Sonoma County keeping COVID-19 variants in check

In the battle for dominance between coronavirus variants, Sonoma County and the entire state of California apparently have come upon good fortune, after more than a year with plenty of pandemic pain.

The county certainly isn’t guaranteed this positive phase will continue, so infectious disease experts say it’s imperative to keep aggressively vaccinating the local population.

Here’s what’s been occurring: The dominant COVID-19 strain in Sonoma County and around the state is a homegrown West Coast variant mutation that is for now “out-competing” other more contagious and deadlier variants, playing crucial interference that could be preventing these other strains from taking hold, said Dr. John Swartzberg, a UC Berkeley infectious disease expert.

And this tamer variant does not appear to be causing another surge of virus infections, according to Swartzberg and other medical experts.

In other parts of the United States, coronavirus strains like the South African, Brazilian and U.K. variants have taken hold and triggered a spring surge of new COVID-19 cases. But in California, that’s not the case. At least not yet.

In short, California has gotten lucky, said Dr. George Rutherford, an infectious disease epidemiologist at UC San Francisco.

“We did not engineer this. It just happened,” Rutherford said. “Whether it was our wonderful weather or our great population or whatever, I don’t know. But for whatever reason (the West Coast variant) appears to have a selective advantage — for now. This could change.“

A future examination of the molecular biology of variants eventually will yield the reasons why some strains became dominant in some parts of the country over others.

“For right now, the observation is that we’re seeing more cases of the West Coast variant and fewer cases of the U.K. variant than in the rest of the country, and buy a lot,“ Rutherford said.

The West Coast or California variant appears to have contributed to a sort of pandemic pause, opening a window of opportunity, Swartzberg said. It’s a chance to get more people vaccinated and continue to keep transmission low to prevent a more deadly homegrown mutation from popping up, he said.

“We need to take advantage of this pause that we’re experiencing,” Swartzberg said. “Every human being who is not immune and gets infected is a viral factory ... so now is the time to get on top of this, while we can.”

Virus hospitalization low

The pandemic outlook continues to improve in Sonoma County since the winter surge. The county is in the orange stage of the state’s community reopening plan, the second least restrictive part characterized by a moderate rate of virus transmission.

According to the state’s most recent assessment of local COVID-19 metrics, the county is seeing 3.9 new daily virus cases per 100,000 people. Test positivity, the share of COVID-19 tests that turn up positive, is only 1.6% and that rate in the county’s most disadvantaged communities is 1.9%

Local health officials say the ongoing vaccination effort, with 38% of eligible adults now fully inoculated and 19% partially vaccinated, is helping keep the virus in check. Officials point to the vaccination rates in area skilled nursing and assisted living centers as a prime example of the success of the three vaccines on the market nationwide.

About 95% of all residents and 85% of staff in senior care homes in the county have been fully vaccinated. As a result, there have been no new COVID-19 infections among senior care home residents since March 5 and no deaths at those properties since Feb. 16.

What’s more, coronavirus hospitalization rates for people 65 and older went into a free fall about six weeks after the local vaccination effort started in late December. Throughout the pandemic that began in March 2020, virus-related hospitalization rates for seniors have been sharply higher than they’ve been for residents younger than 65.

During the winter surge, hospitalization levels for county residents 65 and older were between 4 and 5 individuals per 100,000 local residents, compared to between 1 and 2 per 100,000 people younger than 65. Now, the rates for both groups are about the same, at well below 1 per 100,000.

Variant detection

In California, the so-called West Coast variant — which is actually made up of two closely related strains B.1.427 and B.1.429 — appears to be prevailing sevenfold over the next most prolific strain, the U.K. variant. State health officials have genetically sequenced 13,490 cases of West Coast variants statewide, compared to 1,937 cases of the U.K. variant, according to the latest California public health data on COVID-19 variant cases.

Another 27 cases were determined to be the South African strain and 166 the Brazilian variant.

In Sonoma County, eight cases of variants have been detected, three each of the West Coast strains B.1.427 and B.1.429. and two of the U.K. strain, B.1.1.7.

The county has two ways of conducting genetic sequencing tests, or genotyping, to detect COVID-19 variants. One, a surveillance program with the Centers for Disease Control and Prevention, allows the county to process four local virus specimens every other week. The second is a state-run program that enables processing of up to 20 positive COVID-19 samples a week at a laboratory in the East Bay.

The criteria for the state genotyping effort involves testing: those who have become reinfected with the virus after 90 days of a previous infection; virus cases among those who have been fully vaccinated; anyone in the hospital who is younger than 55; anyone who dies and anyone who has a history of travel outside the country or are visitors from outside the country.

The turnaround time for state genotyping results is anywhere from 21 to 42 days, while the CDC program can take between 30 and 45 days, said Jenny Mercado, a county epidemiologist. Officials said such wait periods do not allow local public health workers to effectively respond to variants and the threats they pose.

But D’Arcy Richardson, head of nursing for the county’s pandemic response, said the county public health lab is awaiting new genetic sequencing equipment that will allow the county to run batches of virus samples every couple of days.

That will greatly improve the county’s ability to track the presence and trajectory of new COVID-19 variants, Richardson said. Local genetic sequencing should be available by summer, she said.

“It would be a game changer for us in terms of being able to manage our cases and intervene quickly when we’re seeing things of concern in the community,” Richardson said.

With local genotyping, public health staff can better determine if certain variants are associated with higher rates of hospitalization, death or viral transmission. Hospital treatment can then be better tailored for patients with certain variants, she said.

On Friday, the entire country got a boost related to this matter. The Biden administration announced it would allocate $1.7 billion to track highly infectious variants and expand state and federal genetic sequencing capacity. The money, which is part of President Joe Biden’s American Rescue Plan, is part of the latest effort to address the emerging pandemic threat in the United States, where nearly half of all new COVID-19 cases are now caused by variants.

Homegrown strains

Dr. Lee Riley, a UC Berkeley infectious disease expert, credited several factors that have led the West Coast variant to outperform other strains in California. Riley said he doesn’t think the state’s homegrown strains are necessarily keeping other variants out, since technically “viruses don’t compete against each other.”

“They independently start new transmission chains among different susceptible groups of people,” Riley said.

The state’s ongoing vaccination rollout, greater compliance with social distancing and other pandemic measures, and the fact that so many people in Los Angeles County were infected during the winter surge are some of the reasons the U.K. variant is having trouble finding new groups of people to infect, he said.

“In Michigan, the U.K. variant began to circulate before the vaccine rollout began and the state also has no mandated restrictions, which made it easier for the U.K. variant to find many new groups of people to infect,” Riley said.

The West Coast variant likely emerged in Southern California communities with very high transmission frequencies.

“Some of the mutations may be detrimental to the virus, while others are advantageous,” he said. “It was just a random event that the variants we got in (California) were not as highly transmissible as the U.K. variant.”

Vaccination urgency

Infectious disease experts think the battle against the coronavirus will stay fixated on variants and vaccinating as many people as possible before a more deadly strain arrives.

Rutherford, the UC San Francisco infectious disease expert, said greater focus needs to be placed on places like Baja California, where large urban cities such as Tijuana are adjacent to nearly 1.5 million people in San Diego.

He said Mexico has highly successful vaccination programs and the best childhood vaccination rates in the world. But right now, he said, Mexico does not have enough COVID-19 vaccines.

“We’ve given them some of our vaccine and we probably need to give more,” Rutherford said. “We need to think more globally, at least more regionally about disease control or otherwise we’re going to keep getting re-introductions.”

During a virtual town hall Wednesday, county health officials expressed optimism the local vaccination push can prevent the spread and increase of variants.

Dr. Urmila Shende, Sonoma County’s vaccine chief, and other infectious disease experts say ongoing success beating virus mutations will depend on continued public adherence to all the preventative measures, particularly mask wearing and social distancing, that have helped reduce local transmission of the virus, in whatever strains.

“We don’t know what variants are going to do, but hopefully we have beat the variants,” Shende said. “Hopefully, we’ve got enough immunity built into our community at this point that we’re going to be able to thwart (variants) and we’re not going to have the same outcomes as other parts of the country and other parts of the world.”

You can reach Staff Writer Martin Espinoza at 707-521-5213 or martin.espinoza@pressdemocrat.com. On Twitter @pressreno.