Two New Omicron Subvariants, BA.2.12 & BA.2.12.1, Are Fueling Rising Covid Cases In New York

SARS CoV 2 molecules NIAID

“At present there are a number of Omicron sub-lineages we’re following closely, including BA.2, BA.4 and BA.5 and another recombinant detected, made up of BA.1 and BA.2,” said WHO Director-General Tedros Adhanom Ghebreyesus today. That recombinant is called XE and, until today was the newest more-transmissible variant raising concern. Now there are subvariants BA.2.12 and BA.2.12.1.

The New York State Department of Public Health today announced the rapid rise of two new Omicron subvariants in the state, dubbed BA.2.12 and BA.2.12.1. They are sublineages of the BA.2 variant, and thought to have a 23%–27% growth advantage over BA.2, which itself had an estimated 30% growth advantage over the original Omicron.

If those numbers hold true, it would make BA.2.12.1 and BA.2.12.2 the most highly-transmissible strains of Covid identified to date. That distinction previously went to the WHO-monitored XE variant, which is thought to be 10% more transmissible than BA.2

“State health officials have determined that these highly contagious new variants are likely contributing to the rising cases,” according to a NY state press release. “For the month of March, BA.2.12 and BA.2.12.1 rose to collectively comprise more than 70% prevalence in Central New York and more than 20% prevalence in the neighboring Finger Lakes region. Data for April indicate that levels in Central New York are now above 90%.”

That rise is paralleled by the rise in the number of cases. At the end of the first week of March, the 7-day average number of daily new cases in the state was well under 2,000. Today, it is over 5,000, according to the New York Times. The total number of new positive cases today, according to state data, was 6,546.

The NYT reports that the subvariants have been detected in more than 40 other countries and in more than 30 states across the United States. Per NYSDPH, “The Department’s findings are the first reported instances of significant community spread due to the new subvariants in the United States. At this time, there is no evidence of increased disease severity by these subvariants, though the Department is closely monitoring for any changes.”

Some states such as California, however, do not break Omicron data out into sublineages, a practice that made it hard to track the rise of BA.2 and is now making it hard to chart BA.2.12.1 and BA.2.12.2.

Nationally, BA.2 lineages — a group which one assumes would includes the two new sublineages — account for about 86% of all new test samples sequenced the week of 4/9. In the three-state region comprised of New York, New Jersey and Connecticut however, BA.2 lineages make up for more than 90% of all newly sequenced samples.

covid variants
Proportion of new cases that are Omicron (pink) vs. other variants (purple) CDC

BA.2.12.1 is said to have North American and European lineage, while BA.2.12.2 is said to derive its lineage from the USA and Canada, with some speculating the first case was identified in Canada.

A new wave of hospitalizations from BA.2 largely did not materialize, even as restrictions were eased. So hopefully the trend with the new sublineages, should they out-compete BA.2, will be similar.

Only time — and good surveillance — will tell.

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