First US case of Omicron variant confirmed in California

by BLOOMBERG / pic by AFP 

THE first confirmed US case of the omicron variant of the coronavirus was detected in California, the Centers for Disease Control and Prevention said, as the recently detected mutation continues its spread around the world.

The infected individual was a traveler from South Africa, according to the CDC. The San Francisco resident was fully vaccinated, had mild symptoms that are improving, and has been self-quarantining since testing positive. All close contacts have been traced and have tested negative, according to the CDC.

The infected person began traveling home on Nov. 21, landed the following day and felt symptoms on Nov. 25, California Governor Gavin Newsom said in a press briefing. Testing was done Nov. 28 and came back positive the next day. The patient wasn’t hospitalized, he said.

“This individual is doing well,” Newsom said in the briefing, adding that the patient is expected to make a full recovery.

Omicron, first detected in South Africa, has been found in locations from Australia to Germany and Canada. Its arrival had been widely expected in the U.S., and researchers are racing to understand the impact of the heavily mutated strain that features some changes that are absent in other major variants.

Sheer Numbers

Omicron’s mutations number about 30, suggesting the strain could evade antibodies produced by existing vaccines, while being equally or more transmissible than delta, the strain that currently dominates. But little is known for sure, as the variant is so new that scientists haven’t had a chance to complete their studies.

Anthony Fauci, President Joe Biden’s top pandemic adviser, said that he wasn’t aware of any other potential cases of the variant in the US right now. Fauci said to his knowledge the infected person hadn’t received a booster dose of a Covid-19 vaccine.

Testing for the infection was done by a Color Health Inc. lab in San Francisco, according to an outside representative of the company. The strain was identified in less than 30 hours from sample collection. The sample was then turned over to the University of California, San Francisco lab of Charles Chiu for confirmatory sequencing.

Chiu said his laboratory heard about the sample on Tuesday afternoon and had received it by 8 p.m. From there, they ran a quick molecular test looking for what’s known as spike-gene dropout, which suggested the sample was possibly omicron.

Small Sequencer

To confirm the finding, the lab sequenced the entire genome of the virus using a pocket-sized sequencing machine made by Oxford Nanopore Technologies PLC. Within five hours, they had confirmed the detection of omicron, and within eight, the entire genome had been decoded.

“At 4 a.m. last night we were able to conclusively demonstrate that this was indeed an infection from the omicron variant,” he said in the press conference.

“All of us have been working furiously for the last 24 hours,” said Grant Colfax, Director of Health for the City and County of San Francisco. “We knew omicron was going to be here. This is cause for concern but this is certainly not cause for panic.”

The patient had earlier received a two doses of Moderna Inc.’s vaccine, but no booster, Colfax said. The city doesn’t plan any additional virus measures or restrictions because of the variant, he said. Likewise, Newsom said he didn’t see shutdowns in the immediate future.

While epidemiologists had said the eventual confirmation of a U.S. case would be unsurprising, given the spread of the variant so far, the milestone carries an emotional punch. Early warnings of possible omicron risks have spooked markets, prompted the U.S. to tighten some travel rules and spurred other countries to shut their borders.

“There’s no reason to panic-but we should remain vigilant,” Newsom said in a tweet. “That means get vaccinated. Get boosted. Wear a mask indoors.”

Post-Thanksgiving Emergence

The World Health Organization warned that the new variant could fuel a fresh surge in infections, though the global agency also said on Wednesday it believes that current vaccines would protect people infected with the variant from severe disease.

The emergence of omicron in the US followed last week’s Thanksgiving holiday, when air travel reached a pandemic high.

South African researchers said omicron appears to be more transmissible than its predecessors but existing vaccines are still likely to offer good protection against severe illness and death. So far, doctors and researchers there have reported that most cases linked to the variant have been mild, but it’s becoming increasingly prevalent in Cape Town, South Africa’s second largest city.

“It was like a tap being turned on from Thursday or Friday last week,” said Anthony Smith, a general practitioner in the suburb of Sea Point. “I’ve probably come across about 20 cases directly or indirectly.”