People wearing masks while shopping at BJ's in Freeport on...

People wearing masks while shopping at BJ's in Freeport on April 3, 2020. Credit: Newsday/J. Conrad Williams Jr.

A new, highly transmissible COVID-19 subvariant is quickly becoming the dominant virus strain circulating across the state and throughout Long Island, just as cases and hospitalizations have begun to tick up during the holiday season, according to state data and medical officials.

The JN.1 subvariant evolved from BA. 2.86, a descendant of the Omicron variant that spread rapidly in 2021 and is now responsible for about 21% of new COVID infections nationwide, according to data from the Centers for Disease Control and Prevention.

As of Dec. 2, 17.5% of new COVID cases in New York State are linked to the JN.1 strain, according to data from the state Health Department. That's up from just 2.6% Nov. 4.

The strain, officials said, is expected to become the leading coronavirus variant around the world in a matter of weeks, in part because of holiday travel and waning vaccine immunity.


  • The JN.1 COVID-19 subvariant is rapidly becoming the dominant strain of the virus, as caseloads and hospitalizations continue to increase both on Long Island and statewide.

  • Medical experts say the subvariant is highly transmissible but does not cause any more serious disease than previous strains of the virus.

  • While health experts insist that staying up-to-date on COVID vaccinations is essential, state figures show only around 8% of Long Islanders have received the most recent vaccine dose.

Dr. Alan Bulbin, director of infectious disease at St. Francis Hospital in Roslyn, said while the subvariant is highly transmissible, the disease does not appear to be any more severe than earlier variants.

“It's still causing similar disease,” Bulbin said. “We don't have any signs that it's going to be more aggressive or lead to more serious illness. So it just falls in line with COVID and the usual concerns about who is at high risk and who needs to be protected.”

JN.1, first detected in the United States in September, is extremely similar to BA. 2.86, with the exception of a slight mutation to its spike protein, the CDC said.

The variant has spread rapidly this past month alone. In November, JN.1 accounted for just 3.5% of cases nationwide, the CDC estimated.

Globally, JN.1 “continues to be reported in multiple countries, and its prevalence has been rapidly increasing globally,” according to an advisory issued this week by the World Health Organization.

“What we're seeing now is a strong increase in the number of infections and significantly more hospitalizations as a result from it,” said Dr. Frank Coletta, a pulmonologist and chief of critical care at Mount Sinai South Nassau Hospital in Oceanside, who added they don't test for specific variants.

The subvariant appears to have similar symptoms as other COVID strains, including fever, congestion, cough and difficulty breathing, although the updated vaccines are expected to increase protection against JN.1, the CDC said.

But state data shows that just 8.6% of Nassau residents and 8.1% of Suffolk residents have received the updated version of the vaccine, below the statewide average of 10.6% and the national average of 18%, data shows.

Meanwhile, as has become a familiar trend in recent years, COVID cases on Long Island have gone steadily up during the winter months.

For example, the seven-day average of new cases on Long Island on Dec. 18 was 1,374, state figures show. That's the highest reported figure since Jan. 5, when the seven-day average in the region was 1,438.

And there were 409 patients hospitalized on Long Island with COVID reported Wednesday, the highest total since the week of Jan. 30 when there 425 individuals hospitalized here, state Health Department data shows. There were 179 patients hospitalized on Nov. 13.

The new variant comes as hospitals are seeing a surge of flu and RSV illnesses across the state, creating, along with COVID, what medical officials call a “tripledemic.”

“The warnings of the tripledemic are actually coming true now,” Coletta said. “We're seeing patients in the hospital with a higher degree of illness than previously from these viral infections.”

For example, there were 10,680 lab-confirmed influenza cases and nearly 800 flu hospitalizations reported during the week ending Dec. 9, the highest totals in nearly a year, according to state figures.

And the rate of New Yorkers testing positive for RSV is just under 10% on a three week rolling average, according to the CDC. Those numbers, however, are trending down slightly from their peak of more than 11% at the start of December, federal figures show.

"The holidays are here and thankfully we are able to gather together and celebrate. It is my hope that no one would miss out on visiting with friends and loved ones because they are sick,” said state Health Commissioner James McDonald. “For the first time in history, we have three safe and effective vaccines available to protect against these three illnesses, flu, COVID and RSV.”

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