How San Francisco confirmed 1st U.S. Omicron case so shortly

SAN FRANCISCO –

A UC San Francisco laboratory analyzing positive coronavirus test results is a major reason for the rapid identification of the Omicron variant in California, the first documented case in the United States.

Dr. Charles Chiu, an infectious disease specialist at UC San Francisco, routinely analyzes positive coronavirus cases in San Francisco for their genome sequence to identify the variant.

Chiu said he first heard of the positive case at 3 p.m. Tuesday. The moderately ill San Francisco resident, who returned home from a trip to South Africa on November 22, became symptomatic on or around Thanksgiving and was tested for the coronavirus on Sunday. The results were positive on Monday.

Chius Labor received a sample of the detected coronavirus at 8 p.m. on Tuesday. Scientists ran a rapid molecular test that gave results within two hours that suggested, but inconclusive, that the coronavirus that was making residents sick was the Omicron variant.

“To confirm this finding, we had to sequence the genome – the viral genome – of this virus,” said Chiu. By 4 a.m. on Wednesday, the scientists had assembled most of the genome and “we were able to conclusively prove that it was actually an infection with the Omicron variant.”

According to Dr. Anthony Fauci, President Biden’s senior medical advisor on the pandemic, has also been confirmed that the sequence matches the Omicron variant at the U.S. Centers for Disease Control and Prevention.

The laboratory sample was sent to UC San Francisco by Color Health, a Burlingame, California-based company that works with the San Francisco Department of Public Health to provide coronavirus testing services.

Virtually all positive coronavirus test results identified by Color Health in San Francisco will be directed to genome sequencing to identify their variant, said Scott Topper, vice president of clinical operations at Color Health.

San Francisco Health Officer Dr. Susan Philip said the quick identification of the Omicron variant would not have been possible without UC San Francisco and Color Health and the resident who chose to get tested for the coronavirus as he acknowledges the recent trip to South Africa and mild symptoms of illness prompted a test.

The resident was at home in San Francisco for a few days before South African scientists announced the discovery of the new variant in question. South Africa announced on November 24th that it had discovered the variant – originally called B.1.1.529.

Two days later, the World Health Organization declared it a “questionable variant” and gave it its Greek letter name Omicron.

The San Francisco resident “realized that he had recently traveled; they realized they had symptoms; and they did what we should all be doing – getting tested, ”said Philip.

The person then contacted the San Francisco Department of Public Health. The person has stayed home, isolated, and the health authorities are in the process of identifying people who may have been in close contact with the resident. Close contact is defined as someone who has been within six feet of someone for 15 minutes or more.

“This person knew about the news from Omicron, so upon their return from the trip they reported appropriately and received their positive test result through the color lab,” said Philip. We “really appreciate this person’s awareness and cooperation in this case.”

Los Angeles County officials also regularly perform genome sequencing of confirmed coronavirus cases – not just to look for Omicron, but to see if any new trends emerge.

“Currently, between 1,500 and 5,000 positive samples from LA County residents are sequenced each week, with results reported to both LA County and the state,” Public Health Director Barbara Ferrer said during a briefing. “And we will continue to rely on our network of commercial and public health laboratories to ensure we get a representative assessment of the prevalent variants.”

These efforts have led to the same result for months: the hyperinfectious Delta variety remains the dominant variety nationwide. In the week of November 20, Delta made up 100% of the specimens sequenced, according to Ferrer.

But on Thursday evening officials also reported their first case of Omicron – a person who had recently returned to the county from South Africa.

“While we cannot know for sure the effects of Omicron at this point, the good news is that we already know how to reduce and slow transmission through pharmaceutical and non-pharmaceutical measures,” Ferrer said in a statement.

The infected San Francisco resident was identified only by age – between 18 and 49 – and had been fully vaccinated with Moderna but had not received a booster, authorities said.

Before the infection, the resident was healthy. The infection caused mild symptoms that did not require hospitalization, officials said.

The person has since recovered, said Dr. Grant Colfax, San Francisco Director of Health.

Close contacts of the resident have so far been tested negatively, said Fauci.

The California Department of Health says everyone “should get tested for COVID-19 immediately if they experience symptoms – regardless of your vaccination status. COVID-19 symptoms can feel like a common cold (including just “the cold”), seasonal allergies, or the flu. The California COVID-19 test is free to anyone who needs it. You can book a free test appointment, find a walk-in testing clinic, or buy a self-test kit at your local drugstore. “

State health officials also advise everyone to wear masks in indoor public places such as grocery stores and movie theaters regardless of vaccination status, and anyone aged 5 and over should be vaccinated. Some California counties require masks in indoor public places, including most in the San Francisco Bay Area, as well as the Los Angeles and Ventura counties.

Fully vaccinated adults should get a booster dose, health officials say. Those who received their second dose of Pfizer or Moderna syringe at least six months ago or their Johnson & Johnson vaccination at least two months ago are entitled to a booster dose.

In some parts of California, the demand for booster shots is increasing. The county south of San Francisco, San Mateo County, recently reported that the demand for booster vaccinations is so great that officials are no longer allowing walk-in vaccinations at the county-operated location at the San Mateo County Event Center.

Booster shots are also in great demand in Marin County. Some pharmacies have run out of doses in the past few days and are working on replenishing supplies, KGO-TV recently reported.