The Georgia Department of Public Health is on high alert, scanning for a new potentially more contagious variant of COVID-19 that has begun spreading around the globe.
Public health workers are using sophisticated machines acquired in the pandemic to perform genetic sequencing on samples from COVID patients looking for the variant, called omicron. Private labs too, which handle the majority of COVID testing and sequencing now performed, are also on the lookout and will report their findings to the state.
DPH spokeswoman Nancy Nydam said each week labs sequence hundreds of samples from the state, but none have yet shown the variant, which leapt to international attention last week. With COVID-19 cases beginning to rise again in Georgia, testing and case numbers will too, as will the number of specimens sequenced.
The omicron variant, first detected in Southern Africa, and classified as a “variant of concern” by the World Health Organization, has already been found in at least a dozen countries. Two cases have been reported in Canada as of Sunday.
While the CDC said no omicron cases had been confirmed in the United States as of 11 a.m. Monday, Dr. Anthony Fauci said on ABC’s “This Week Sunday” that the question isn’t if there will be a case in the U.S., but when.
On Monday, the U.S closed its borders to non-U.S. citizens coming from eight Southern African countries.
There is still much unknown about the omicron variant, such as whether it’s more contagious or causes more severe - or less severe - illness. It’s also not yet known if existing COVID-19 vaccines will maintain their effectiveness against the virus.
The vaccines will likely continue to prevent severe illness and death, although booster doses are advised to protect most people. The makers of the two most effective vaccines, Pfizer-BioNTech and Moderna, are preparing to reformulate their shots if necessary.
Testing will continue to be important and health officials say the more simple PCR test can provide a clue whether the strain is the omicron variant. This could be key in quickly spotting likely cases.
Like the Alpha variant earlier in the pandemic, a specific pattern in the COVID-19 virus’ genetic material can be detected by at least one brand of PCR tests, signaling it may be the omicron variant. A more involved test — full genomic sequencing — is needed to confirm it’s omicron.
PCR tests, considered the gold standard for testing, begin with a sample from a patient’s nose or throat. The next step is to process the genetic material so that the presence of even a small amount of the virus can be confirmed. This is done using a technique called a polymerase chain reaction. PCR tests are widely used by commercial pharmacies, doctor’s offices and mass vaccination sites and can typically be completed within a few hours.
Genetic sequencing is a much more complex process done on a small percentage of positive coronavirus samples. The process begins with extracting the genetic material from the sample. Then, sequencing machines map out the entire SARS-CoV-2 virus genetic code — all 29,903 individual building blocks. The machine can take three days to complete that step, and then scientists must manually review the findings.
Dr. Anne Piantadosi, an assistant professor in the department of pathology and laboratory medicine at Emory University, and who has been doing sequencing since the earliest days of the pandemic, says most variants of concern have a number of mutations from the original iteration of the virus, but “omicron has even more than what we are used to.”
She said while some of the mutations in omicron have been associated with faster replication, increased transmissibility, and partial immune evasion, it’s too soon to know if the variant will lead to more serious illnesses and deaths.
Josh Arant, chief operating officer of the commercial testing company Mako Medical, said that the company is staffed up for a winter surge in positive COVID test results and already looking for omicron. Mako operates all the state drive-up testing sites, around 50 in Georgia, and genetically sequences every positive result.
Mako was fortunate to find out that the brand of assay that it uses to run COVID tests, by Thermo Fisher Scientific, can detect the if a positive COVID sample might be the omicron variant. They have not yet found an omicron patient.
”Labs have been preparing for this for almost two years now,” Arant said. “I hope that everyone’s taken the same kind of precautions that we have.”
Dr. Michael Eriksen, founding dean of Georgia State University’s School of Public Health, said it will take a little time, likely a week or two before more is known about the seriousness of the variant and level of protection from vaccines. Early signs, he said, suggest it may be more infectious but that doesn’t necessarily mean it will cause more severe illness.
He said it’s particularly important for those at high risk, such as older adults and the immune-compromised including those who are vaccinated, to take the same strict protective measures as they did early in the pandemic: strict mask wearing and social distancing in public.
Eriksen said people should not panic but need to be vigilant. And for those who are not yet vaccinated, Eriksen said, “now is the time.”
“At this time, the big takeaway message is that everyone should get vaccinated as soon as possible, not just here in the U.S., but everywhere in the world. Given today’s travel patterns, a virus anywhere is a virus everywhere,” he said.
