COVID in California: Latest subvariant of concern, BN.1, takes off in state – San Francisco Chronicle

Kaiser nurse Marilyn Antonio, left, gives a Moderna booster shot to Ted Naifeh, right, from San Francisco, at Kaiser Permanente City Center Vaccine Clinic in San Francisco on Thursday September 22, 2022.
UPDATE: Here are the latest updates on COVID in the Bay Area and California.
Winter is nearing, and COVID-19 isn’t the only respiratory disease circulating. With cases of respiratory syncytial virus surging nationwide, and the U.S. already over the “epidemic threshold” with influenza, experts explain how to tell if your symptoms are due to the coronavirus, flu, or RSV, and what should you do once you know. In the Bay Area, UCSF chair of medicine Dr. Bob Wachter says he’s once again avoiding indoor dining, citing a rise in COVID-19 case and positive-test rates.
Latest news:
Commonly used rapid antigen home tests fail to reliably detect an omicron COVID-19 infection in asymptomatic people, according to a study published Monday in the journal Clinical Microbiology and Infection. Dutch researchers tested 3,600 asymptomatic people with suspected COVID-19 between January and March, when omicron accounted for up to 99.5% of cases in the Netherlands, using self-administered rapid antigen tests and PCR tests. The overall sensitivities for the three bands used — sold under the retail names of Flowflex, MPBio, and Clinitest — were 27.5%. A quarter of the participants who tested again within 10 days of getting a negative result from a rapid test were positive. “Self-testing in asymptomatic individuals may only detect the minority of infections,” the authors wrote. “Repeated self-testing in case of a negative self-test is advocated to improve the diagnostic yield, and individuals should be advised to re-test when symptoms develop.”
President Biden on Monday repeated the promise that most Americans will only need to receive an annual booster shot against COVID-19 despite widespread skepticism from infectious disease experts who think waning vaccine efficacy will necessitate more than one dose every 12 months. Touting the updated bivalent booster as part of the federal government’s “Countdown to Thanksgiving Vax Up America Tour,” Biden encouraged people to schedule their vaccine appointments today. “Omicron did not even exist when the first vaccines against COVID were developed,” the president tweeted. “Now, we’ve got an updated vaccine that’s highly effective against omicron that most folks only need to get once a year.” Kevin Munoz, the White House’s assistant press secretary, said federal officials want people to get maximum protection before an anticipated winter surge. “Ahead of Thanksgiving, we’re making a new push to get Americans their updated vaccines so we can all gather safely this holiday season,” he said.
Despite repeated calls from public health officials for Americans to get their updated booster shots against COVID-19 before the holidays, demand is on the decline. The seven-day daily average of vaccine doses administered in the U.S. fell to 508,761 as of Nov. 2, the date with the most recent data from the U.S. Centers for Disease Control and Prevention — marking a 17% dip from the daily average of 614,669 in the previous week. So far, 31.4 million Americans have received the updated bivalent COVID booster that targets the original virus and the omicron variants, which is about 10.1% of those eligible for the shots.
The Biden administration plans to request billions of dollars in additional funds for the U.S. coronavirus response before the year ends, the Washington Post reports. Officials will reportedly seek $8.25 billion for domestic COVID-19 response efforts, including developing future vaccines and treatments for virus variants and research into long COVID. The request is expected to meet pushback from GOP members who oppose further funding for COVID-19 response and question how some previous funds were used, according to the Post. The move would come amid concerns about a winter uptick in cases driven partly by new omicron subvariants. Case and hospitalization rates remain relatively low nationwide compared to earlier in the year but ticked up the past two weeks, according to data from the Centers for Disease Control and Prevention, which reports that 10.1% of eligible people age 5 and older have received their bivalent booster.
Over the weekend, the U.S. Centers for Disease Control and Prevention added another subvariant of concern to its growing list of omicron offshoots. BN.1, a descendent of BA.2.75, made up a 4.3% proportion of sequenced COVID-19 cases in the U.S. last week, joining a  “variant soup” that includes BF.7. BA.5.2.6, BA.4.6, BA.2.75, BA.2.75.2, BA.4, BA.1.1.529 and several other strains. BN.1 is predicted to have high immune escape by infectious disease experts and has already taken off in the Western region of the U.S., including California, accounting for 6.2% new cases last week — substantially higher than the national average. The subvariant caused a surge of hospitalizations in Austria in the fall. The omicron subvariants BQ.1 and BQ.1.1 made up 6 out of 10 of the total coronavirus cases circulating nationally last week, quickly edging out the previously dominant omicron BA.5 variant.
Several Southern California hospitals have begun using overflow tents outside emergency rooms to cope with a rising number of patients with flu and other respiratory illness, the Associated Press reports. The move comes amid a rise in flu symptoms in emergency room patients in San Diego County. About 9% of these patients had flu symptoms last week, up from 7% two weeks ago, according to a county report that also flagged an increase in patients with COVID-19 symptoms, though not as quickly. Scripps Memorial Hospital in Encinitas reported 1,695 positive flu tests since Sept. 1, up from 471 in the same period last year. “The fear is that everything is just sort of bouncing off everything else and once you’ve been through the flu you could still get hit by COVID or whatever other virus you’re going to get,” said Dr. Ghazala Sharieff, Scripps Health’s chief medical officer of acute care operations and clinical excellence. “I’m hopeful, but we’re still kind of planning that it’s going to be this way through February.”
Moderna said on Monday that its bivalent booster shot provides “significantly higher” protection against the omicron BA.4 and BA.5 subvariants compared to its original formula, based on findings from a clinical trial with more than 500 adults who received both shots. “We are pleased to see that both of our bivalent booster vaccine candidates offer superior protection against Omicron BA.4/BA.5 variants compared to our original booster, which is encouraging given COVID-19 remains a leading cause of hospitalization and death globally,” Stéphane Bancel, the biotechnology company’s CEO said in a news release. The data was not published in a medical journal and was not peer-reviewed.
Moderna said it also has preliminary evidence that the bivalent booster neutralizes the emerging BQ.1.1 omicron subvariant. “Our bivalent boosters also show, in research assays, neutralizing activity against BQ.1.1, an increasingly dominant emerging variant, confirming that updated vaccines have the potential to offer protection as the virus continues to evolve rapidly to escape our immunity,” Bancel said.
The Biden administration plans to keep the COVID-19 public health emergency in effect until April, according to sources who spoke with Reuters on Friday. The declaration allows Americans to have access to free tests, vaccines and treatments. The officials cited an anticipated winter surge in coronavirus cases and the need for more time to transition out of the public health emergency as the primary factors for the decision to keep the order, which was initially declared in January 2020, in place. In August, administration officials had suggested the order might expire in January, but that deadline passed on Friday. The U.S. Department of Health and Human Services has said it will give states 60 days notice before letting the emergency expire.
A reader who described herself as petite and was concerned about booster side effects after experiencing a strong reaction to initial COVID vaccination wrote to The Chronicle’s Pandemic Problems Advice Team asking why dosage doesn’t differ according to body weight. Experts consulted for the column said emphatically that your body size does not matter when it comes to dosage of COVID vaccines — or any vaccine, for that matter — and urged following booster guidelines to make sure you remain protected against the coronavirus.
The medical explanation hinges on how vaccines operate in your body as opposed to most medications. “The vaccines are dosed based on the ‘weight’ of the immune system, not the ‘weight’ of the body, while resulting in as few side effects as possible,” said UCSF infectious disease expert Peter Chin-Hong. “This is the way most vaccines are given, not just COVID shots.”
Read the column from The Chronicle’s Kellie Hwang.
Dr. Bob Wachter, the UCSF chair of medicine, reversed his personal stance on indoor dining in San Francisco in a Twitter post Friday, citing a rise in case and test positivity rates. Wachter posted in September that he felt ready to dine indoors and remove his mask, calculating that his chances were about 1 in 200,000 of dying from an indoor mask-less dinner and about 1 in 1,000 of getting long COVID. Wachter said he would stop again if risk increased markedly. “Alas, it has,” he wrote Friday. Wachter noted San Francisco is averaging 16 daily cases per 100,000 residents, a 122% increase from two weeks earlier, according to New York Times data. He also cited UCSF data showing an uptick in test positivity rate for asymptomatic cases and CDPH data showing a rise since mid-October in SARS-CoV-2 concentration in San Francisco wastewater. “Still OK w/ small groups w/ testing (poker tonite) but no indoor restaurants till” numbers decline, Wachter wrote.
Aidin Vaziri is a staff writer at The San Francisco Chronicle.
Anna Buchmann is The San Francisco Chronicle’s engagement editor. She joined the newsroom staff in 2019 as an online producer for Previously, she worked at The Sacramento Bee in a variety of roles, including digital senior editor, senior editor for topics and breaking news, regional news desk director and copy desk chief. She also trained newsroom reporting interns in the fundamentals of journalism. Buchmann began her journalism career at the San Jose Mercury News, where her roles included news editor, wire editor, copy editor, page designer and education reporter. She earned her bachelor’s degree in English literature from Georgetown University and her master’s degree in journalism from Stanford University, where she also taught editing in the journalism M.A. program.


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