SAN JOSE, Calif. — Santa Clara County health officials Tuesday said they have identified two COVID-19 cases of a worrisome sub-lineage of the fast-spreading omicron variant.
Health officials had little information Tuesday about the two cases of the sublineage, known as BA.2, and said it’s not yet known whether it is more transmissible or virulent than the dominant omicron sublineage, known as BA.1.
“The BA.2 sub-lineage is much rarer, but has begun to pop up in places, including California and Santa Clara County and other places around the world,” Santa Clara County Deputy Health Officer Dr. George Han said Tuesday.
Han said it’s unclear how troubling the new variant might be, and he had little information to share about the two local cases.
“The main thing about this sublineage is that because it’s so much less common, we don’t know much about it,” Han said. “Early indications are that it probably behaves much like the omicron BA.1 sublineage, but it’s hard to tell because of the small number of cases so far.”
According to the World Health Organization, the omicron variant has four lineages known as B.1.1.529, BA.1, BA.2 and BA.3. While the BA.1 lineage has previously been the most dominant, recent trends from India, South Africa, the United Kingdom and Denmark suggest that BA.2 is increasing in proportion, the WHO said.
“Drivers of transmission and other properties of BA.2 are under investigation but remain unclear to date,” the WHO said in a Jan. 21 update.
BA.2 has been dubbed “stealth omicron” because most omicron variant sequences include a deletion in the S gene, which can cause what scientists call an “S gene target failure” in PCR tests that has been used to identify variants as omicron. The BA.2 sublineage, however, lacks that S gene deletion, the WHO said, so using that S gene target failure to identify omicron might miss the BA.2 lineage.
Han said that the BA.2 sublineage can be identified by a full genetic sequencing, which is not commonly done on most virus samples, but was used to identify the Santa Clara County cases.
BA.2 also has been reported in Washington state and Texas. The Centers for Disease Control and Prevention and California Department of Public Health have not been separately tracking the sublineage publicly.
The California Department of Public Health said Tuesday that as of Jan. 24 there were a total of 11 confirmed BA.2 cases in the state.
“New variants will continue to evolve as long as there are large pockets of unvaccinated people,” the department of public health said in a statement. “Strengthening our protection against COVID-19 through vaccination and boosting is more important than ever.”
Denmark’s Staten Serum Institut in Copenhagen last week reported that the proportion of BA.2 cases in the country had risen in just weeks from 20% to 45%, and told the the Washington Post on Monday it now accounts for 65%.
On Friday, the United Kingdom Health Security Agency designated BA.2 a “variant under investigation,” on the basis of “increasing numbers of BA.2 sequences identified both domestically and internationally.”
The Health Security Agency said a total of 40 countries have uploaded 8,040 BA.2 sequences since Nov. 17 and it is unknown where the sub-lineage may have originated. The first sequences were submitted from the Philippines, and most samples have been uploaded from Denmark — 6,411. Other countries that have uploaded more than 100 samples are India (530), Sweden (181), and Singapore (127), the agency said.
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