, testing, and sequencing of SARS-CoV-2 samples in Oregon communities were funded by OSU, the David and Lucile Packard Foundation, PacificSource Health Plans, Oregon Health Authority, and the National Science Foundation .
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About the Center for Genome Research and Biocomputing: One of OSU’s interdisciplinary research centers and institutes, the Center for Genome Research and Biocomputing facilitates genomic and big data-driven research in the life and environmental sciences at OSU and across the ‘State. Research in the affiliated laboratories of the CGRB and the faculty aims to improve health, make better use of natural and agricultural resources, understand our global environment and develop new bio-based products and energy sources.
About the TRACE project: TRACE – short for Team-based Rapid Assessment of Community-Level Coronavirus Epidemics – is an OSU public health project designed to collect timely information on the presence of the novel coronavirus responsible for COVID-19 in communities around in Oregon and on OSU campuses. TRACE is funded by the David and Lucile Packard Foundation, PacificSource Health Plans, Oregon State University, and the Oregon Health Authority. See https://trace.oregonstate.edu.
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