New York’s struggle with the new Omicron variant BQ is trying to tell us something

As scientists speculate what an autumn COVID wave might look like in the U.S., all eyes are on the Empire State. That’s because it’s considered a “bellwether” when it comes to viral conditions, and what happens there often provides a preview for the rest of the country.

Right now, New York is seeing mounting cases of the extremely transmissible, immune-evasive BQ family of COVID variants, which includes BQ.1 and BQ.1.1. Experts tell Fortune that because such variants are thriving there, they’re likely to thrive elsewhere in the country too.

BQ variants—along with XBB variants surging in other parts of the world—are believed to be the most immune-evasive strains of COVID yet. The jury is still out on how severe these strains are, but there are early reports that monoclonal antibody treatments, reserved for high-risk patients, can’t stand up to them. 

“We are really worried about BQ.1.1 and looking closely at New York data,” variant tracker Raj Rajnarayanan, assistant dean of research and associate professor at the New York Institute of Technology campus in Jonesboro, Ark., recently told Fortune.

Together, Omicron spawn BQ.1 and BQ.1.1 are “following the same script” as other previously dominant variants—like the original strain of COVID, Delta, and the original strain of Omicron—by starting a swelling in the northeast that could eventually wash over the rest of the U.S., fellow variant tracker Dr. Ryan Gregory, a professor of evolutionary biology at the University of Guelph in Ontario, Canada, told Fortune.

New York’s concerning hospitalization rate

New York is a veritable crystal ball when it comes to COVID forecasting for a couple of reasons: its volume of incoming international travelers, and its robust capabilities to genetically sequence COVID virus samples, experts say.

When a variant gains traction in Europe, as the BQ family has, trackers like Rajnarayanan and Gregory know to look for it in the U.S. The first place they check: New York.

Levels of BQ variants nearly doubled this week in the CDC’s New York region, which also includes New Jersey, Puerto Rico, and the Virgin Islands. The BQ family rose from a combined estimated 9% last week to more than 17% this week, according to agency data.

The rapid growth rate concerns scientists, including leading U.S. infectious disease expert Dr. Anthony Fauci, who recently called the viral family’s doubling time “pretty troublesome.”

What concerns Rajnarayanan more though, is that hospitalizations in New York are also on the rise. In mid-September they sat at around 2,000 a day. A month later, they’re nearing 3,000, according to data from the state.

The state’s current hospitalization wave is “pretty close, if not higher than the Delta peak,” he said, referring to the deadly COVID wave that rocked the U.S. late last year, right before Omicron hit. 

Another sign of rising viral activity: Google searches in New York for “cough” are five to seven times higher than usual, Rajnarayanan said, citing a dashboard he created with data from Google Trends. And searches for “nasal congestion,” “headache,” and “migraine” are also up, in addition to those for “sore throat” and “diarrhea.”

“Something is going on there,” he said. 

‘An ugly peak’

The U.S. likely isn’t far behind New York in seeing a surge in BQ cases, Rajnarayanan says, as other parts of the country are also seeing the family of variants slowly rising.

Estimated cases of BQ.1 and BQ.1.1—dubbed “Typhon” and “Cerberus” respectively by some public health experts on the Twitterverse—rose from about 12% nationally last week to nearly 17% this week, the U.S. Centers for Disease Control and Prevention announced Friday. Experts say that national BQ levels are likely lagging those in New York, where most of the first sequences in the U.S. were identified.

No one can predict which variant comes out on top this winter. But BQ.1.1’s extreme immune evasiveness and transmissibility “sets it up to be the principal driver of the next U.S. wave in the weeks ahead,”  Dr. Eric Topol, a professor of molecular medicine at Scripps Research and founder and director of the Scripps Research Translational Institute, tweeted last week.

Waves of COVID variants used to be fairly sequential, often with a valley or plateau in between. But now, more than 500 Omicron variants are circulating, according to Rajnarayanan—some, like members of the XBB family, with the potential to cause their own subsequent surges.

The coming U.S. COVID wave, he predicts, won’t be just one wave, but a series of waves—each fueled by a different variant—that form a “table mesa” or “table-like plateau.”

The extended wave will have an “ugly peak because of a combination of different lineages peaking and then going down,” he said. “I won’t celebrate when one goes down, because something else is going to pop up.”

It’s possible that the coming winter wave won’t be all that dissimilar to what the U.S. has already experienced, in terms of hospitalizations and deaths. But that doesn’t mean it will be without consequence, experts say.

“Even if 200,000, 300,000, 400,000 people get infected, some of them are probably going to develop Long COVID,”  Rajnarayanan said. “It’s going to affect the workforce, those who cannot do remote work. It’s a huge problem.”

“That’s something I don’t think we have a proper plan for as a country,” he continued. “I would like to see a long COVID plan before we start declaring the pandemic is over.”