Will a contagious subvariant lead California to a spring COVID-19 surge? What we know
As a more contagious subvariant of omicron known as BA.2 represents a steadily climbing portion of COVID-19 cases in California, experts are still working to determine whether that means another surge is on the horizon — and if so, when and how severe it might be.
For now, California has nestled into one of its lowest points of COVID-19 activity of the two-year pandemic. The only period with lower case rates and hospital numbers was spring 2021, after vaccines began to roll out but before the delta variant took hold.
But BA.2, which researchers have determined as more transmissible than the original omicron strain known as BA.1, has been increasing in prevalence for several weeks and appears to have recently become the dominant strain in some of California including parts of the Bay Area, according to genetic sequencing and wastewater data.
Infections and hospitalizations are currently surging in several European countries in which BA.2 recently gained a foothold, including the United Kingdom, health data show.
California’s two most recent surges, spurred by the delta and omicron variants, began a few weeks after those variants began to spread rapidly in the United Kingdom. The current surge overseas started in late February.
Experts have given a range of estimates in recent weeks, most of which peg BA.2 as at least 50% more contagious than BA.1 – which was already far more transmissible than earlier dominant variants.
BA.2 does not appear to cause more severe illness than BA.1.
How prevalent is BA.2?
The Centers for Disease Control and Prevention on Tuesday estimated BA.2 made up 35% of U.S. cases for the week ending March 19.
That’s up from 22% the week of March 12 and from 13% the week of March 5.
The growth has been quicker in the CDC region that includes California, Arizona, Nevada and Hawaii, rising from 13% to 28% to 41% over the last three weeks with data available.
Healthy Davis Together, a partnership between the UC Davis Genome Center and the county health office that provides the Sacramento region’s most robust surveillance of genetic variants, reported that 34% of Yolo County’s cases for the week ending March 12 were BA.2. That’s up from 29% the previous week and 16% two weeks earlier.
CDPH has a data tracker for variants in California, but as of its latest update it did not distinguish between the different subvariants of omicron. It shows all lineages of omicron making up 100% of recent cases statewide.
The CDC and the World Health Organization have not labeled BA.2 as a distinct variant of concern on its own, so the subvariant still falls under the omicron umbrella, without its own Greek letter.
Increasing virus and BA.2 levels in California wastewater
The Sewer Coronavirus Alert Network, a Stanford-based research project that measures viral loads of COVID-19 in wastewater, was recently updated after scientists developed a method to track indicators of BA.2.
The subvariant’s prevalence varies significantly across cities in the capital region, Bay Area and Central Valley being monitored by the Stanford research group.
BA.2 as of Sunday made up 65% of samples taken from Davis wastewater, more than double the 26% recorded two weeks earlier.
The subvariant made up 43% of Sacramento wastewater samples, compared to 19% on March 6.
BA.2, the so-called stealth variant, comprised 68% of wastewater samples in Palo Alto, 60% in San Jose and 31% in Merced, according to recent measurements.
Additionally, overall amounts of SARS-CoV-2 genes being shed have started to tick up at least slightly in Davis, San Jose and Palo Alto, the Stanford data show. It remains too early to determine whether the upticks are the start of exponential growth or a smaller blip. That should become clearer within the next couple of weeks.
Overall virus levels in wastewater haven’t started to climb in Sacramento or Merced, where BA.2 made up less than half of samples, according to the Stanford data.
Gov. Gavin Newsom and state health leaders unveiled the state’s endemic plan, known as SMARTER, in February. The first R in that acronym, readiness, called for the state to “maintain wastewater surveillance in all regions.”
Another wastewater monitoring project, the CDC’s National Wastewater Surveillance System, includes about three dozen wastewater sampling sites spanning California.
The network showed different parts of the state trending in vastly different directions as of mid-March.
COVID-19 activity in sewershed for Fresno County, for instance, jumped more than 400% between March 3 and March 17, according to the CDC tracker. In San Diego County, viral activity spiked by 386%.
Like with the Stanford data, it will likely take another week or two to determine whether those spikes end up being reflected in the two counties’ case rate and positivity metrics, due to the delays associated with traditional diagnostic testing.
Case and test positivity numbers remain flat in Fresno and San Diego counties, and at much lower levels than during winter’s omicron surge, state and local health data showed as of Tuesday.
Meanwhile, the largest sewershed area within Los Angeles County, which serves about 3.5 million people, observed a 92% drop between early and mid-March. The Bay Area was split, with activity mostly steady in San Francisco and Santa Clara County but more than doubling at one wastewater site in Contra Costa County.
As with the Stanford wastewater network, the CDC surveillance showed minimal change in Sacramento wastewater. Levels dropped by 3% in the past two weeks.
The National Wastewater Surveillance System does not include data on variants.
If BA.2 is so contagious, why haven’t cases spiked?
Yolo County health officer Dr. Aimee Sisson, during a virtual panel last month hosted by UC Davis, cited an estimate of BA.2 being 30% to 50% more contagious than BA.1. She said the county is watching the new subvariant “closely.”
“But as we’ve been seeing the proportion of cases caused by BA.2 increasing, we have not seen any increases in our case rate,” Sisson said of Yolo County during the Feb. 28 event. “So that’s reassuring.”
But will it last?
The downward trend in case rate has continued through the first three weeks of March. Yolo’s daily rate fell to 7.9 per 100,000 as of Monday, compared to 21 per 100,000 at the end of last month. The rate peaked near 250 per 100,000 in January at the peak of the omicron surge.
As in Yolo County, California Department of Public Health data shows statewide COVID-19 activity continuing to plummet this month.
CDPH on Tuesday reported a daily case rate of 5.6 per 100,000 residents and 1.3% test positivity, the best measurements in each metric since early last summer.
The state recently dropped below 2,000 patients hospitalized with confirmed COVID-19 for the first time since last July, reported at 1,850 on Tuesday.
But Tuesday also saw increases in the number of COVID-positive hospital patients and ICU cases over the previous day. The increases were small, adding just 17 hospitalizations and eight intensive care patients compared to Monday, and it’s only a single-day sample size.
Still, the additions marked the first day-over-day increase for each figure since late January.
Most of Tuesday’s patient increase came from an assortment of counties including Fresno, Placer, Monterey, San Mateo, Santa Barbara and Tulare.
Dr. Anthony Fauci, the nation’s leading infectious disease expert, said Sunday on ABC’s “This Week” that he expects an “uptick” but not a surge in the U.S. as BA.2 spreads in the coming weeks.
However, he also said the nation shouldn’t be caught “flat-footed.”
A key factor will be waning immunity.
For now, reinfection with BA.2 in those who contracted BA.1 appears to be relatively rare, experts have said in recent weeks.
That could change as more time elapses from California’s omicron surge, which peaked at about 305 daily cases per 100,000 for the week ending Jan. 10.
Vaccines appear to maintain strong protection against hospitalizations and deaths, as they have with the original omicron variant, Sisson and other experts have said. And booster doses appear to restore efficacy against infection.
The likelihood of a major BA.2 surge will probably depend on how quickly immune protection afforded by booster doses and by recent infection with omicron begins to fade. Those facets aren’t yet clear.
Vaccines and boosters: ‘Relying on hope’
California, like the U.S. as a whole, has a much lower booster rate than the United Kingdom, prompting extra concern in the event that the surge over there turns out to be another bellwether for here.
Only 42% of Californians ages 12 and older are fully vaccinated and boosted, compared to 67% in the United Kingdom, according to figures updated Monday by CDPH and the National Health Service, respectively.
Booster uptake is poor. About 43% of fully vaccinated Californians who are eligible for a booster dose haven’t yet received one, CDPH data show.
“Right now we’re mainly relying on hope as our defense, when it ought to be boosting at scale,” Dr. Eric Topol, director of the Scripps Research Institute in San Diego, tweeted Sunday.
Vaccination rates are also low in young children. CDPH reports that a little less than one-third of Californians ages 5 to 11 are considered fully vaccinated.
U.S. health officials are determining whether to recommend a second booster dose for the mRNA vaccines by Pfizer and Moderna. Moderna last week asked the Food and Drug Administration to authorize a second booster dose for adults.
BA.2 increase comes as measures loosen
The growing presence of BA.2 coincides with the recent end of most of California’s mask requirements, another factor prompting some worry about a significant surge.
California dropped its indoor mask mandate for the fully vaccinated in mid-February, for the unvaccinated at the start of March and at K-12 campuses last week.
Other entities plan to drop mask requirements in the weeks to come.
Sacramento City Unified School District announced this month that it would keep its mandate in place until Sacramento County has been classified in the CDC’s “low” community level for four straight weeks, which appears on track to happen upon return from spring break in early April.
Sacramento State and UC Davis also dropped their face covering requirements for most indoor areas on campus at the end of last week, ahead of their spring break this week.
The state on April 1 will also loosen restrictions on indoor “mega” events.
This story was originally published March 23, 2022 at 5:00 AM with the headline "Will a contagious subvariant lead California to a spring COVID-19 surge? What we know."
