Amid concerns about a potential winter wave of COVID-19, cases linked to newer subvariants of the coronavirus are beginning to rise in California as officials in Los Angeles County and the San Francisco Bay Area warn that a long-term decline in new infections appears to be stalling.
It’s unclear whether this trend in coronavirus cases can be blamed on the rise of newer strains — especially since the Omicron subvariant BA.5 remains the dominant version across the country, as it has been for months.
But officials have long warned that any new subvariant could threaten progress in the fight against COVID-19, either by being inherently more infectious or better able to evade protection from vaccination or previous infections.
The latest generation of alphanumeric Omicron subvariants may have such an advantage, even over the hyperinfectious BA.5.
BA.5 “appears to be gradually accounting for fewer sequenced samples, indicating that other variants may become more dominant in the future,” says Los Angeles County Public Health Director Barbara Ferrer.
The erosion of BA.5’s dominance was slow but steady. Such changes “could indicate the beginning of a growth advantage for some other strains,” Ferrer said Thursday during a weekly briefing.
According to the latest data from the US Centers for Disease Control and Prevention, BA.5 accounts for about 62% of all new coronavirus cases nationwide. However, that proportion has dropped significantly since mid-August, when it was thought to be behind more than 86% of cases.
In the southwestern part of the US, which includes California, Arizona, Nevada, Hawaii, and the US Pacific territories, BA.5 remains more common, accounting for about 72% of all new cases during the last analysis period.
Several other Omicron sub-variants also rose to prominence. BQ.1.1, which some officials have cited as a potentially problematic strain, has risen from an estimated 0.2% of cases nationwide in mid-September to 7.2% this month. At the same time, BQ.1 increased its estimated share from 0.5% to 9.4%, while BF.7 — also known as BA.5.2.1.7 — rose from 1.9% to 6.7%.
In L.A. County, data from the week ending Oct. 1 also indicated a decline in BA.5 dominance and new subvariants accounting for an increasing proportion of cases.
But while BQ.1 and BQ.1.1, both descendants of BA.5, are gaining popularity across the country, only a few such cases have been documented in L.A. County. Seven are attributed to BQ.1, and three to BQ.1.1.
Another Omicron subvariant, BA.2.75.2, accounts for only 0.2% of cases per week in L.A. County, a rate that has been stable for three weeks. L.A. County also reported no cases of the XBB subvariant spreading in Singapore, according to Ferrer.
Some researchers in China found evidence that XBB “can evade the antibody protection developed after infection with BA.5. We don’t know the full implications of this yet,” Ferrer said.
“Some of these mutations make it easier to evade previous immunity, meaning that many of us can be reinfected even if we were infected with the Omicron strain earlier this year,” she added. “And while there is no immediate risk given the relatively small number of recently sequenced specimens of these new hosts in L.A. County, we must be vigilant.”
Although newer strains have some mutations that could provide a growth advantage, it is unclear whether some will cause more severe symptoms than their predecessors.
Many officials and experts remain generally optimistic that available vaccines — especially the recently released bivalent boosters — should continue to provide strong protection against the latest round of subvariants.
“We understand that there can be fatigue from COVID, but we cannot let our guard down,” the California Department of Public Health wrote in a recent statement to The Times. “Our statewide COVID-19 vaccination campaign is still working with community partners across the state to emphasize the importance of keeping their COVID-19 vaccines and boosters up-to-date.”
The updated boosters are designed to target the original version of the coronavirus – which includes the same formula as the vaccines available from late 2020 – and the BA.4 and BA.5 Omicron subvariants. Many newer strains are descendants of those subvariants.
“Do I worry about an alphabet soup of new varieties of concern, today’s big ones: BQ.1 & XBB? Of course, but there is nothing we can do about them except to monitor their distribution; boost – even if they are partially immune, you will be better protected with a boost than not,” Dr. Robert Wachter, chair of the UC San Francisco Department of Medicine, wrote on Twitter on Wednesday.
Wachter added that, on a societal level, he is “most concerned about the low level of adoption of the new booster,” which he said only about 5% of eligible Americans have received.
“That small intake will translate into tens of millions of preventable cases and thousands of preventable deaths — most of the latter in high-risk groups,” Wachter wrote.
California has made significant progress since the peak of last summer’s COVID wave, with the number of cases and hospitalizations falling in recent months. But those declines may be slowing.
L.A. County reported 874 cases of the coronavirus a day in the seven-day period ending Friday, or 61 cases a week for every 100,000 residents. That represents a drop of 8% compared to the previous week. In contrast, the previous week-on-week decline was 17%.
The San Francisco Bay Area reported 60 cases per week for every 100,000 residents during the seven-day period ending Tuesday — unchanged from the previous week. The previous drop compared to the week was 15%.
In addition, “we are no longer seeing significant declines in wastewater concentrations, which may mean that virus transmission is no longer decreasing in L.A. County. We will have to see,” Ferrer said.
Her observations resonated with those of Dr. Matt Willis, Marin County Health Officer. Willis warned a week earlier that the rate at which laboratory tests for the coronavirus give positive results is starting to rise, from 4.5% to 6.5%, in recent weeks.
“Since the beginning of the pandemic in Marin, every surge has been preceded by an increase in the percentage of positivity,” Willis said. “The previous trend of the decline of our wastewater has also stopped. And we’ll have to keep a close eye on that.”
Willis warned that developments in Europe and the eastern US suggest that pandemic trends are worsening.
“There is a clear increase in cases and hospitalizations in Europe. And we’re seeing a significant increase in virus levels in Massachusetts wastewater,” he said.
But in those cases, Willis said the increase was not largely driven by a newly emerging strain.
“It’s important to note that these spikes are fueled by our regular BA.5 variant of Omicron, which means this: BA.5 can apparently spike, subside for a few months, and reappear in the same communities,” he said. “We really haven’t seen that much before.”
Previous spikes in COVID-19 have mostly coincided with the emergence of a new variant or sub-variant of the coronavirus. That BA.5 could apparently strike twice “implies that the culprit is a weakened immune system, a change in weather and/or a change in behavior,” says Willis.
“Regardless of the reason, it’s a concern to us because as a community we’re a lot like Massachusetts and those parts of Europe where there’s growth,” he said. “We’re highly vaccinated, we’re getting colder weather and we’re getting the BA.5 spike a few months ago.”
In addition, new subvariants circulating overseas could add to the fall surge, Willis said.
“BQ.1 is growing in Europe and appears to be even more infectious than BA.5,” he said. “The good news, if we can call it that, is that most of these newer variants that are circulating — and that may appear here — are actually closely related to BA.5,” so it was a good decision for federal officials to ask the vaccine manufacturers to focus on an updated booster designed to protect against BA.5.
Ferrer said she thinks it’s likely that a new strain or subvariant will eventually start to displace BA.5. But “how quickly that happens and how much of an impact it has on the winter waves, I can’t judge at this point,” she said.
While the newer subvariants have been slowly increasing, “that doesn’t mean you can’t have a big acceleration of expansion if something can crowd out the other variants that are out there—especially as we get into the colder months; people will be inside more, people will not wear masks,” said Ferrer.
The good news is that the updated Pfizer-BioNTech and Moderna bivalent enhancers are designed to protect against the BA.4 and BA.5 Omicron subvariants, “and we expect this to provide good protection against the BA.4 and BA.5 subvariants and BQ strains.”
On Wednesday, the CDC allowed the Novavax vaccine against COVID-19 to be used as a booster for adults. But that offer was designed only against the original strain of the coronavirus, not the BA.4 and BA.5 variants.
For most people, a recent infection does boost the immune system, but that immunity can vary from person to person. Overall, Ferrer suggests that residents receive incentives by late October or early November.
“I hope that as we approach the holidays and cooler weather and more gatherings, each of us can be sure to continue to do our part by staying home when sick; testing when they are exposed, sick, or congregating indoors with others at increased risk; and primarily taking advantage of the new boosters that protect against Omicrons,” she said.
Vaccines are not the only option for preventing COVID-19. A number of therapeutic drugs — including remdesivir and bebtelovimab, which are given intravenously, and paxlovid and molnupiravir, which can be taken orally — can help prevent severe disease and death.
“Over 85,000 doses of oral therapeutics are currently available in L.A. County,” Ferrer said. “We have no shortage.”
Anti-COVID drugs are not intended to replace vaccines. But infections can still happen, “and these drugs are invaluable in our toolkit to combat severe outcomes,” she added.