New York watching for COVID variant appearing in other states that's 'highly divergent' from prior strains

A new variant of the virus that causes COVID-19, not yet in New York State, is substantially different from its predecessors, drawing the attention of state researchers who are expanding their early detection efforts.

The strain, BA.2.86, represents "a huge evolutionary jump,” said Yen Pottinger, a virologist and senior lab adviser for ICAP at Columbia University. "We don’t know enough about 2.86 to be ringing all the alarm bells yet,” but any change to the virus makeup is a potential cause for concern, she said. “The virus, in its evolution, will continuously look for improvements, its way of looking for how to more effectively infect its host.” 

In a news release, New York State Department of Health officials said the strain appears to be “the most genetically different strain since the original omicron variant." Those mutations could allow the strain to evade immunity built up from prior infection or vaccine, officials warned.

“We continue to diligently work as new strains have emerged, with a particular focus on one highly divergent strain being seen elsewhere,” New York State Health Commissioner Dr. James McDonald said in a release from his department, referring to the BA.2.86 strain.

The Centers for Disease Control and Prevention said it was too soon to tell how transmissible the variant is, or if it can cause illness more serious than previous strains. Tests used for detection and medications used to treat COVID appear to be effective against the variant, the CDC said in a risk assessment released Thursday. The effectiveness of a new vaccine scheduled to be released this fall is being evaluated, according to the CDC, though the agency currently assesses the "updated vaccine will be effective at reducing severe disease and hospitalization."

Early detection is important because it gives public health officials time to shape their response.

The new strain has been found in at least nine cases: in Michigan, Virginia, Israel, Denmark and South Africa, but not in New York. After the new strain was identified in those cases, researchers from New York State’s Wadsworth Center labs, with colleagues from Syracuse University, searched the last six months of data from wastewater surveillance and lab testing to confirm that the strain was not present, according to the news release.

That work, which can detect the virus in wastewater up to a week before any swings appear in testing or hospitalizations, draws in part on sampling from 17 treatment plants on Long Island. Health officials are discussing expanding the work, and the state Department of Health is increasing the number of samples it tests, department spokeswoman Danielle DeSouza wrote in an email. 

While experts said it might be weeks before the potential impact of the new strain is understood, the scale of change in its makeup was immediately notable. 

Pottinger, at Columbia University, said the current dominant strain, EG5, has one mutation compared with its predecessor. BA.2.86 has 36, she said. 

The World Health Organization has BA.2.86 as a “variant under monitoring," highlighting the need for all countries to maintain surveillance. 

While COVID hospitalizations in the United States and on Long Island have risen this summer, the CDC said in the risk assessment that the national increase did not appear to have been driven by the variant. 

About 30 variants are in circulation across the United States, according to the CDC. 

In an email, Suffolk County Health Commissioner Dr. Gregson Pigott said his department will continue to “closely monitor hospitalizations and COVID-19 trends. We encourage our residents to get the new booster shot when it becomes available in the fall." 

A Nassau County spokesman did not respond to a request for comment. 

Dr. Sharon Nachman, chief of pediatric infectious diseases at Stony Brook Children's Hospital, said discovery of the new strain was a sign that the public health system was working: “We are using our infrastructure to do a better job tracking this variant.” That means that health care professionals have an opportunity to communicate with high-risk populations and can warn parents to expect COVID circulating in schools. Most of her colleagues believe vaccines will be effective at preventing hospitalizations, if not infections, she said.

Dr. David Hirschwerk, an infectious disease expert and medical director of the North Shore University Hospital, said the new strain had “raised a flag” among experts. In the three years since COVID emerged, some variants “turn out to be impactful, some are much less so.” But “It’s too early to know” with this one,” he said.

Hirschwerk said the new variant eventually will reach Long Island, if it hasn’t already. 

His advice: “People should stay up-to-date with the vaccine.” While the boosters scheduled to become available in the fall were designed before this variant began circulating, they will “likely offer some degree of protection, and maybe significant protection,” he said.

Wastewater has become an important public health resource because people shed virus in their waste days before they turn symptomatic, and because it gives access to a vast, unbiased sample population. 

Dave Larsen, professor and chair of Syracuse University’s Public Health Department, said that his group compiles one to two wastewater samples per week from each of about 200 sites across the state, using a CDC-supported tool called Freyja to identify the abundance of different lineages of COVID. 

While the technique relies on samples from waste treatment plants, it works even in areas like Suffolk County, where many people rely on individual septic systems, because waste from the populations of those served and not served by sewers tend to mix, he said.