A “Stealth omicron” subvariant found in Santa Clara County
Santa Clara County health officials said on Tuesday they had identified two cases of a worrisome sublineage of the fast-spreading omicron variant of the virus that causes COVID-19 that quickly overtook the most common version in d other parts of the world.
Health officials had little information on Tuesday about two cases of the subline, known as BA.2, and said it was not yet known whether it was more transmissible or virulent than the sub. – omicron dominant lineage, known as BA.1.
“We have reports here in Santa Clara County of two cases of the BA.2 sublineage of the omicron variant,” Santa Clara County Deputy Health Director Dr. George Han said Tuesday. . “The omicron variant that has caused big breakouts around the world, which is driven by the BA.1 subline. The BA.2 subline is much rarer, but has started showing up in places like California and Santa Clara County and other places around the world.
Han said it was unclear how troubling the new variant might be and that he had little information to share about the two local cases.
“The main thing about this subline 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 subline, but that’s hard to say due to the small number of cases so far.”
According to the World Health Organization, the omicron variant has four lineages called B.1.1.529, BA.1, BA.2, and BA.3. While the BA.1 lineage was previously the most dominant, recent trends from India, South Africa, the UK and Denmark suggest that BA.2 is increasing in proportion, the WHO said.
“The transmission drivers and other properties of BA.2 are under investigation but remain unclear at this time,” 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 “S gene target failure” in tests. PCR which were used to identify variants like omicron. The BA.2 subline does not have this S gene deletion, however, the WHO said, so using this S gene target failure to identify the omicron could miss the BA.2 line.
Han said the BA.2 sublineage can be identified by complete genetic sequencing, which is not routinely performed on most virus samples but has been used to identify Santa Clara County cases.
BA.2 has also been reported in Washington State and Texas. It is not known how many other cases are in California. The Centers for Disease Control and Prevention and the California Department of Public Health have not tracked the sublineage separately.
At On Friday, the UK Health Security Agency designated BA.2 as a “variant under study”, based on the “increasing number of BA.2 sequences identified both nationally and internationally”.
The Health Security Agency said a total of 40 countries have uploaded 8,040 BA.2 sequences since November 17 and it is unclear where the subline may have come from. The first sequences were submitted from the Philippines and most of the samples were uploaded from Denmark – 6,411. Other countries that uploaded more than 100 samples are India (530), Sweden (181) and Singapore ( 127), the agency said.