As cases of the omicron variant of COVID-19 pop up across the U.S., scientists at a Bar Harbor lab are likely to detect when the new variant has arrived in Maine.
The Jackson Laboratory performs most of the coronavirus genomic sequencing that’s happening in Maine. It is likely, though not guaranteed, that it will be the first to identify the state’s first case of the omicron variant.
Maine Center for Disease Control and Prevention Director Nirav Shah said Wednesday that it was “a matter of time” before the variant comes to Maine, though he warned residents not to panic.
The lab’s work detects when a new virus strain shows up in Maine and how prevalent it is. Earlier this year, those efforts revealed that the delta variant had become the most pervasive coronavirus strain circulating in Maine.
The lab has been sequencing coronavirus genomes since May 2020, with the work becoming more routine in December 2020. Some of its early work involved finding out more about how the coronavirus first arrived in Maine. It is now doing sequencing weekly and publishing the results in reports published on the Maine CDC’s website.
The latest report shows that 99 percent of the samples it sequenced in November were delta variant cases.
Though the lab’s work is primarily surveillance of Maine coronavirus samples, its data help other researchers in the U.S. and internationally, said Ryan Tewhey, an assistant professor at the laboratory who leads a team of researchers who do genome sequencing.
“The sum of all those efforts is much greater than any one single state,” Tewhey said.
None of the 150-190 samples sequenced this week contain the omicron variant, Tewhey said. Maine usually doesn’t see new coronavirus variants until weeks after the rest of the country, he said. But the lab is ready to identify the variant when it comes.
“If this is to follow the trajectory of alpha and delta, it’s usually a few weeks after we first start to see it really circulating at high frequency at a national level and then, more specifically, at a regional level,” Tewhey said.
Like other health experts have done since South Africa reported the variant to the World Health Organization on Nov. 24, Tewhey warned that there was still a lot that experts don’t know about the variant.
The next couple of weeks will likely provide better answers, Tewhey said, including how transmissible it is and if it can overcome the protections from the COVID-19 vaccine or a prior coronavirus infection.
“It’s important to be concerned,” Tewhey said. “You want to take precautions, be prepared. But we don’t want to panic because we don’t have all the information.”
What really distinguishes this variant from others, besides its report of faster spread within South Africa, are the 30-plus mutations in the variant’s spike protein. That spike protein is on the outside of the virus, and is how the virus infects hosts.
“Spike is the one we’re always focused on because that’s the one that is kind of outward-facing,” Tewhey said. “It interacts with your immune system as well as your cells.”
Each week, the Maine CDC sends The Jackson Laboratory extracted RNA — residual material from diagnostic COVID-19 tests. The lab tends to receive the samples early in the week and takes a day or two to process them. It generally has the genome sequences ready by Thursday or Friday.
The RNA is converted to DNA, a similar molecule that is more stable, Tewhey said. Scientists then perform a PCR (polymerase chain reaction) to isolate virus cells from the sample. After a couple of other steps, those amplified fragments are then placed onto large sequencing instruments that read the nucleotides — the basic components of DNA — of those pieces.
Clusters derived from that sequencing are then compared with the initial clusters of the virus that were found in Wuhan, China, in late 2019.
The lab tends to sequence 100 to 200 samples a week culled from across Maine, Tewhey said. It is important that they are geographically diverse, he said, to have broader surveillance over the state’s 16 counties.
Scientists identified the first U.S. case of the omicron variant at a University of California, San Francisco lab at around 4 a.m. Wednesday morning. That lab’s work is not too different from the sequencing done in Bar Harbor — it works closely with the California Department of Public Health and San Francisco Department of Public Health on genome surveillance.