How sewage led researchers to the contagious variant of COVID-19 in central Oregon

Sewage sampling played a key role in helping researchers detect the presence of the highly contagious UK variant COVID-19 in central Oregon.

Scientists at Oregon State University’s Genome and Biocomputing Research Center said on Friday that they collected wastewater samples as part of a partnership between the Oregon Health Authority and the university’s TRACE project.

Long before global concerns about the spread of more contagious variants emerged, this Oregon project has been collecting wastewater samples to monitor the spread and distribution of coronavirus in dozens of communities across the state.

The program proved valuable in detecting variants when samples collected from Bend on December 22 were sequenced last week by OSU, revealing the variant’s presence in the UK.

The UK variant, called B.1.1.7, spreads faster than the versions that dominated the pandemic last year. It has been detected in three Oregonians so far.

“We will see the variants of COVID-19 increase and decrease in abundance in our population over time, and the increase in a new variant is not necessarily a cause for alarm,” said the Oregon Health Authority’s director of viral respiratory pathogens, Dr. Melissa Sutton. launch. “However, monitoring for variants is critical to our understanding of disease transmission, disease severity, evasion capacity, vaccine effectiveness and resistance to treatment.”

People infected with the coronavirus eliminate the virus in their stool. Scientists have developed a technique to detect genetic material from the virus in the wastewater stream. Depending on where the sewage samples are collected, it is possible to isolate neighborhoods, hospitals, schools and other facilities to monitor outbreaks.

Using these samples to identify specific mutations in the coronavirus is a new and developing use of this technique. It moves the capabilities of scientists in addition to testing whether the coronavirus is present; by sequencing the virus genome, researchers can determine specifically which variants are present.

On Monday, the OSU laboratory completed genetic sequencing on more than 1,100 samples – 936 samples of wastewater and 174 individual samples from the TRACE project.

Related: Coronavirus wastewater surveillance expands to communities across Oregon

The OSU Genome and Biocomputing Research Center and TRACE co-investigator Brett Tyler said that another variant of COVID-19 was also detected in recent samples.

“We detected the genetic fingerprint of another variant that is under surveillance,” said Tyler during a news conference on Friday. This variant is known as L452R, or the “California variant”, in honor of the state where it spread after reaching the United States. It was first identified in Denmark.

The variant was detected in four samples of wastewater from the OSU campus and samples from wastewater treatment plants in Albany, Forest Grove, Klamath Falls, Lincoln City and Silverton, Tyler said.

The L452R variant has been around since last March, but recently it has been the cause of major outbreaks in Santa Clara County in California and has spread throughout southern California. Tests have shown that COVID-19 vaccines may be less effective against the variant.

“We are a little concerned about this strain, but it is not as worrying as the strains in the UK, South Africa and Brazil,” said Tyler. “But we want to keep an eye on that.”

Recently, researchers at the center have been particularly alert to identify any evidence of different variants of COVID-19, especially those in the United Kingdom, South Africa and Brazil that have been shown to be more contagious than common variants of the virus.

These three variants have a mutation in the virus’s spike protein that can allow individual virus particles to bind to a person’s cells more effectively.

A different variant detected in South Africa appears in the results released so far to be less responsive to some versions of the COVID-19 vaccine. It was detected in the United States just this week.

The Oregon Health Authority and OSU plan to expand the practice of collecting wastewater samples to all counties in the state and conduct sequencing weekly to track the arrival and spread of variants.

A scientist who recently published a study on this type of research said that, as valuable as it is, it is also difficult work.

“That’s when we can start to distinguish between these different mutations. The problem is that there is so little of it in wastewater compared to everything else in wastewater, ”said Rose Kantor, a researcher at the University of California at Berkeley. “It is simply difficult to get a good sample and do it well.”

Kantor’s article was published in mid-January in the mBio newspaper.

Now that their Bay Area research team knows what to look for, they are working with other groups to develop targeted tests to detect whether specific viral mutations are present, she said.

“This would be much more feasible and faster than sequencing,” she said. “That said, sequencing can reveal variants that we don’t know about.”