As the world scrambles to make sense of the new omicron variant of the coronavirus, Northeastern is ready to spot it if it enters our community.
Northeastern’s COVID-19 testing laboratory can already detect the omicron variant through existing protocols. And that could save the university community precious time in identifying and responding to any threat the variant might pose.
“We take a more targeted approach, which gives us a head start,” says Jared Auclair, who runs Northeastern’s COVID-19 testing facility, the Life Sciences Testing Center in Burlington, Mass. “We have a test in line that really helps us identify these variants. We, as a university, did the right thing and continue to do the right thing to be able to track these things, so the population should feel confident that they are still safe.”
Auclair’s team has been monitoring variants in the Northeastern community for months by testing all positive samples for distinctive markers of strains of the virus identified as “variants of concern.” That approach reveals a result within just a few hours, rather than the days it can take to sequence the entire genome of every positive sample (although the Northeastern scientists do that, too, so they don’t miss anything). Those results are reported on the university’s daily COVID-19 dashboard.
There isn’t a test specifically for the omicron variant just yet, but the approach to COVID-19 testing that the team at the Life Sciences Testing Center uses will still catch cases, Auclair says. That’s because the omicron variant has a key similarity to the alpha variant, which the lab is already screening for.
Here’s how it works: When swabs come into the testing facility from Northeastern’s asymptomatic surveillance testing center or symptomatic testing center, they are first run through a 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: the ORF1ab gene, the N gene, and the S gene.
Many labs just scan for one or two of the virus’s genes, and often the S gene is not among them. But Northeastern opted to include the S gene because it allows the testing system to scan for more mutations.
That choice is proving critical now, Auclair says.
When the testing center finds a sample with all three of those genes, it has found a clearly positive COVID-19 case. But if the test results are positive for only one or two of the genes, it could be a variant in which mutations have occurred on the missing gene.
That’s the case for the alpha variant. The S gene has “dropped out,” as scientists call it. So far, that has indicated to lab technicians that the alpha variant may be present in a sample.
The omicron variant includes mutations on the S gene, too. So the S gene would also drop out if a sample contains the omicron variant.
“We can prioritize those immediately. Right after we get the test result, an S gene can be flagged.” Auclair says. “It’s either alpha or omicron, generally speaking, and we’ve already seen alpha travel the world, so it likely would be this new variant.”
Next, the lab technicians would sequence the S gene or the whole viral genome to be sure that omicron is the culprit. The Northeastern testing team fully sequences positive test results for an even closer look at which strains of SARS-CoV-2, the coronavirus that causes COVID-19, are circulating.
Auclair and his team at the Life Sciences Testing Center are working with their partners to develop probes specific to omicron as well. He expects that system to be online within the next few weeks. President Joe Biden has urged Americans to remain cautious, but not panic, as the omicron variant is detected in more places around the world.
“We’ve come a long way from March of 2020,” Auclair says, offering “kudos” to the South African COVID-19 surveillance teams that identified the omicron variant. “I think it speaks to the infrastructure that the world has set up and the ability to track and monitor and identify and sequence.”
Northeastern currently requires everyone on its campuses to undergo COVID-19 testing once a week. The surveillance testing strategy is accompanied by a vaccine requirement for all students, faculty, and staff.