COVID in California: BQ.1 and BQ.1.1 strains are now CDC's 'greatest concern' – San Francisco Chronicle

Faustino Salazar prepares to receive his COVID-19 booster while daughter Maria Guadalupe Salazar helps roll up his sleeve at the community testing and vaccination clinic United in Health/Unidos en Salud in San Francisco’s Mission District.
UPDATE: Here are the latest updates on COVID in the Bay Area and California.
The White House is upping its messaging about a potential winter upsurge in COVID cases. President Biden got his “bivalent” dual booster shot live online, while the White House rolled out its fall playbook for businesses on how to get through another potential surge and outlined a plan to offer free delivery of Paxlovid treatments to underserved communities. But will there even be a winter surge? One influential research organization predicts that cases will rise by about a third between now and February but that hospitalizations and deaths won’t spike. And if it’s any comfort, the wild outbreak of the immune-evasive XBB subvariant in Singapore appears to be dying out as fast as it emerges.
Latest updates: 
U.S. health officials are watching the BQ.1 and BQ.1.1 COVID subvariants “very carefully,” said the director of the Centers for Disease Control and Prevention. Speaking at a virtual event hosted by the University of Virginia School of Medicine on Wednesday, Dr. Rochelle Walensky described the emerging omicron descendents as “our greatest concern right now, both for the number of mutations, but also for the impact and the phenotype that we are worried that they may imply.” BQ.1 and BQ.1.1 made up 16.6% of the total coronavirus variants circulating in the United States last week, up from 11.4% the week before, according to data published Friday by the CDC.
They could soon crowd out the dominant BA.5 variant. The “doubling time” for both BQ versions versus those of the earlier BA.4, BA.4.6 and BA.5 has been faster, said Walensky, who herself tested positive for the virus on Friday. She reiterated that there is some indication the subvariants are resistant to the monoclonal antibody treatments Evusheld and bebtelovimab. “There are no current data to suggest decreased vaccine effectiveness, but something we are watching very carefully,” she said.
With the threat of another swell of coronavirus infections alongside a steady rise in RSV and influenza cases, the U.S. is facing the threat of a “tripledemic” that could overwhelm hospitals this coming winter, said Dr. Ashish Jha. But the White House COVID-19 response leader said there are steps people can take to ease the risk. “We’re not powerless against it,” Jha said in a Tuesday interview with CBS News. He said the combination of a flu shot and updated COVID booster will help people avoid serious illness and stay out of the hospital as they get ready to celebrate Thanksgiving and other holidays with friends and family. “We need everyone to step up and do their part,” he said earlier in the day at another press event. “This is literally about saving lives of tens of thousands of Americans this fall and winter,” he said. “The great news here is that, unlike past winters, we are in control.”
Federal health officials have expressed growing concern about RSV cases, for which no shot is available. About 75% of the nation’s 40,000 pediatric beds are currently occupied according to the latest Department of Health and Human Services data. “We need hospitals for all sorts of things, not just those viruses,” Jha told CBS. “So right now, our focus is, get people vaccinated, get people treated, and keep people out of the hospital.” He also encouraged people to use “standard” mitigation measures to avoid spreading the viruses, such as staying home when sick, washing hands, and avoiding people who show symptoms of illness. “Those are things that really make a difference in keeping RSV levels low,” he said.
California’s planet-warming emissions dropped nearly 9% in 2020 compared to the year before as pandemic restrictions kept people at home, out of their cars and away from the workplace for much of the year, the Associated Press reports. The data released Wednesday marks California’s largest single-year emissions drop and tracks with a similar reduction nationwide. An official cautioned that the data can’t be used as a marker for future trends because the pandemic caused unprecedented yet temporary economic changes. “This year will be looked at as an outlier,” Steven Cliff, executive officer for the California Air Resources Board, told reporters ahead of the data’s release. Indeed, data from the Global Carbon Project pointed to a rebound in global emissions 2021 once pandemic restrictions across the world began to ease.
Oakland’s ordinance requiring anyone attending a large indoor event of 2,500 attendees or more to wear a mask will expire Nov. 1, the city announced Wednesday. People are still required to wear a face mask when entering city facilities, libraries, senior centers, recreation centers and other government buildings. Public health guidelines issued by the State of California and Alameda County Public Health department strongly recommend that everyone, regardless of vaccination status, continue to wear masks indoors to protect against exposure or spread of COVID-19.
Don’t shrug off that sneeze or scratch at the back of your throat. As coronavirus variants continue to evolve and become more difficult to detect, so do COVID symptoms, allowing more people to spread the virus without realizing it. Signs of infection are increasingly hard to tell apart from symptoms of a common cold or flu, according to the latest update from the ongoing Zoe Health Study, a joint project by researchers at Harvard, Stanford, and King’s College in London. A mild runny nose, headache, or sore throat could now precede a positive test result with one of the many offshoots of omicron. Other indicators commonly reported during earlier phases of the pandemic, such as loss of taste and smell, have dropped down the list. Read more about the changing symptoms of COVID and how they may be affected by your vaccination status.
Some fungal diseases have surged during the COVID-19 pandemic as health-threatening fungi expand worldwide due to global warming and increased international travel and trade, a new World Health Organization report says. The WHO on Wednesday released its first-ever list of fungal “priority pathogens” — the 19 fungi that represent the greatest threat to public health. They are both increasingly common and resistant to treatment, with only four classes of antifungal medicines currently available, the WHO said. The report identified four of “critical” priority, including Aspergillus fumigatus and Candida albicans — the two most common fungal pathogens globally — as well as Cryptococcus neoformans, a leading cause of death in people with HIV. Aspergillus fumigatus mainly affects the lungs, while Candida albicans is the most common cause of thrush. Infection rates of both pathogens rose in many countries during the COVID-19 pandemic, with high mortality rates among vulnerable patients from invasive infections, the Guardian reported. The fourth critical priority pathogen — Candida auris, which grows as a yeast — is “intrinsically resistant to most available antifungal medicines” and has “high outbreak potential,” the report found.
Around 40% of Americans who live in rural areas say they have had COVID-19, according to a federally funded survey published Wednesday. In a poll conducted in July and August of 2,000 adults, parents and teens who live in a “non-urban” zip code, a majority of the respondents said they had some type of personal experience with COVID-19. Three out of four rural adults know someone who has had COVID-19 (76%), and two-fifths have been infected themselves (38%) — marking a 15-percentage point increase from a previous survey conducted in February.
Despite their close contact with the disease, 59% said it did not have a more or less favorable effect on their intent to get vaccinated. Vaccination rates among the rural population have stalled since the prior poll. Around 63% of rural adults reported being at least partially vaccinated, with 68% of those vaccinated also receiving their booster shot. About 43% of rural parents and 44% of teens said they are fully or partially vaccinated. “Data show how opinions have further solidified, especially among unvaccinated individuals,” the National Rural Health Association said in a press release. “Responses also indicate that while most respondents believe COVID-19 is here to stay, this does not impact their decisions to accept or reject vaccination.”
Howard Stern will return to his SiriusXM studio in Manhattan for the first time in more than two years to interview Bruce Springsteen on Monday. Stern, 68, has been exceedingly cautious about becoming infected with COVID-19 since the start of the pandemic in 2020. But he said on Wednesday that the Boss convinced him to come out of isolation. “Bruce was saying he thinks it would be nice if we’re sitting together in the studio — I’ve spoken to Bruce and agreed to do that,” Stern said, according to the New York Daily News. “You know me, I haven’t been out of the house in two years.” Stern added that he initially tried to get the Rock and Roll Hall of Famer to do the interview remotely, but Springsteen, who has never been on his show, wanted to meet in person. Everyone in the studio will test for the virus before doing the interview. “If I was going to get COVID, I wouldn’t mind getting it from Bruce,” Stern said, adding he felt incredible “pressure” over the upcoming segment. Springsteen is planning to bring his guitar. “It should be the second coming of Christ — like Bruce walks in, and suddenly something magical happens,” Stern said. “I just want him to have a good time and be comfortable.”
Entertainer Selena Gomez canceled her scheduled appearance on “The Tonight Show Starring Jimmy Fallon” on Wednesday after testing positive for the coronavirus. “I’m not going to be on Fallon tonight,” Gomez wrote in an Instagram post. “I ended up getting covid but am resting and feeling ok. A friendly reminder that covid is still out there.” The singer and star of “Only Murders in the Building” was set to promote her upcoming Apple TV+ documentary, “Selena Gomez: My Mind & Me,” which highlights her battles with lupus, depression, and other health issues. “Get updated on your boosters,” she told her fans in the post. “I was actually scheduled to get mine this week. Love you all.”
While the northern hemisphere can expect infections to slowly rise through the winter, they are unlikely to lead to the dramatic spikes in COVID-19 hospitalizations and deaths seen in the first two winters of the pandemic, according to the latest forecast from the University of Washington’s Institute for Health Metrics and Evaluation. The model estimates that daily infections in the United States will increase by about a third between now and February, largely due to an uptick of virus spread in schools and general winter seasonality.
In a weekly update, researchers said the impact of the immune-evasive XBB subvariant is likely to be blunted by the number of people infected by BA.5 in the past three months — and that the strain does not appear to lead to more severe outcomes. They did express some concern over the “rapid increase in hospital admissions” in Germany due to the BQ.1 and BQ.1.1 subvariants that appear to be spreading across Europe but were “cautiously optimistic” that it would not be too disruptive. “We don’t have good data at all separating out admissions due to COVID as compared to admissions with COVID, and so we’re not really sure how consequential this big surge in Germany is and how consequential it will be for the rest of Europe,” they said.
The IHME researchers also highlighted their latest insights on long COVID, finding the risk of developing persistent symptoms is tied to the severity of the disease and is more common in women than men. “With the milder variants, we also expect to see a lower probability of long COVID,” they said. Their current estimates show about 5% or 6% of individuals have long COVID symptoms three months after their original infection, with that figure dropping to about 1% at 12 months. “But if you take the huge volume of COVID infections in the world, those numbers do translate into a very large number of individuals globally who will be suffering at three months from symptoms of long COVID and many millions suffering even at 12 months with symptoms of long COVID just because of the incredible ubiquity of COVID infection,” they said. “Even though the probabilities are not that high, individual by individual, they add up to a big toll on society.”
Qatar will no longer require travelers to test for COVID-19 before entering the country to attend the World Cup next month as part of a nationwide change in policy, the country’s health ministry announced Wednesday. The agency asks visitors to “continue to follow standard precautionary measures to reduce the risk of infection,” including getting vaccinated against the virus and “following a healthy lifestyle.”
A surge of cases driven by the immune-evasive XBB omicron subvariant and a wave of reinfections seems to have peaked in Singapore, health ministry data show. New cases in the country quadrupled between late September and mid-October when the seven-day average hit 8,243 daily cases on the 17th. Since then, that number has fallen as quickly as it ascended, with the country reporting a daily average of 5,704 cases as of Tuesday. About one in five of those cases is reinfections, said Health Minister Ong Ye Kung. “We have to continue to watch to see whether (the number of cases) bounces again because it can happen,” he told reporters, according to Straits Times. “But if it continues to come down from here, that means our modeling actually was a bit more pessimistic. We thought it would peak by the first half of November.”
The highly mutated strain of the coronavirus called XBB, or BA.2.10, caused the number of cases in Singapore to double in a day when it first became dominant in the country, with some outlets describing it as a “nightmare variant.” The subvariant was first detected in August in India and has since been sequenced in more than 17 countries, including India, Japan, and Australia. It is believed to have similar changes to its spike protein as the BQ.1 and BQ.1.1 omicron subvariants surging in Germany and growing in proportion in the U.S., and there are indications that XBB evades the monoclonal antibody treatments Evusheld and bebtelovimab, according to a pre-print study from researchers in China.
But it appears Singapore’s highly vaccinated population — 95% of those eligible have received two shots and 79% of those have received boosters — and strict virus mitigation measures have blunted the impact of the new strain when it comes to the worst outcomes of the disease. Of the 167,233 people infected over the past 28 days, 99.7% had no or mild symptoms. So far, 62 sequences from XBB have been detected in the U.S., including 12 in California, based on data from GISAID, an international research organization that tracks virus variants.
People who experience common side effects after receiving the mRNA vaccine against COVID-19 tend to have a greater antibody response to the jabs, according to a new study published in JAMA Network Open. Post-vaccination symptoms such as fever, chills or muscle pain are a good sign, said the researchers from Columbia University, the University of Vermont and Boston University. “These findings support reframing postvaccination symptoms as signals of vaccine effectiveness and reinforce guidelines for vaccine boosters in older adults,” they wrote. And for those who don’t experience the side effects? The study shows they exhibited a positive antibody response too after completing their primary two-dose vaccination series.
As part of President Biden’s efforts to increase access to COVID-19 treatments, Walgreens has partnered with Uber and DoorDash to provide free delivery of the antiviral treatment Paxlovid to Americans living in underserved communities. Patients with a prescription for Paxlovid being filled at Walgreens who live in a socially vulnerable community will be able to have their prescription delivered to their home at no cost via Walgreens.com and the Walgreens app, according to a White House fact sheet. The initiative will formally launch in the coming weeks.
President Biden received his updated COVID-19 booster shot on Tuesday and urged other Americans to follow his lead ahead of the holiday season. “Virtually every COVID death in America is preventable,” he told reporters on the same day the White House announced a detailed plan to make therapies and the reformulated vaccine targeting omicron variants of the coronavirus more accessible across the United States. The strategy includes key partnerships with major retailers as well as local health leaders. Biden reiterated that people should get the shots ahead of Halloween to have maximum protection going into the winter. About 20 million people have received the updated shots, according to federal health data — a figure that represents less than 10% of the more than 216.2 million people eligible. “Your old vaccine or your previous COVID infection will not give you maximum protection,” Biden said.
When given as a fourth dose, the updated bivalent mRNA vaccine targeting the omicron BA.4 and BA.5 subvariants does not induce superior neutralizing antibody responses in humans compared to the original monovalent vaccine formulation, according to a preprint study published Monday that has not yet been peer-reviewed. The updated shots manufactured by Pfizer and Moderna were not tested in humans but in mice before they were given emergency use authorization by the U.S. Food and Drug Administration in August.
In a real-life clinical trial, researchers at Columbia University and the University of Michigan found that after three to five weeks, individuals who received the new booster dose “had similar neutralizing antibody titers as those receiving a fourth monovalent mRNA vaccine against all SARS-CoV-2 variants tested, including BA.4/BA.5.” They added that “the findings may be indicative of immunological imprinting,” the phenomenon where exposure to a virus strain limits development of immunity against later minor variant strains of the virus, also sometimes called “original antigenic sin.”
Eric Topol, executive vice president of Scripps Research in San Diego, who was not involved in the study, said the result was to be expected. But he added that the vaccines are still effective at reducing deaths and hospitalizations, even as newer omicron subvariants such as BQ.1 and BQ.1.1 become dominant and encouraged people to maintain their protection. “Bottom line: Until more data are available, regard the bivalent booster as equivalent to a booster which augments and broadens immunity, without specific anti-BA.5 properties,” Topol said. His comments set off a lively Twitter discussion.
“In March 2020 I contracted a mild COVID infection,” writes San Francisco resident Charlie McCone in a powerful Chronicle op-ed. “I had just turned 30, was in perfect health and living ‘my best life.’ The Centers for Disease Control and Prevention told me it would take two weeks to bounce back. But it’s been 2½ years, and I’ve spent my entire 30s disabled by a post-infection illness — housebound and barely holding onto what little I can of my former life. I truly cannot relay the misery.”
“We are now well past the point of plausible deniability,” McCone says. “And the fact there is still not a warning, in the face of overwhelming evidence of the prevalence and severity of long COVID, is unconscionable.” Read more of his essay and his call for greater awareness of long COVID and its devastating impact.
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 SFChronicle.com. 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.
Sarah Ravani covers Oakland and the East Bay at The San Francisco Chronicle. She joined The Chronicle in 2016 after graduating from Columbia University’s Graduate School of Journalism. Previously, she covered breaking news and crime for The Chronicle. She has provided coverage on wildfires, mass shootings, the fatal shooting of police officers and massive floods in the North Bay.

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