Omicron BA.2 variant now dominates in local counties

The BA.2 strain of the SARS-CoV-2 virus has overtaken other variants in Santa Clara and San Mateo counties, wastewater surveillance shows.

The strain, which is a subvariant of the omicron virus that caused a large surge in cases in January, constitutes nearly 100% of the coronavirus strains in some local sewersheds throughout both counties, according to Santa Clara County’s Wastewater Surveillance Program and data from Stanford’s Sewer Coronavirus Alert Network (SCAN).

The surveillance program samples wastewater for evidence of the virus’ ribonucleic acid (RNA), a part of its genetic signature. The average percentages of BA.2 in Santa Clara County wastewater ranges from 65% to 100% of all variants in the north county. The levels are still consistently below 30% in the southernmost county areas, county staff said in an email.

The high presence of BA.2 started in the Palo Alto sewershed, which includes Palo Alto, Mountain View, East Palo Alto, Los Altos and Los Altos Hills, according to Stanford’s SCAN. Stanford SCAN presents the percentage of the variant in the wastewater compared to other variants as a trimmed mean over five days, which eliminates the high and low numbers.

The five-day trimmed mean percentage was as low as 2% on Feb. 8, but it reached 93% at its peak on March 6. It dropped to 63% as of March 21, according to Stanford SCAN data.

Other sewersheds also showed BA.2 in single-digit percentages around the same time in February. They also rose significantly in the past few weeks. On March 21, the percentage of BA.2 in Codiga (Stanford University), a subset of the Palo Alto sewershed, was 89%; and San Jose was 71%. Sunnyvale’s percentage was 96%.

In Gilroy, however, at the extreme end of Santa Clara County, the BA.2 percentage represented 34% of the variants present in wastewater, according to the Stanford SCAN data.

In San Mateo County, the BA.2 percentage in the Silicon Valley Clean Water sewershed, which serves the cities of Belmont, San Carlos, Redwood City and the West Bay Sanitary District, was 93% on March 21, according to the Stanford SCAN data.

“The trends are consistent with state and national trends of BA.2 increasing among sequenced specimens from people with COVID,” Santa Clara County noted.

The county cautioned, however, against focusing only on recent readings.

“Wastewater surveillance, particularly for COVID-19 and variant detection, is still an emerging science,” the county said.

Wastewater data can also vary over short periods. Sunnyvale’s BA.2 five-day trimmed mean percentage was 96% on March 21, but on March 22 it dropped to 71%. Researchers and health officials must look at sustained trends rather than focusing on only the most recent readings, both for COVID-19 concentrations overall as well as proportions of a given variant, the county said.

The rapid rise of a variant is not completely unexpected, Michael Balliet, county deputy director for public health, said in a recent phone interview.

“It’s a pretty good indicator of what’s going on. The overarching message is that the virus is still actively circulating in the community,” he said.

The prevalence of BA.2 in the wastewater doesn’t necessarily mean there are abundant COVID-19 cases, just that the strain has taken over, Dr. Jorge Salinas, hospital epidemiologist for Stanford Health Care, said by phone this week.

“Most variants have faded out and new variants tend to outcompete past variants. One potential conclusion is that BA.2 is perhaps more transmissible. It’s possible that the BA.2 variant has a bit of a competitive advantage,” he said.

While BA.2 is the dominant strain in the wastewater, so far it hasn’t translated to a high number of known infections, which is somewhat baffling to health officials. The number of hospitalizations and case rates remain low, health leaders in Santa Clara and San Mateo counties said. It’s unknown if the BA.2 variant, which is 30% more transmissible, is going to cause milder illness, health officers in both counties have said.

Santa Clara County also hasn’t yet put its number of BA.2 cases on its online COVID-19 wastewater surveillance dashboard. The time required for laboratories to sequence the genetic material and report the variant cases to public health departments can take a month or more, according to the county.

Still, epidemiologists think another wave is coming.

“It is fair to expect an increase in cases in the coming weeks,” Salinas said.

Cases have exploded in some other countries, particularly in Asia.

BA.2 now accounts for 75% of the world’s COVID-19 cases, said Dr. Maria Van Kerkhove, the World Health Organization’s COVID-19 technical lead.

“This is the most transmissible variant we have seen of the SARS-CoV-2 virus to date,” she said.

‘It is fair to expect an increase in cases in the coming weeks.’

Dr. Jorge Salinas, hospital epidemiologist, Stanford Health Care

While each country and region faces different challenges, a reduction in testing in many areas means the current cases are “just the tip of the iceberg,” Dr. Tedros Adhanom Ghebreyesus, WHO director-general, said during a press conference on March 16. Regions that have done away with precautions such as masking and social distancing and that have low vaccination rates are going to be the most impacted, he said.

“The pandemic is not over. I repeat: The pandemic is not over,” he said.

In the Bay Area, with its high vaccination rate and high number of cases of the omicron BA.1 variant just two months ago, the region will be better protected against death and severe illness than other places, Salinas said.

“I believe there will be another wave. It probably won’t be as high as the January wave,” he said.

It’s hard to predict how big the wave might be and how impactful, he added.

“It means in the coming weeks … we will need to implement preventative procedures: masking, vaccination, social distancing; avoid crowded inside spaces.

“It’s like living in an area with frequent earthquakes or tornadoes. You know what to do,” he said.

Salinas said he is concerned that the country, so anxious to put the pandemic in the past, will rapidly jump to the conclusion that BA.2 is milder. He noted that was the assumption with omicron BA.1 — but people died from BA.1.

“With BA.2, we need to remain humble and nimble in our response,” he said.

Salinas also wouldn’t be surprised if there is another variant and a subsequent surge as long as there is an uncontrolled, large amount of infection anywhere in the world.

Louise Rogers, chief of San Mateo County Health, also told the San Mateo County Board of Supervisors on Tuesday that it’s too soon to say whether BA.2 will cause a surge. The county continues to be prepared and expects at some point there will be an uptick.

“Unfortunately, at this point we don’t know what will happen,” she said, which is why county health officials continue to urge people to get vaccinated and boosted.

“The vaccination rates do seem to be correlated with how severe the impacts are in other parts of the world,” she said.