Once again, COVID-19 cases are rising sharply across the world, along with hospitalizations and death. That also means more cases of so-called long COVID, in which some people take months or years to recover from this illness. We're in the midst of this year's winter wave of respiratory illness, including flu and RSV, but COVID-19 is by far the most worrisome. How bad will this winter be? No one can say for sure, but one of the ways experts can make predictions is by analyzing the genetics of the viruses responsible and gauging caseloads.
The virus that triggers COVID-19, SARS-CoV-2, keeps mutating, as viruses naturally do, which can change the landscape of the ongoing pandemic. As of Friday, JN.1 is now the most dominant strain the United States, according to estimates from the Centers for Disease Control and Prevention (CDC.) The agency also reported more than 25,000 Americans were hospitalized from COVID the week ending Dec. 16, a 10 percent increase from the previous week, while the CDC director Mandy Cohen has said we're not yet near the peak.
The coronavirus subvariant has gone from being the third most prevalent strain in the U.S., after EG.5 and HV.1., to surpassing EG.5 and becoming the second most prevalent strain, to now becoming the first over the course of a month. This news comes after the World Health Organization announced earlier this week that it was classifying the variant JN.1 as a separate variant of interest from its parent variant BA.2.86 (nicknamed Pirola.)
As Salon has previously reported, JN.1 is largely contributing to this year’s surge of winter illnesses. But it didn't come out of nowhere. In August, virus trackers first discovered BA.2.86 and noted that it was significantly different from Omicron. With nearly double the number of mutations on the spike protein than previous strains, experts warned BA.2.86 likely had a stronger ability to bind to our cells making it more infectious. It also had a mutation similar to the “FLip mutation” in the virus’s spike protein. (The name FLip comes from a shift in two amino acids labeled F and L.) This specific mutation, experts said, increased the chances of immune evasion to the disease. Until now, the two have been grouped together with experts referring to them and tracking them as the so-called "Pirola clan.”
But the WHO’s move shows that virus trackers are narrowing a focus on BA.2.86’s descendant, JN.1. At the time of its discovery, JN.1 didn’t appear to be spreading as quickly throughout the population as other variants with similar mutations. And yet, it’s showing that it’s not going anywhere — leaving many to wonder: Is this the new Omicron on the brink of sparking a tidal wave of infections like previous winters?
Dr. T. Ryan Gregory, an evolutionary and genome biologist at the University of Guelph in Canada, explained to Salon that scientists have been referring to clans of variants “to capture the idea that evolving lineages is what matters, rather than any individual variant per se.” The “pirola clan,” which not only includes BA.2.86 and JN.1, but also other descendants that have been identified, like JN.10 and JQ.1, are ones we haven’t heard so much about. However, Gregory agreed the most notable of the clan is JN.1 which continues to evolve and increase in prevalence.
Experts have previously speculated that Omicron hit so hard and fast because it evaded immunity from both natural infections and vaccination. But with JN.1, vaccine manufacturers said the latest shots hold up against the Pirola lineage. Additionally, the CDC said antibody therapies like Paxlovid, Veklury and Lagevrio should work against it as well. For these reasons, experts who have been following JN.1 don’t believe it will cause an Omicron-like wave this winter like it did in winter 2022.
“Since summer 2022, the pattern hasn't been ‘one variant, one wave,' but rather a soup of variants that keep the baseline number of infections and hospitalizations elevated,” Gregory said via email. “This doesn't overwhelm hospitals like early big waves did, but it does put sustained (and unsustainable) pressure and it does mean more long COVID, more variant evolution.”
When asked if JN.1 is the next Omicron, Dr. Scott Roberts, an infectious disease expert, said he thinks it is similar, but he doesn't think it will look like the winter 2021 surge.
"There is a much greater degree of immunity in the population, both from natural infection and vaccination that will still be effective in reducing the impact of JN.1," Roberts said via email, adding that he is still concerned about JN.1. "I think we are already seeing the start of waves where JN.1 is the most prevalent subvariant."
The WHO hasn’t assigned any new Greek letters to a variant since November 2021 when it gave BA.1 the name Omicron. Since then, they have changed their definition so that only variants of concern will receive a new letter, a process that is done for the sake of simplicity. Notably, the WHO’s latest announcement was that JN.1 is a variant of interest, not of concern. Gregory said he would be very surprised if the organization gave JN.1 a new Greek letter, which would be “Pi,” and classified it as a variant of concern.
That being said, this doesn’t mean that the WHO’s recent move is insignificant or that everyone agrees that a Greek letter is not in JN.1’s future. Dr. Rajendram Rajnarayanan, of the New York Institute of Technology campus in Jonesboro, Arkansas, told Salon the WHO’s move holds “crucial significance” and suggested that the classification of variants of interest came too late.
“Many countries rely on WHO cues to shape or adjust their public health policies, and international aid often aligns with WHO statements and guidelines,” Rajnarayanan said. He added he believes JN.1 “is now on the brink of being designated a Variant of Concern (VOC),” adding that a good way to think of it is like “a great great great, grandkid of Omicron.”
“Its rapid spread, substantial growth advantage over existing lineages, and ability to evade immunity have contributed to a rise in COVID-19 hospitalizations in regions where it prevails,” Rajnarayanan said. “The clinical aspects of this variant remain unclear, but it is gaining prominence as the leading variant of the season.”
As the SARS-CoV-2 virus continues to evolve, it’s hard not to wonder at what point does this become a new virus? At least when it comes to JN.1, that’s unlikely to happen. Experts say it's possible that it could eventually receive a Greek letter, but it’s unlikely to be dubbed SARS-CoV-3 any time soon.
“By contrast, JN.1 (BA.2.86.1.1) differs from BA.2.86 by a few mutations, including only one in the spike protein – it just happens to be a mutation with a significant effect on the success of JN.1 relative to BA.2.86 and the previously dominant XBBs,” Gregory said. “So, JN.1 isn’t likely to be considered a new virus if BA.2.86 wasn’t.”
No matter how the virus changes, our response largely hasn't. Masking in public and staying up-to-date on vaccinations are two of the best ways to protect oneself from this winter's scourge of illness.
