Mary Ngim of San Jose holds her daughter on her lap as she receives a COVID-19 vaccine at a clinic in San Jose on June 21, 2022.
UPDATE: Here are the latest updates on COVID in the Bay Area and California.
California emerged from its summer surge on Thursday, reporting its lowest daily case rate in four months, and the Biden administration officially ended the emergency phase of the pandemic. Confirming that omicron was less deadly than its predecessors, the CDC’s Morbidity and Mortality Weekly Report on Friday showed that mortality risk among patients hospitalized primarily for COVID-19 decreased to 4.9% in the period from April to June, about one-third what it was during the delta period. Some worries persist, however: another study released Thursday found that 7.3% of adult COVID survivors were experiencing persistent symptoms of long COVID as of July.
Latest updates: 
Despite the “great progress” the U.S. has made in the pandemic, the White House coronavirus response coordinator on Friday cautioned that it is too soon to declare victory against COVID-19. “Three hundred and fifty Americans are still dying every single day of COVID. Annualized that’s over 100,000 a year,” Dr. Ashish Jha told the second annual Boston Globe Summit. “I think all of us would agree that is an unacceptably high toll on our society.”
Speaking at the three-day virtual conference, Jha said as long as Americans take advantage of updated vaccines, therapies, and basic mitigation measures, they can avoid the most severe outcomes of the disease. “We have managed to blunt the worst of the virus,” he said. “We have managed to defend against the virus as long as people actually avail themselves of these things.” He added that while his children do not mask in school, he still wears a mask when in a crowded indoor space and prefers to sit outside when dining out. Jha added that the winter could bring another surge, especially with more people gathering. And he slightly walked back an earlier statement that said the COVID shot would become an annual event like the flu shot. “High-risk people may be more than once a year,” he said. “We’ll see what the data shows, but I think for a vast majority of people, this is now an annual shot and that’s how people should be thinking about it.”
Nationwide supply of the Moderna bivalent COVID-19 booster is limited, but people seeking a shot can get the Pfizer version instead since mixing and matching COVID shots is safe and effective, said Bay Area health care providers. Sutter Health, Kaiser Permanente and UCSF say there is a nationwide shortage of the Moderna bivalent shot and that supply at some of their locations is limited. It’s not clear what’s causing the issue. Moderna did not immediately respond to questions about what the problem may be or when it would be resolved. “There is a nationwide shortage, or will be some shortage of the Moderna bivalent vaccine,” said Dr. Darvin Smith Scott, clinical vaccine lead for Kaiser Permanente Northern California. He encouraged people to get the Pfizer bivalent shot instead, of which there is plenty. “It doesn’t really matter which one you get based on your prior vaccine,” he said. You can mix and match safely.”
While the omicron BA.5 subvariant remains the dominant strain of the coronavirus in the U.S., making up nearly 85% of sequenced COVID-19 cases last week, its cousin BA.4.6 is now circulating in more than 10% of new cases for the first time, according to data published Friday by the Centers for Disease Control and Prevention. The agency also flagged two variants of concern that are climbing the charts. The emerging omicron BF.7 sublineage made up nearly 2% of new cases, while BA.2.75 — which got some traction this summer but then appeared to fade — is now showing up in 1.3% of cases. Ian Williams, the deputy director of the CDC, said last month that the agency started tracking these variants because mutations may make them resistant to available treatments. “We’re very interested in this because BA.4.6 has an additional spike substitution at position 346, which might impact the performance of monoclonal antibodies,” he said. “So we continue to watch variants, watch for the next variant, collaborate very closely with our partners around the globe to sort of see what is happening there.”
Only 8% of the U.S. population still lives in an area designated as having “high” COVID-19 community levels, based on hospitalization and case rates, according to the Centers for Disease Control and Prevention. Most regions nationwide are showing improving trends with 35% of Americans living in a region classified as being in the “medium” tier and 57% in “low” — including all the Bay Area counties except Marin and Sonoma. Despite the positive changes in the community levels, 83% of all counties remain in the “high” virus transmission category, based on a separate metric that tracks the rates of new cases and positive tests.
While federal health officials are still “working to update visualizations and metrics” to tally exactly how many doses of the new bivalent COVID-19 vaccine booster have been administered so far, the CDC’s daily count of overall vaccines doses administered across the U.S. indicates that people are not rushing out to get the shots. Despite a small bump in the numbers last week — about 423,000 individuals got a shot on Sept. 9, the highest number since May — the figures plummeted back below 200,000 per day as of this week and remain among the lowest rates since the life-saving vaccines first became available. The nation’s top health experts are urging people to get the new boosters to prevent another fall and winter surge, saying the shot “can help restore protection that has waned since previous vaccination and were designed to provide broader protection,” according to Rochelle Walensky, director of the CDC.
Officials at San Francisco’s beleaguered Laguna Honda nursing home, which is under threat of closure, said the facility experienced its largest COVID-19 outbreak to date among residents in August. Resident cases peaked at 55 on August 25, interim CEO Roland Pickens told a Board of Supervisors meeting Tuesday. “We made plans to open a second COVID unit at Laguna if needed,” he said, noting that due to the staff’s swift action and enhanced use of mitigation measures, including the distribution of N95 masks, they were able to control the outbreak. Pickens said there were 11 cases among the 600 residents at the 156-year-old hospital and rehabilitation center as of Monday. “Thankfully, we didn’t have to use the second unit but we made it ready.” As part of the changes, Laguna Honda visitors are now being tested upon entry, gathering spaces like the cafe have been temporarily closed, and most staff meetings are being held virtually. There have been three COVID deaths among residents this year, and eight in total since the start of the pandemic in March 2020, according to city data. There have been a cumulative 206 cases among residents at Laguna Honda in 2022, compared with 32 in 2021 and 46 in 2020. Among staff, there have been 810 cases this year, 158 last year, and 129 in the previous year.
New variants of the coronavirus may impact the performance of rapid antigen tests, according to a nationally funded study published Thursday. A research team backed by the National Institutes of Health found that commercially available rapid antigen tests can detect past and present variants of concern, but noted that potential mutations that may affect test performance in the future. “Rapid antigen tests remain an important COVID-19 mitigation tool, and it is essential to ensure that these tests can detect the SARS-CoV-2 virus as it continues to evolve,” said Bruce J. Tromberg, Ph.D., director of the National Institute of Biomedical Imaging and Bioengineering, in a statement. The researchers said there will likely be specific mutations to the N protein of the virus that could affect diagnostic antibody recognition. “Our study provides information about future SARS-CoV-2 mutations that may interfere with detection,” said senior study author Eric Ortlund, Ph.D., a professor in the department of biochemistry at Emory University. “The results outlined here can allow us to quickly adapt to the virus as new variants continue to emerge, representing an immediate clinical and public health impact.”
During the period of omicron variant predominance, the crude mortality risk among patients hospitalized primarily for COVID-19 decreased to 4.9% between April and June — lower than any previous time in the pandemic and approximately one-third of what it was during the period of delta variant predominance, according to a report that will be published Friday in the CDC’s Morbidity and Mortality Weekly Report. “In the later omicron period, COVID-19 patients at lower risk were hospitalized less often, and hospitalized COVID-19 patients at higher risk experienced less severe disease and lower mortality,” the authors write. Researchers credit several factors for the improvement in mortality rate, including advances in early treatment for patients at risk for severe disease, lower pathogenicity of omicron subvariants, and the effectiveness of two to three doses of the mRNA vaccines. Hospitalizations not primarily for COVID-19 — patients admitted “with COVID” — were excluded from the study.
An estimated 7.3% of adult COVID survivors — about 18.5 million people — are experiencing the persistent symptoms of long COVID as of July, according to a population-representative survey by researchers at City University of New York. The pre-print study, published Thursday, found that about one-quarter of a random sample of 3,042 respondents said the condition severely affected their day-to-day activities and nearly one-third said they experienced symptoms more than a year after their initial infection. The age- and sex-adjusted prevalence of long COVID was higher among respondents who were female, had comorbidities, or were unvaccinated or unboosted. “We found that the duration of long COVID symptoms extends to more than 12 months for many people, but that the impact of long COVID on daily living decreases with time since the most recent infection, suggesting possible improvement in long COVID symptoms over time,” said Denis Nash, one of the authors of the study, in a Twitter thread.
California officially emerged from its summer surge on Thursday, reporting its lowest daily case rate in four months. The state is averaging 12.1 cases per 100,000 residents, state data showed. That marks a 30% decrease from the previous seven-day average and is on par with numbers reported in April before the omicron BA.5 subvariant became dominant. California’s test positive rate also dropped to 6.2% — a marked improvement from the 16.2% it reached in late July, but still above this year’s low of 1.2% recorded in March. The California Department of Public Health cut back on its coronavirus reporting starting this week, updating numbers just once a week on Thursdays, as opposed to the previous cadence of two weekly updates on Tuesdays and Fridays. There are 2,580 patients hospitalized statewide with confirmed COVID-19 as of Thursday, including 316 in intensive care unit beds. That is roughly half the figures reported at the peak of the most recent surge. An average of 28 state residents are still dying each day in California due to COVID-19.
The Biden administration said it aims to end the emergency phase of the pandemic today, but asserted that the United States must continue to work with its international partners to minimize COVID-19-related cases, hospitalizations and deaths. The White House on Thursday released an updated COVID-19 Global Response and Recovery Framework, noting that the United States has so far donated over 620 million doses of COVID-19 vaccines to 116 countries for free, averting nearly 20 million deaths in 2021 alone. It estimates that almost 70% of the world’s population is now vaccinated. “While this is real progress, inequities persist, and our work is not finished. Too many countries lack equitable access to vaccines, tests, treatments and oxygen, and the capabilities needed to effectively deliver them,” spokesperson Adrienne Watson said in a statement.
Aidin Vaziri is a staff writer at The San Francisco Chronicle.
Catherine Ho covers health care at The San Francisco Chronicle. Before joining the paper in 2017, she worked at The Washington Post, the Los Angeles Times and the Daily Journal, writing about business, politics, lobbying and legal affairs. She’s a Bay Area native and alum of UC Berkeley and the Daily Californian.