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Expert: COVID BA.2 variant likely widely spreading in San Diego County

San Diego’s weekly COVID-19 report shows steady new-case numbers, but there are signs, experts say, that BA.2, the new subvariant that has caused surges in Europe and Asia, has already taken a significant hold here.

The county’s latest variant report lists only 140 confirmed BA.2 cases across the region. But confirming the variant’s presence requires time-consuming genetic sequencing work. A happenstance feature of the original Omicron variant helps see the current picture more quickly. Omicron, like other variants that came before it, omits a part of its S gene that is targeted by some commonly used coronavirus tests.

Those deletions were intact in Delta, Omicron’s predecessor, which provided a useful benefit. When test results started coming back with the targeted part of the S gene failing, it could reasonably be assumed that a shift in the prevalent strain was underway.

It’s a similar situation today, noted William Lee, chief science officer for Helix, a San Diego-based testing company with a national footprint that has delivered more than 10 million results during the pandemic. The targeted portions of the S gene are intact for BA.2, Lee noted, just as they were for Delta. It was not too long ago that nearly 100 percent of test results had omitted the S gene target, suggesting that Omicron was everywhere. But local results, Lee noted, have changed dramatically. The most recent update on March 20 shows that only about 20 percent of results were missing that gene target, strongly suggesting that the remainder are BA.2.

“The latest data I have from San Diego suggests that BA.2 is probably over half of cases already, if not even higher,” Lee said.

While the current moment feels like a lull, the greater transmissibility of BA.2, Lee warned, is likely to cause a surge in infections relatively soon.

“I do think this BA.2 wave is going to come sooner than many people thought,” Lee said.

Omicron caused fewer severe cases than the variants that came before it and, while BA.2 seems to be more easily spread, early studies have indicated that it is not expected to cause significantly more hospitalizations and deaths. While the variant does seem to have evaded some drugs called monoclonal antibodies, antiviral drugs are thought to still have efficacy.

Another wave is most concerning for those at greatest risk of complications, especially for people with compromised immune systems or chronic diseases such as diabetes. The risk also increases with age.

A total of 2,774 coronavirus cases were reported over the past week compared to 2,987 the previous week, according to the county’s update Wednesday. The report included 13 additional deaths of which four were fully vaccinated and nine were not. All, save two whose medical histories are pending, had other underlying conditions present at the time of their death.

Cumulative coronavirus hospitalizations continue to shrink, falling under 200 countywide Sunday.

Many have recently turned to the amount of virus detected in local wastewater samples as an extremely effective indicator of a new coronavirus wave arriving.

It was not clear Wednesday evening whether the community’s wastewater detections have changed significantly. The most recent update posted to San Diego’s SEARCH coalition, a collaborative wastewater analysis effort led by UC San Diego, was posted on March 14, more than one week ago. There were 1.2 million viral copies detected per liter of wastewater, a number that is well below the 47 million copies per liter at the height of the winter surge. However, the community will need more frequent updates if it is to use wastewater to help detect the arrival of a new coronavirus surge. University microbiome expert Rob Knight said in an email Wednesday afternoon that an update will be made soon, and the group is working to find a way to post three updates per week.



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