2ND OMICRON CASE DETECTED IN COUNTY
Man in 30s was vaccinated, had booster and hadn’t traveled; symptoms were mild
San Diego County officials announced on Friday that a second case of the Omicron variant of the coronavirus has been detected in the region.
The person is a man in his 30s who has not recently traveled, so local officials believe he was infected locally. He was fully vaccinated and received a booster at least two weeks ago, according to a county news release. His symptoms, which were mild, have already cleared up, and he’s currently isolating at home.
The news comes just a day after the first case was reported on Thursday. And the fact that this case appears to be the result of local transmission suggests there are other infections that haven’t been detected. Public health investigators are now contacting those who’ve recently been in contact with the man to see if they’ve been infected, too.
“Omicron variant is now spreading in the community. While the Delta variant remains the main strain circulating in San Diego, we expect to see more Omicron cases,” said Dr. Wilma Wooten, the county’s public health officer, in a statement. “San Diegans should continue taking the recommended precautions, especially getting all the recommended COVID-19 vaccine doses.”
The case was spotted by the San Diego Epidemiology and Research for COVID Health Alliance, a joint effort by local research institutes to track the scope and spread of the coronavirus.
Their first clue? A weird COVID-19 test result from UC San Diego’s lab on Wednesday.
Scientists found a sample that was positive for the coronavirus but didn’t seem to have the gene that codes for the spike protein, the part of the virus that allows it to latch onto your cells and slip inside them.
This finding, known as S gene dropout, happens when a viral sample has a mutation in the spike gene that causes molecular tests to miss the gene entirely. The Alpha variant, formerly known as the U.K. strain, has that mutation. So does Omicron, though The Guardian reported this week that a “stealth” version of the strain lacks the mutation needed to produce the anomalous test result.
A team led by Scripps Research immunologist Kristian Andersen confirmed that the sample was Omicron by sequencing the virus. UCSD then corroborated the finding with its own sequencing. By late Thursday evening, experts were certain the sample contained the new variant.
In an email to The San Diego Union-Tribune last week, Andersen had said he expected the first
local case to be reported this week. Omicron has also been detected in other parts of the state, including San Francisco and Los Angeles, and wastewater samples suggest the variant has been in the Golden State for weeks.
The news brings fresh urgency to scientists’ race to understand key questions surrounding the strain. How transmissible is it? If infected, are you more likely to get seriously ill? And how well do the vaccines protect you?
Early answers are coming from South Africa, one of the first countries to spot the variant. New infections there are rapidly climbing, and there’s evidence the virus is reinfecting those who’ve recovered from COVID-19.
But the rise in cases has yet to result in a flood of hospitalizations. And initial reports from South African hospitals suggest that many of those infected with Omicron have had milder symptoms than what public health officials have seen with Delta and previous strains.
That could be encouraging. But Dr. Davey Smith, UC San Diego’s chief of infectious disease research, isn’t so sure.
“That’s good-ish news,” he said. “It is a little shaky, epidemiologically speaking.”
Smith points out that many of the infections in South Africa have been among younger people, a group at low risk of severe COVID-19. It’s still unclear how Omicron affects seniors and those with serious underlying health conditions.
Researchers are also hustling to understand how well vaccines fare against the variant. Both Omicron cases have been San Diegans who were fully vaccinated and received a booster. But it’s impossible to draw sweeping conclusions from two people, vaccines are never 100 percent effective, and neither resident had a severe case of COVID-19. The county also hasn’t shared any details on whether either person had underlying medical conditions that made them more vulnerable to the virus.
This week, Pfizer announced that three shots of its vaccine were as effective against Omicron as two doses were against previous variants. The findings were based on laboratory experiments that measured antibodies, Y-shaped proteins that can latch onto a virus and block infection if they grip tightly enough at the right spot.
And while the pharma company’s latest announcement focused on antibodies, there are other key players in vaccine responses. That includes T cells, which kill infected cells before they spew out more virus. Alex Sette, a researcher at La Jolla Institute for Immunology, is part of a team that’s now looking at how well T cells from vaccinated people respond to Omicron. To do this, Sette and colleagues are taking T cells from blood samples and exposing them to cells coated in little pieces of the virus.
Researchers have used this approach in the past to show that T cell protection has held up across variants. That makes these cells an important bulwark in people with low antibody levels, which is likely part of the reason that coronavirus breakthrough infections tend to be mild.
Erica Ollmann Saphire, president of La Jolla Institute for Immunology, is leading an effort to test hundreds of different antibody treatments to see how well they work against Omicron. That’s particularly important given initial reports that an antibody treatment from New York biotech Regeneron doesn’t work well against the variant.
Unlike vaccines, which spark an array of antibody and T cell responses, these treatments infuse patients with a large dose of one or two antibodies to help keep those who’ve been recently infected from ending up in the hospital.
In its announcement, the county stressed that indoor masking, vaccination and testing remain key strategies to limit the spread of the virus. And local officials said they would include any new cases of Omicron in their weekly variant report.