New Omicron subvariants spreading fast in New York

Two new Omicron subvariants that appear even more transmissible than the highly-contagious BA.2 are driving an uptick in Covid cases in New York, the state’s health department said Wednesday.

While there’s no evidence that either causes more severe disease, the department estimates they have a 23% to 27% growth advantage over the BA.2 variant that was itself more infectious than the original Omicron. It’s the first reported instance of significant community spread due to the two subvariants in the US.

“We are alerting the public to two Omicron subvariants, newly emerged and rapidly spreading in upstate New York, so New Yorkers can act swiftly,” State Health Commissioner Mary Bassett said in a statement. “While these subvariants are new, the tools to combat them are not.”

The discovery of the two new subvariants in the US comes as both cases and hospitalizations increase nationwide due to the BA.2 subvariant. With more people using at-home tests, there is also concern the numbers could be an underestimate. On Wednesday, US officials extended the pandemic public health emergency and the mask mandate for travelers, citing the rise in cases.

A few weeks ago, the state health department started investigating an unusual uptick in cases in Central New York, a region of upstate New York. Using open access genomic sequences available through the GISAID database, as well as information sent to the Wadsworth Center from labs in New York, they identified the two subvariants now known as BA.2.12 and BA.2.12.1. They currently represent 90% of cases in the Central New York region and have also been detected in the neighboring Finger Lakes region.
State data released Wednesday show the seven-day average of cases per 100,000 people in Central New York, where the subvariants were identified, is higher than any other region. They are almost twice as high as those in New York City.

The department is continuing to urge residents to get vaccinated and consider wearing masks while indoors. They also suggested upcoming Easter and Passover celebrations be moved outdoors to reduce infection risk.