Sonoma County gets new tool to quickly detect COVID-19 mutations

With new COVID-19 cases on the rise and the more infectious delta variant spreading especially among unvaccinated people, Sonoma County public health officials have added a new weapon in the fight against the evolving coronavirus.

It’s a state-of-the-art, $275,000 diagnostic machine they hope will narrow their aim on the types of virus strains circulating in the community by speeding certain test results that allow experts to track the emerging variants in close to real time.

On Tuesday morning, county microbiologists put the device to work for the first time at the public health lab in Santa Rosa. It specializes in genetic sequencing of COVID-19 specimens — a task that up until now has been handled by a state lab, with a lag time of up to four weeks.

The long waits have hampered the public health response, authorities said.

“By the time you wait for weeks like that, the outbreak is perhaps over, people have recovered, you’re getting information after the fact,” said Dr. Rachel Rees, director of the public health lab. “But if they can get the information within, like, two days then the outbreak is still ongoing, they still have an opportunity to curtail the size of the outbreak.”

The county’s new device shortens the turnaround time to less than 24 hours.

It uses robotics to conduct hundreds of repetitive tasks, combining complex DNA sequencing and cloud-based analytics to give officials a vital head start in the race against a resurgent virus and its now-dominant strain, the delta variant.

The testing device, Clear Dx Whole Genome Sequencing, is made by San Carlos-based Clear Labs. It can process up to 32 COVID-19 specimens in 18 hours.

The genetic sequencing equipment comes to Sonoma County at a key moment in the pandemic, which only a month ago appeared to be petering out.

But transmission of local cases and the share of COVID-19 tests that turn up positive have now increased, Dr. Sundari Mase, the county’s health officer.

Mase warned that a surge of new cases is being driven largely by infections among unvaccinated residents and the emergence of the delta mutation, which now accounts for 29% of locally detected strains that have been identified by the federal Centers for Disease Control and Prevention as “variants of concern.”

Mase told the Board of Supervisors on Tuesday that the current transmission rate for those who have been vaccinated is 2 per 100,000 residents, while the same rate for unvaccinated residents is 13 per 100,000.

“The increased rate in our unvaccinated population is driving our increasing case rate at this time,” Mase said.

According to the latest public health data, 68 cases of the delta variant, technically known as B. 1.617.2 have been detected in Sonoma County. That’s more than twice the 32 cases of the U.K. variant, B.1.1.7. The homegrown West Coast variants, B. 1.427 and B. 1.429, still make up the largest share of local mutations, at 47 and 86, respectively.

Local health officials are concerned about spread of the delta variant, which is reportedly 60% more transmissible. As current COVID-19 vaccines do provide significant protection against variants, including the delta strain, public health officials said the current surge is hitting hard local residents who have not yet been vaccinated.

This week the World Health Organization reported that while fully vaccinated people are contracting the delta variant, the inoculations are protecting most people from becoming severely ill or dying.

With so many older Sonoma County residents vaccinated, health officials said the virus has now set its crosshairs on younger residents. Mase said 78% of cases are among people 49 and younger.

“The age of cases in the past 60 days and has gone down. We’re seeing the most cases in 20- to 29-year-old age group,” she said, adding that younger people are now more frequently being hospitalized than before.

During her pandemic update to county supervisors, Mase said coronavirus-related hospitalizations increased from an average of 10 per day in mid-June to a current level of more than 40 per day. She said 92% of hospitalized COVID-19 patients and 100% of ICU patients are unvaccinated.

“We’re seeing an increase in younger people being hospitalized because those are the ones that are unvaccinated,” she said.

That group accounts for 294 cases in the past 60 days, followed by 229 cases each for the 10-to-19 and 30-to-39 age groups.

“The rise in our case rate does coincide with when we first detected the delta variant,” Mase said.

Prior to receiving the new genetic sequencing equipment, the county’s ability to detect COVID-19 mutations was limited. Positive COVID-19 samples had to be sent south to a state public health lab in Richmond. Rees said the county stopped sending specimens at the end of June because of the delay in results and in anticipation of the new tool’s arrival.

The new genetic sequencing equipment will allow the county to examine four to six times more samples, up to 64 in a week with current staffing, and return those results far faster, Rees said.

She called the equipment a game changer in the local battle against the virus.

“It’s a momentous change to bring this new technology in-house and I hope that it really helps our effort with the COVID pandemic,” she said.

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