When the Northeastern community returns to weekly surveillance COVID-19 testing in the fall for everyone, regardless of vaccination status, the COVID-19 wellness team won’t just be monitoring positive or negative cases. They’ll also be keeping track of the variants of the virus that are infecting the community—and they will be able to quickly identify which strains are responsible.
“The pandemic is not over, but it has evolved,” says Jared Auclair, who runs Northeastern’s COVID-19 testing facility, the Life Sciences Testing Center in Burlington, Massachusetts. “There are a couple of important things to think about in our testing strategy: We still need to provide the binary positive or negative, which we’ll do, but we are supplementing that with additional tests to determine what is going on in those positive patients, what’s happening within our Northeastern population.”
Many testing labs will sequence the full genome of viral samples that test positive for COVID-19 in order to determine what strain of the coronavirus is causing the disease. That approach, says Auclair, director of biotechnology and bioinformatics in the College of Science, is great for researchers who are studying how the virus mutates. And the Northeastern lab also takes this approach.
But sequencing the entire genome of the virus takes time, he says, and waiting a few days to know that a variant of concern is circulating in the community could mean precious time lost in stopping the spread. So the Northeastern team is adding in another step to determine which strain of the virus is behind a positive COVID-19 test within just a few hours.
The goal, Auclair says, is “that the university can be more proactive as opposed to reactive.”
The procedure for testing a sample for variants is largely the same as conducting the polymerase chain reaction (PCR) test for COVID-19 in general. In that process, the scientists are looking for three genes unique to the virus in a patient’s sample. They don’t use all of the cells in an individual person’s sample so that they can run more tests if needed. If it comes back positive, the sample will glow in the lab. Then, the team will run the same kind of test on it again, but this time, instead of checking the sample for the markers of COVID-19, they will probe it for distinctive markers of known variants of concern.
There are four variants currently considered worth monitoring: Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2). The technology for this testing system comes from a partnership between Northeastern and Thermo Fisher Scientific. “One of the reasons the partnership is so great is that if there are new variants that come up that we want to track,” the scientific instrumentation company is poised to add it to the testing panel quickly, Auclair says.
Once the Northeastern COVID-19 testing team determines which variant is responsible for the positive test, the viral genome in the sample will then be fully sequenced for an even closer look at which coronavirus strains are circulating.
This system also could help Northeastern better monitor when variants of the coronavirus that causes COVID-19 evade vaccine protections.
“One thing that we’ll be tracking with the variant panel is people who are vaccinated,” Auclair says. Northeastern has required all of the university’s students, faculty, and staff that will be on campus in the fall to be fully vaccinated against COVID-19. “What is the variant, or what is the DNA sequence of the virus that they have? With this testing strategy, we can correlate a vaccinated person to a positive test so that we can start helping inform the community at large,” he says, about how readily a given variant causes breakthrough infections, whether booster shots might be needed, and any other unanswered questions.
In addition to these measures, the university is installing special air filtering devices, called AerosolSense, to monitor the virus in indoor spaces around campus.
Each device is about the size of a microwave oven, and can capture particles of airborne pathogens, like the coronavirus or the flu onto a filter. The filters are collected and then sent to the laboratory for Auclair’s team to test.
“It’s a great tool for us now to monitor the air for COVID-19,” Auclair says. “But it’s also an interesting tool that could be used for pathogen surveillance all the time in the future.”
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