Coronavirus subvariant JN.1 growing fast in US, already dominant in the Northeast

(CNN) — The US Centers for Disease Control and Prevention estimates that the coronavirus subvariant JN.1 is now causing about 20% of new Covid-19 infections in this country, and it’s the fastest-growing strain of the virus. It’s already dominant in the Northeast, where it is estimated to cause about a third of new infections.

JN.1 is descended from BA.2.86, or Pirola, a subvariant that came to the world’s attention over the summer because of the large number of changes to its spike proteins: more than 30. Scientists feared that it was so mutated that it would completely escape the protection of vaccines and antibodies against Covid-19, perhaps sparking another tidal wave of illness the way the original Omicron variant did in 2021.

That never happened, but BA.2.86 hung around, growing very slowly in some countries, including the US. Some studies suggested that it never really took off because it may have lost some of its ability to infect our cells.

Enter JN.1, which is two generations removed – a granddaughter, so to speak – of BA.2.86. JN.1 has only one change to its spike protein compared with its ancestor, but that seems to have been enough to make it a fitter and faster virus.

The CDC estimates that prevalence of JN.1 more than doubled in the US between late November and mid-December. It seems to be getting an assist from holiday travel and waning immunity.

“When I just look at the growth curve, it is rising quite sharply, and it seems to coincide with the Thanksgiving break in terms of timing,” said Dr. Shishi Luo, who heads infectious diseases for the genomic sequencing company Helix.

Variant trackers say they expect JN.1 to become the leading coronavirus variant around the world in a matter of weeks. The World Health Organization named it a variant of interest on Tuesday because of its “rapidly increasing spread” but noted that the additional public health risk remains low.

“It’s already pretty clear that it is highly competitive with existing XBB variants and looks like it’s on track to become the next sort of globally dominant group of variants,” said Dr. T. Ryan Gregory, an evolutionary biologist at the University of Guelph in Ontario, who has been tracking the evolution of the virus that causes Covid-19.

The mutation in JN.1’s spike is at a position that Gregory said seems to help the virus escape our immunity.

Studies by researchers at Columbia University and in China suggest that there’s about a twofold decrease in the ability of our antibodies to neutralize this subvariant. Although that’s not a huge drop, it could portend another wave of infections on the horizon.

Several countries in Europe – including Denmark, Spain, Belgium, France and the Netherlands – have seen exponential growth of JN.1 and, with it, rising hospitalizations. It’s also growing quickly in Australia, Asia and Canada.

That’s happening in the United States too, thanks to waning immunity. Too many Americans have chosen to forego the latest round of vaccination for Covid-19, and they may also have passed it up last year. As a result, their immunity hasn’t had the important upgrades that help the body fend off the worst consequences of Covid-19 infections.

As of December 9, only about 18% of adults had received the latest Covid-19 vaccine, about the same low proportion of the population that got them last year, according to the CDC.

The CDC has called on doctors to work harder to get their patients vaccinated, emphasizing that it’s not too late in the season to benefit from the shots.

The CDC also warned that in the past four weeks, hospitalizations for Covid-19 have risen 51%. With hospitalization rates for flu and RSV also on the rise, the agency noted that a continued increase could strain hospital capacity.

The good news is that a recent study from Dr. David Ho’s lab at Columbia University found that the current Covid-19 vaccine, which was designed to boost the body’s ability to fight of the XBB family of variants, also offers good protection against BA.2.86 and its offshoots, including JN.1.

That finding “strongly supports the official recommendation to widely apply the updated Covid-19 vaccines to further protect the public,” the study’s authors wrote.

Last week, WHO issued a statement supporting the upgraded Covid-19 vaccines against XBB.1.5 because of the broad protection they offer against a variety of variants.

“Fewer people are getting the booster, and fewer people are getting Paxlovid,” an antiviral that can reduce the risk of hospitalization and death from Covid-19, said Dr. Alex Greninger, assistant director of the Clinical Virology Laboratory at the University of Washington.

“There was a lot of work to get those vaccines and get those drugs available, so it’s just extra sad when those tools aren’t being used,” he said.