Sewage sampling played a key role in helping researchers detect the presence of the highly contagious U.K. COVID-19 variant in Central Oregon.
Scientists with Oregon State University’s Center for Genome Research and Biocomputing said Friday they had been collecting wastewater samples as part of a partnership between Oregon Health Authority and the university’s TRACE project.
Well before global concerns had arisen about the spread of more contagious variants, this Oregon project has been collecting wastewater samples to monitor the spread and distribution of the coronavirus in dozens of communities around the state.
The program proved valuable in detecting variants when samples collected from Bend on Dec. 22 were sequenced last week by OSU, revealing the U.K. variant’s presence.
The U.K. variant, called B.1.1.7, spreads faster than the versions that have dominated the pandemic for the past year. It’s been detected in three Oregonians so far.
“We will see COVID-19 variants rise and fall in abundance through our population over time and the rise of a new variant is not necessarily cause for alarm,” Oregon Health Authority Medical Director of Respiratory Viral Pathogens Dr. Melissa Sutton said in a press release. “However, monitoring variants is critical to our understanding of disease transmission, disease severity, the ability to evade testing, vaccine effectiveness and treatment resistance.”
People infected with the coronavirus shed the virus in their feces. Scientists have developed a technique to detect genetic material from the virus in the wastewater stream. Depending on where the sewer samples are taken, it’s possible to isolate neighborhoods, hospitals, schools and other facilities to monitor for outbreaks.
Using those samples to identify specific mutations of coronavirus is a new and developing use of this technique. It moves scientists’ capabilities beyond testing if the coronavirus is present; by sequencing the genome of the virus, researchers can determine specifically what variants are present.
As of Monday, the OSU lab has completed genetic sequencing on more than 1,100 samples – 936 wastewater samples and 174 individual samples from the TRACE project.
OSU’s Center for Genome Research and Biocomputing and co-principal investigator of TRACE Brett Tyler said another COVID-19 variant was also detected in recent samples.
“We’ve detected the genetic fingerprint of another variant that’s on the watch,” Tyler said during a Friday press conference. That variant is known as L452R, or the “California variant,” named for the state where it has spread after arriving in the U.S. It was first identified in Denmark.
The variant was detected in four wastewater samples from the OSU campus and in samples from wastewater plants in Albany, Forest Grove, Klamath Falls, Lincoln City and Silverton, Tyler said.
The L452R variant has been around since last March but has recently been the cause of large outbreaks in California’s Santa Clara County and has spread throughout Southern California. Tests have shown COVID-19 vaccines may be less effective against the variant.
“We’re somewhat concerned about this strain, but it’s not as concerning as the U.K., South African and Brazilian strains,” Tyler said. “But we do want to keep a close eye on it.”
Recently, researchers at the center have been particularly alert to identifying any evidence of different COVID-19 variants, especially the U.K, South African and Brazilian variants that have been shown to be more contagious than common variants of the virus.
Those three variants have a mutation in the virus’ spike protein that may allow individual particles of the virus to latch onto a person’s cells more effectively.
A different variant detected in South Africa is appears in 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 wastewater sample collecting to every county in the state and conduct sequencing on a weekly basis to keep up on the arrival and spread of variants.
A scientist who recently published a study on this kind of research said that as valuable as it is, it’s also difficult work.
“That’s when we can start to distinguish these different mutations. The catch is just that there’s so little of it in the wastewater compared to all the other things that are in wastewater,” said University of California, Berkeley researcher Rose Kantor. “It’s just difficult to get a good sample and do it well.”
Kantor’s paper was published in mid-January in the journal mBio.
Now that her 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.
“That would be a lot more feasible and rapid than sequencing,” she said. “That said, sequencing can uncover variants that we don’t know about.”