New COVID variants with ‘extreme transmissibility’ take hold in San Diego County

Confirmed COVID-19 cases remain high in San Diego county, with more than 7,000 cases reported for the most recent week data is available, and experts fear that new strains of Omicron might create a surge in infections, even among those with natural or vaccine immunity, in the coming weeks.

The sub-variants BA.4 and BA.5 are quickly taking hold and, like other iterations of Omicron, are increasingly more contagious and equipped to evade existing antibodies. 

Experts are worried that these new strains could cause more breakthrough cases down the line, as immunity in those who are fully vaccinated or boosted wanes and additional booster shots are not yet widely available.

“We’re seeing people who have been very careful for two-and-a-half years becoming infected with these strains of virus, which I think reflects their really extreme transmissibility,” said Robert Schooley, chief of the UC San Diego Health Division of Infectious Diseases.

The number of daily confirmed COVID-19 cases in the county has remained fairly consistent since May when the spread of earlier variants of Omicron, BA.2 and BA.2.12.1, caused daily case numbers to climb to levels rivaling the Delta surge last summer. 

For the week of June 12, the county had three days in a row where the number of reported cases exceeded 1,600, similar to the daily counts at the height of the Delta wave.

While the majority of cases reported by the county up to this point have most likely been earlier strains of Omicron, potential spread in the future could increase even more as BA.4 and BA.5 take hold and more activity occurs due to the lack of restrictions, experts say.

“We’re at a level right now that each case generates slightly more than one new case,” Schooley said. “Through a combination of increased intensity of activities and less vaccination, less masking, we’re allowing the virus to kind of smolder.”

The most recent data available from wastewater sampling, which has been used to monitor the prevalence of the virus and its variants, show that BA.4 and BA.5 accounts for about 46% of the virus’s caseload as of June 15, while previous iterations of Omicron, BA.2 and BA.12.1, make up about 51%.

This sampling also suggests that current reported case numbers might be an undercount, due to the increasing practice of at-home testing.

While rates for hospitalization and death still remain lower for those who have been vaccinated, some of the communities with the highest rate of transmission over the last two weeks have been in places with high rates of full vaccination. 

Areas such as San Ysidro, Mission Valley, Chula Vista, La Jolla and Oceanside are among those with the highest rates of transmission in the county, despite rates of vaccination that suggest a majority of residents have received at least two doses. 

Other factors, such as occupation and social exposure, are important to consider when looking at this overlap and potential break-through cases in the future, according to Susan Kiene, professor of global health at San Diego State University.

“It’s not necessarily any kind of correlation between vaccination and then getting infected,” Kiene said. “It’s certainly that people are having risk in daily life (doing things like) just going to work, even though they’re doing the right thing in terms of getting vaccinated.”

Experts say that the most important factor influencing the current surge in cases is diminishing immunity in those who might have been fully vaccinated or boosted. 

A report from the Center for Disease Control published earlier this year found that vaccine effectiveness against COVID-19 was higher after receiving the third dose than after the second but decreased strength over time. 

During the “Omicron-dominant period,” the report says that vaccine effectiveness against emergency department or urgent care visits two months after a third dose was around 87%, decreasing to 66% by the fourth month. 

The strength of the booster in preventing these hospital visits is reported to fall to around 31% after five months of receiving it, however, the CDC says this estimation might be imprecise. For those without a booster, effectiveness drops to about 37% after about five months after getting the second dose.

Both Kiene and Schooley emphasize the importance of getting a booster if you are eligible for one and taking personal precaution to avoid infection, like wearing a mask indoors.

“It’s inevitable that almost all of us are gonna get infected,” Schooley said. “I think kind of a takeaway message here is that this virus is much more capable of getting into the population than the previous ones … If you let your immunity wane, you can get really quite sick.”

“We’re at a very different place than we were probably a year ago,” Kiene said. “COVID is much more manageable now, (but) it’s not that there is no risk anymore. We still need to exercise caution.”