As the novel coronavirus – known to scientists as SARS-CoV-2 – reproduces, variations appear in its genetic code. Accumulating over time, these changes are like fingerprints, leaving a telltale trail of clues about where the virus has been, and where it might be headed.
University of New Mexico scientists Darrell L. Dinwiddie, PhD, and Daryl Domman, PhD, are playing the role of genomic detectives trying to crack the case.
They are part of a newly formed national consortium of research universities and public health departments seeking to track the disease. Dubbed SARS-CoV-2 SPHERES, the program is sponsored by the National Center for Emerging and Zoonotic Infectious Diseases (a branch of the Centers for Disease Control and Prevention) as a way to pool crucial information about the virus.
Dinwiddie, an assistant professor in the UNM Department of Pediatrics, has been sequencing hundreds of coronavirus samples obtained from the New Mexico Department of Health and the Wyoming Public Health Laboratory in his molecular genomics lab over the past few weeks.
“We recently completed the first 48 genomes from New Mexico,” he says. “There’s strong indication that the majority of the first infections in the state were travel-related from around the world.”
Dinwiddie has been collaborating in the analysis with Domman, PhD, an assistant professor in the Department of Internal Medicine. “He does a lot of what we call genomic epidemiology,” Dinwiddie says, adding that Doman has experience following outbreaks of cholera around the world. “We’re using very similar methods to investigate SARS-CoV-2.”
The novel coronavirus genome is encoded in strands of a molecule called RNA. Minor changes in the sequence of nucleotides in the strand provide information about how closely related one viral sample is to another.
Scientists like Dinwiddie and Domman are hard at work building a library of these samples to create a viral family tree.
A preliminary analysis of samples collected in New Mexico suggests there were multiple introductions of the virus into the state, which is consistent with early reports of cases among people who had traveled abroad or domestically.
“We can also say from the early genomic analysis the majority of samples are more similar to the strains coming out of Europe or New York,” he says. “We’re not seeing very many that are closely related to the ones in China.”
Genomic variation in viral reproduction is a natural process. “For the SARS-CoV-2 S the rate of genomic change has been fairly stable,” Dinwiddie says. “We know how quickly it changes. Based on that information we can make predictions about how far back different samples have gone.”
The viral samples are taken from nasal swabs collected from patients who have tested positive for coronavirus infection. They are handled using biosafety procedures and inactivated so that they are no longer infectious, Dinwiddie says.