The emergence of omicron, a new variant of concern, has shined a spotlight on the way that coronavirus cases are sequenced.
Keeping an eye on changes in the genetic code of viruses over time and in different regions allows scientists to alert the public and help control the spread. Scientists look for mutations that might spread rapidly, cause different symptoms, evade immunity or even not show up on tests.
The U.S. Centers for Disease Control and Prevention has labeled omicron a variant of concern because its detection in South Africa coincided with an increase in infections.
A global consortium for sharing genomic data, GISAID, notes that the United States has sequenced 2.9 percent of its cases. That’s higher than where omicron first emerged: South Africa sequences 0.56 percent of its cases. But it’s below 21 countries, including Iceland, which sequences half its cases.
California’s whole genome sequencing initiative, COVIDNet, includes public and private laboratories, as well as academic institutions such as UC San Francisco, which tracked the first omicron case in the country.
Kern County Public Health Services Lead Epidemiologist Kim Hernandez said the county is watching very closely what happens with omicron cases.
Right now, most cases in Kern County are not sequenced. When they are, they’re largely handled by the state’s laboratory.
“There is not the capacity at the state level,” Hernandez said.
The ones chosen for further investigation are the most severe — the ones that would land a Kern County resident in the hospital, Hernandez said.
It takes two to three weeks for Kern County to receive results from the state laboratory, Hernandez said. The county updates the variant count continuously, though results tend to arrive in batches.
More than likely, it is the severity of the case that flags the need for more investigation, but a certain pattern of travel may also do that, Hernandez said.
That is how the earliest cases of omicron were discovered in the United States. The first case was discovered in a fully vaccinated San Francisco resident who was only experiencing mild symptoms but had recently traveled to South Africa, according to UCSF.
Before the arrival of omicron, state modeling forecast that, without an uptake in COVID vaccine booster shots, the county would see the worst surge on record. The scenario assumes waning immunity. The worst-case scenario of the model still shows that a surge is possible, though the model now pushes the peak later to February and forecasts an even higher surge: 994 cases a day at the peak.
Kern County Public Health officials said that its message when it comes to a potential surge or a new variant is the same: Prevention is key.
“Our focus has been to put the public on notice to prevent that fourth surge,” said Brynn Carrigan, director of Kern County Public Health Services.
Getting vaccinated and boosted, wearing a mask, avoiding crowds and washing your hands all help limit transmission, said public health spokesman Michelle Corson. That in turn limits the development of new variants.
Carrigan notes that the county is still able to activate an alternate care site at the Kern County Fairgrounds for COVID patients should cases surge beyond the capacity of local hospitals. But currently, the Fairgrounds serves as a site for Kern residents to get their first, second and booster shots of the COVID-19 vaccine.
The county has also rolled out mobile clinics at local schools to offer pediatric doses of the vaccine to the newly eligible 5- to 11-year-olds. There is one mobile unit focused on it, but a second one to fulfill demand is on the way.
“I think vaccination is the safest, most effective way to reduce transmission and reduce severe illness,” Carrigan said.
You can reach Emma Gallegos at 661-395-7394.