Has the winter COVID variant arrived? Here's why experts are closely monitoring the JN.1 strain

SARS-CoV-2 continues to mutate, as is natural for a virus, always trying to evolve news ways of infecting us. Though the pandemic has seemingly slipped from most people's minds, there are still dedicated teams of virus trackers who are closely monitoring these microscopic changes, to see if they can predict which ones may prove problematic, like the Omicron variant.

In August, virus trackers discovered a new strain — BA.2.86, nicknamed “Pirola” — that was as genetically different from Omicron as Omicron was from the original "wild type" strain from Wuhan, China. With nearly double the number of mutations on the spike protein than other strains, Pirola has a stronger ability to bind to our cells and is thus more infectious. However, without a specific mutation in which neighboring genes swap places called the “FLip mutation,” Pirola didn’t spread throughout the population as quickly as many other variants that do have this mutation did — like EG.5 and HV.1, which together account for over 47% of estimated cases in the U.S.

Now, the virus has once again mutated, and this time, BA.2.86 underwent a mutation very similar to the FLip mutation in a new strain called JN.1, making its ability to bind to our cells even stronger than most other Omicron variants still currently dominating as well as increasing its transmissibility. 

First detected in Luxembourg in late August, JN.1 has since been identified in 130 infections, including cases in England, France, the U.S. and 15 other countries. However, because very few COVID-19 cases are sequenced and testing, in general, has fallen by the wayside after the public health emergency ended in May, virus trackers believe this is only a fraction of the true number of JN.1 cases in circulation. With the winter and holiday season approaching, this strain is expected to become “the winter variant,” said Dr. Rajendram Rajnarayanan, of the New York Institute of Technology campus in Jonesboro, Arkansas.

“With travel and the holidays coming up, we know that it's gonna spread everywhere,” Rajnarayanan told Salon in a video call. “This has all the features of becoming a dominant lineage like EG.5 or XBB.1.16.6.”

Although JN.1 has characteristics that suggest it could become a dominant strain, the landscape of COVID-19 variants has transformed since last summer when one variant could cause a new wave of cases, said Dr. T. Ryan Gregory, an evolutionary and genome biologist at the University of Guelph in Canada. Instead, cases have been sustained at a high baseline over the past year with highs and lows caused by dozens of different variants coming and going within an “alphabet soup” of circulating variants. 

The Centers for Disease Control and Prevention (CDC) are currently monitoring 35 variants, but there are hundreds more that haven’t reached the level of community spread to appear on their radar. In August, the CDC and the World Health Organization (WHO) added the original Pirola “parent,” BA.2.8.6 to the agencies’ respective lists of variants to monitor.

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“I am not so concerned about any one variant causing a huge wave anymore,” Gregory told Salon in an email. “I don’t think wondering if any particular new variant will take over and cause a huge wave is the right way to think about variants anymore.”

Instead, it’s more about the cumulative effects of multiple strains circulating and putting a constant stress on health systems, Gregory said. JN.1 isn’t the only mutation stemming from the BA.2.86 lineage. JN.1, JN.2, JN.3 and JQ.1 have all diverged from the original strain in what trackers are calling the “Pirola clan.” Other variants, including HK.3, have diverged from the EG.5 variant, nicknamed “Eris,” that has been dominating in the U.S. since August. 

Vaccine manufacturers said the latest shots hold up against the Pirola lineage, and the CDC said antibody therapies like Paxlovid, Veklury and Lagevrio should work against it as well. Because sequencing has been minimal and virus trackers are relying on hospital or wastewater data for their analyses, it’s still unclear whether the BA.2.86 lineages will cause differences in COVID-19 symptoms or whether they increase the chance of things like long COVID.

“We’re really just getting a glimpse of what is out there, so it is a certainty that any of the variants appearing in multiple countries are more common and widespread than the number of sequences alone would indicate,” Gregory said. “This is a good reminder that the virus continues to evolve in many different ways and that our best approach is not to rely only on one measure but to take a layered approach that includes vaccination but also mitigation.”

JN.1 isn’t yet a cause for alarm, but it is a signal to vaccine manufacturers that can help them ensure future vaccines and therapies continue to protect against new variations in SARS-CoV-2, Rajnarayanan said. At the moment, there are plenty of mitigation measures in the country’s toolkit to prevent JN.1 and other strains from spreading further, including vaccination, public health measures like masking and improving air filtration in closed buildings, he added.

Although data released last week showed just 3% of the population had gotten the latest COVID-19 vaccine, many Americans at this point have also had a COVID-19 infection, meaning they have some natural immunity as well. However, a study published in August in the International Journal of Molecular Science found the risk of long COVID increases with multiple COVID-19 infections, and many people like those who are immunocompromised still are not able to get vaccines and protect themselves from what could be a life-threatening infection. 

“Right now we have so many things that are protecting us from having the big catastrophe that we had with Delta or Alpha or variants before that, and we are not in that situation yet,” Rajnarayanan said. “If we go there, we do have the tools and the capability of quickly mitigating it compared to previously.”

Those tools, of course, entail the same advice since the beginning of the pandemic: wearing masks in public, testing when exposed or experiencing symptoms, improving indoor air quality and staying up to date on vaccinations.