When COVID-19 reached Arizona State University back in January, state agencies weren't yet performing coronavirus testing. All samples were handled by the Centers for Disease Control and Prevention.
But the university felt it needed to get a handle on the virus.
"We were concerned whether this virus was circulating in the community, and we needed to be able to pick it up," said ASU virologist Efrem Lim.
So ASU researchers quickly retooled an existing influenza surveillance project to SARS-CoV-2, the virus that causes COVID-19.
Disease surveillance, an essential tool in epidemiology, involves amassing and analyzing data from a variety of sources to understand which strains are circulating and which health measures are effective.
"You can see how that sort of framework can be very easily leveraged to understand, of people who are presenting with respiratory symptoms in the clinic, how many of these cases are due to SARS-CoV-2 itself?" said Lim, a project researcher and coauthor on the Journal of Virology paper.
Now, that project has turned up a sample with a sizable mutation in an intriguing area.
In the 2003, the SARS virus used a protein called ORF7a to stymie the body's immune system. Some have since hypothesized changes in the gene associated with that protein helped end the SARS epidemic.
Now, ASU researchers have found a mutation in the ORF7a gene in a single isolate of the current coronavirus. An isolate is a version of an organism separated from others of its kind. In virology, an isolate is a less significant variant than a strain.
Genetic sequencing of the isolate revealed a deletion of 81 nucleotides within the 30,000 or so "letters" that make up the virus's genetic code.
Such a sizable change at such a potentially consequential genetic site could provide a good target for future research, but Lim cautions against jumping to any conclusions, good or bad.
"This is one isolate and is very interesting, but we do need more functional studies to really understand what it means," he said.
After all, viruses mutate. It's what they do. Sometimes those error accumulations matter, but more often they don't.
So, while it's tempting to hope such a mutation implies the coronavirus is winding down, there's no support for such a conclusion. As yet, researchers can only infer the ORF7a gene's role in the current coronavirus.
Moreover, the isolate is only one of thousands that together make up only a small percentage of all the SARS-CoV-2 isolates out that no one has yet sampled.
But it's a place to start, said Lim.
"All of these mutational studies give us a point of reference to prioritize parts of the virus genomes that we should look into to do the functional studies."
