When Northeastern began outlining its COVID-19 testing plan last spring, Jared Auclair, director of Northeastern’s testing lab, had a hunch: The university needed a monitoring system that could adapt to inevitable mutations of the virus in the future.
As the pandemic unfolded, viral mutations were top-of-mind for Auclair, whose background in drug resistance in HIV patients prepared him for the havoc mutations could wreak, disguising viruses in diagnostic tests and negating the effects of medication.
Considering these possibilities, Auclair helped Northeastern design a system that detects positive cases of COVID-19 by scanning for three of the virus’s genes, a more thorough system than most labs, which usually monitor for only one or two genes.
Adding extra genes to the watchlist allows the system to scan for mutations—changes in the virus’s genes—that could otherwise enable positive cases to go unnoticed, Auclair explains. Plus, monitoring for more genes, especially those that are prone to mutations, enables Northeastern to identify new variants faster than other labs.
Monitoring three genes is a costlier and more complicated process than the standard set by the Centers for Disease Control and Prevention, which recommends monitoring for only one gene, Auclair says. But he believes the decision has paid off, as new variants of the virus infiltrate communities around the globe, threatening to evade standard testing and bypass the vaccine.
Right now, scientists and healthcare workers are worried about three variants in particular that each have mutations in the virus’s spike protein. Changes to the spike protein—the mechanism the virus uses to enter and infect healthy cells—are alarming because they could potentially increase transmissibility or reduce the efficacy of vaccines.
Most labs don’t look for the spike protein’s gene (the S gene) when testing for COVID-19. But Northeastern’s lab does, making it easier for the lab to detect positive cases caused by new variants, Auclair says.
In layman’s terms, here’s how testing works: When searching for positive cases, the testing center looks for the presence or absence of three genes (S gene, N gene, and ORF1ab gene) in each sample. A perfect match equals a positive COVID-19 case. A partial match of one or two genes equals a negative case or a positive case of a new variant, Auclair explains.
Samples with two positive gene matches are prioritized for genomic sequencing, especially cases where the S gene is not detected. Similar to the genomic sequencing done in services such as 23andMe to determine the ancestry of a person, genomic sequencing done at Northeastern’s lab determines the ancestry of the virus.
Lab technicians can use this information to determine whether the case is caused by a previously identified variant or a new variant, recognizable by the mutations on the S gene, explains Auclair.
Other labs are capable of finding new variants also. But searching for the S gene gives Northeastern a time advantage, Auclair says. Instead of sequencing the entire genome of every single test sample to look for new variants—a laborious and time-consuming process—Northeastern can prioritize which samples to sequence based on which ones match the N gene and the ORF1ab gene but lack the S gene, he explains.
“Other institutions don’t have this capability. They have to brute-force sequence everything, whereas we can be smarter about prioritizing our sequencing to determine exactly which variants are on campus,” Auclair says. For reference, it takes about 36 to 48 hours to sequence the DNA of one sample.
As of now, Northeastern has no identified cases caused by the current variants of concern, but in the event that those new variants make their way to campus, the university’s lab is well equipped to find those cases quickly and efficiently.
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