Subclade K, a new flu strain, detected in San Diego County

Subclade K, the flu variant that caused fall outbreaks in the United Kingdom and Canada, has been detected in San Diego County, the region’s public health department confirmed Wednesday.

Genetic analysis performed at the county’s new public health lab on four samples collected from local patients confirmed subclade K’s presence. Three of the samples collected in December showed the specific set of mutations associated with K, which is part of the H3N2 group of flu viruses. An analysis of a fourth sample collected in late September also showed K’s genetic fingerprint, suggesting that the rapidly spreading strain was present at some level, though the specific prevalence is not known.

With the U.S. Centers for Disease Control and Prevention’s most recent flu report, released on Dec. 20, showing that 90% of the H3 influenza viruses it analyzed were subclade K, it is no surprise that it has already gained a foothold in the region. Standard community-level characterization of circulating flu viruses does not routinely include the level of genetic analysis that goes beyond the hemagglutinin and neuraminidase proteins on virus surfaces, which leads to the commonly-referenced H and N numbers that many who follow the flu are familiar with.

But San Diego County’s new $96 million public health laboratory, which opened in June, has the staffing and equipment necessary to begin deeper genetic analysis of seasonal flu for the first time locally, providing an opportunity to spot smaller mutations. Similar analysis became commonplace during the COVID-19 pandemic when the coronavirus mutated rapidly, causing waves of illness.

Dr. Sayone Thihalolipavan, San Diego County’s public health officer, noted that early information out of Europe, where subclade K sent case rates soaring before coming to America, show that while this year’s vaccine is less of a perfect match than the public health community hoped it would be, it is still far far better than nothing.

Indeed, a study published Nov. 20 by researchers at the UK Health Security Agency using preliminary data estimates that this season’s vaccines are 72% to 75% effective at preventing emergency department visits and hospital admissions in children and adolescents and between 32% and 39% effective for adults.

“It is important to highlight that this is still a moment where it’s not too late to vaccinate,” Thihalolipavan said, noting that the level of mutation seen with subclade K is nowhere near as severe as was the case in 2009 when a “novel” version of H1N1 flu filled emergency departments.

While it does appear that subclade K has put the spurs to the flu season in America, with flu test positivity rates jumping from 14.8% to 25.6% in a single week, San Diego County has thus far not seen such a jump, though the federal government has not updated its numbers since fives days before Christmas and notified the public this week that its final update of the year, expected on Monday, will not be posted until Jan. 5.

San Diego’s weekly respiratory virus surveillance report, released Wednesday, has test positivity rates climbing but still below 20%. While 6% of emergency visits nationwide were showing flu symptoms as of Dec. 20, the figure was 2.9% in San Diego County emergency departments.

There is no thought that San Diego, and other communities that have not yet seen the heavy flu activity that has been reported in other parts of the country, have somehow escaped the onslaught of subclade K.

“What we hear from colleagues across the country is that it is already severe in many areas,” Thihalolipavan said. “We’ve seen in prior years that sometimes we are a week or two behind, but we start to catch up in San Diego, and so we anticipate that may be a likely possibility, that it will get worse here, too.”

So far this season, San Diego County has recorded 4,231 confirmed flu cases through Dec. 27. That’s less than half of the 10,222 flu cases documented through the same date last season. COVID-19, while still very present, has so far had a similarly low prevalence with 10,708 reported cases since July 1, compared to 21,075 during the same period last season.