In-Depth: Omicron expected to become dominant variant in San Diego by early January, if not sooner

Scripps Research Institute Sequencing
Posted at 3:13 PM, Dec 14, 2021

SAN DIEGO (KGTV) – Based on omicron’s rapid spread around the world, San Diego researchers expect it will become the dominant variant locally and throughout the United States by early next month at the latest.

Scientists at Scripps Research Institute in La Jolla process hundreds of COVID samples each week, hunting for the genetic sequence of omicron in San Diego County. Together with UC San Diego, they confirmed two local omicron cases last week, including one in a man without a travel history.

“Omicron is spreading like wildfire. It’s a really fast-spreading variant. It will hit San Diego soon. I fully expect cases will go up by early January at the latest and possibly sooner,” said Mark Zeller, a staff scientist in Dr. Kristian Andersen’s lab at Scripps Research.

The Scripps Research team released a paper earlier this year correctly predicting when the Alpha variant, first detected in the UK, would take over in the US. This time, the shift from delta to omicron is happening so fast, the team doesn’t have time to publish a similar analysis, said Karthik Gangavarapu, a scientific collaborator of the Andersen Lab.

“We fully expect it to be dominant very quickly,” Gangavarapu said. “Like Mark said, by the end of December, we think 100 percent of the cases would probably be Omicron.”

That’s based, in part, on the rate of spread in other countries. The Andersen Lab tracks and reports global trends on a website called

“If South Africa is any indication, then it takes about three weeks for the virus once it’s first detected to become the predominant strain,” said Dr. Davey Smith, head of the infectious diseases division at UC San Diego.

With previous variants, Dr. Smith said an infected person might spread the virus to three or four other people during a bad surge.

“With this virus, it looks like it doubles what delta was,” he said. “So we’re probably hitting 10, 11 people in a fully susceptible population who would be infected for every one person who’s infected.”

Scientists in Denmark and Norway predicted this week that omicron will become dominant there in just days. Both countries have similar vaccination levels to the US.

Early data from South Africa suggests two doses of the Pfizer vaccine are just 33 percent effective against an omicron infection, but they are 70 percent effective against hospitalization.

Doctors say a booster shot improves protection significantly, raising it to 75 percent against infection in one UK study.

San Diegans should get one right away, Zeller said, with omicron just weeks from being widespread.

“That’s where we are right now. It’s really important to get your booster shot and make sure you protect yourself by wearing masks in indoor or crowded areas,” he said.