Sonoma County joins national effort to track dangerous virus variants

As Sonoma County finally pushed down coronavirus infections and hospitalizations, local public health officials have joined critical work going on around the country of trying to outmaneuver virus mutations, some more transmissible and lethal than the dominant viral strain the world has battled for a year.

The county is participating in state and federal surveillance programs aimed at identifying coronavirus variants before they can spread, infect and kill many residents. Both efforts are in their infancy and local health officials have yet to receive confirmation that any COVID-19 variants have been found in the county.

After a year of fighting the ongoing pandemic, there’s now a race to vaccinate as many county residents as possible, knowing a powerful variant could be lurking. This all-out effort is being replicated in other parts of California and in many areas of the country and world.

“We need to know if there are any mutations, or small changes in the genetic material of the virus that could make it more transmissible, could make it have worse (health) outcomes,” said Dr. Sundari Mase, the county’s health officer.

“If we find somebody who’s been vaccinated in our county, but then comes down with COVID, we’d want to know right away, is this a variant of COVID or is it the same we’ve had before?”

The disturbing reality is mutations could result in new viral strains resistant to COVID-19 vaccines now available in the United States. Case in point is the persistent battle against influenza, which requires an annual update to that plentiful vaccine.

The county’s engagements in state and federal variant detection efforts comes as the Biden administration has pledged to inject $200 million into biotechnology capabilities across the country to bolster local efforts to detect emerging coronavirus variants.

Meanwhile, congressional Democrats in Washington are proposing to spend $1.75 billion to ramp up the nation’s genetic-sequencing capabilities — studying DNA to learn characteristics of organisms — with the goal of checking 15% of all confirmed COVID-19 human samples for variants. That proposal is part of the $1.9 trillion relief package making its way through Congress.

Local health officials on Friday said it will take time for these federal actions to gain traction, and they are uncertain when Sonoma County will begin receiving regular reports on the virus specimens local public health leaders began submitting last month to the Centers for Disease Control and Prevention for analysis.

Strains of concern

Medical experts said viruses mutate all the time and so it’s likely variants will be found in this county. The question is, will these mutations make it more difficult to contain COVID-19, or to treat the respiratory illness caused by the virus?

Public health concerns over variants has intensified the past two weeks with news of more highly transmissible coronavirus mutations making their way around the state and nation.

One of these known as the U.K. variant, B.1.1.7, which was first detected in the United Kingdom and thought to be more contagious, has been detected in Southern California.

A variant first detected in South Africa, B. 1.351 is thought to be resistant to the Moderna vaccine.

And another variant, P. 1, identified in mid-January among Japanese travelers to Brazil, has been detected in the Bay Area. This variant is also thought to be more contagious.

A homegrown variant, known as the California variant, B. 1429, has been detected in Marin and Lake counties. State officials are worried this mutation could more easily attach itself to human cells, making it more contagious.

Mase and other local medical professionals say there have been no epidemiological events in Sonoma County, such as significant or uncommon COVID-19 outbreaks pointing to the presence of a more virulent coronavirus mutation.

Dr. Wanhua Yang, laboratory medical director at Santa Rosa Memorial and Petaluma Valley hospitals, said one positive sign is the dramatic decline in new COVID-19 cases and hospitalizations in the county. However, she said it’s likely the California virus variant already is present in Sonoma County.

Providence St. Joseph Health, which operates Memorial, Petaluma Valley and Healdsburg hospitals, does have the capability to conduct genome sequencing at its molecular laboratory in Oregon. But the big health care provider has been focusing its genotyping efforts in Southern California, which has been hammered with virus cases, including the U.K. and South Africa variants.

Yang said St. Joseph Health could begin sequencing coronavirus samples from Northern California in March.

“The California variant has been found in many other states,” she said. “I wouldn’t be surprised if we find them (here).”

State and federal surveillance

Since Jan. 14, Sonoma County has been sending four positive COVID-19 samples every two weeks to the CDC for its national SARS-CoV-2 strain surveillance program for genetic sequencing.

The federal program is expected to expand sequencing capacity threefold, according to the CDC. The project, which was started with virus samples from state and local public health agencies in November, was scaled up to process 750 requested coronavirus specimens a week beginning Jan. 25.

By contracting with large commercial diagnostic laboratories to sequence COVID-19 samples across the country, the CDC has accelerated processing to nearly 7,000 samples weekly. The $200 million pledged by President Biden will kick-start the CDC’s goal of sequencing 25,000 virus specimens a week.

County health officials said they hope the expanded CDC effort to discover coronavirus variants enables the county to send more samples for analysis.

“I certainly hope we can scale up,” said Mase. “The more specimens that we can get genotyped, the better understanding we’ll have of what’s happening on the ground in terms of variants.”

Another option for analyzing local coronavirus specimens is the state’s Viral Rickettsial Disease Laboratory in Richmond.

Dr. Rachel Reese, director of the county’s public health lab, said the director of the Richmond lab has been coordinating and developing a genome sequencing surveillance program called COVIDNet.

County health officials are finalizing participation in that state program, and the local public health lab soon should be able to send COVID-19 samples there. Samples processed through the state lab as part of COVIDNet will not be limited to a few biweekly, as they are with the CDC surveillance program.

“We can send quite a few more than four samples every two weeks,” Reese said. “We just have not determined how many we’re going to send or how many we need to send to know what’s going on.”

COVID-19 testing key to variant search

As county health officials move to outflank coronavirus variants, they underscored the importance of continuing with yearlong pandemic safety strategies, COVID-19 testing chief among them.

D’Arcy Richardson, Sonoma County’s director of nursing for COVID-19 response, said it’s crucial for residents to continue getting tested when potentially exposed to the pandemic disease to help identify new mutations of the deadly virus that could be spreading locally.

“That’s another reason for people to get tested right now ... the new strains that are circulating,” Richardson said. “One of the things that's really important in terms of controlling the pandemic is making sure that we are on top of what strains are circulating in our county.”

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