This winter, there’s another new SARS-CoV-2 variant contributing to surges around the world. The World Health Organization (WHO) classified this variant, called JN.1, as a “variant of interest” on December 19, signifying that it is worth the attention of scientists and healthcare workers.
In the U.S., JN.1 may lead to higher levels of coronavirus spread this month than we saw last year, though it’s hard to make definitive conclusions thanks to our dismantled testing infrastructure. Luckily, the 2023 vaccines appear to help protect against it, based on several laboratory studies.
But most people haven’t received these latest vaccines. Unchecked disease spread will only lead to more viral evolution, as millions of people around the world get infected with this variant — and hundreds of thousands likely develop Long Covid as a result.
Here’s what you should know about JN.1.
JN.1 descended from BA.2.86, which drew concern this summer
This past August, scientists called public attention to a variant called BA.2.86. While BA.2.86 was in the Omicron family — like all variants that have gained dominance since fall 2021 — it had an unusual evolutionary history. Rather than descending from Omicron mutants that had recently circulated, BA.2.86 evolved from an older strain, called BA.2, which was widespread in early 2022.
At the time, scientists expressed concern that BA.2.86 might easily reinfect people who had been sick with more recent variants. They also worried that this strain might evade this year’s vaccines, tailored for the XBB.1.5 strain; according to genetic analysis, BA.2.86 is about as different from XBB.1.5 as Omicron was from Delta. (For more details, see my explainer on BA.2.86 at the COVID-19 Data Dispatch.)
But as it turned out, BA.2.86 didn’t cause a major new surge. It wasn’t the reinfecting, vaccine-evading threat that scientists had feared. Instead, this variant evolved further: with a few additional mutations, we got JN.1. JN.1 now appears to be living up to the feared potential of its parent variant, leading to new surges globally.
JN.1 is causing spikes in SARS-CoV-2 levels in wastewater around the world
Now that public health systems around the world have largely dismantled their Covid-19 testing infrastructure, anyone hoping to keep an eye on disease trends must primarily rely on wastewater surveillance data. Wastewater surveillance is much patchier than the testing systems we had earlier in the pandemic, as it depends a lot on local resources.
But enough places are screening their sewage that we can see a clear picture: in this case, JN.1 contributing to major surges in many countries. The countries seeing JN.1-driven surges include nations across Europe (Spain, France, Belgium, Denmark, the Netherlands, the U.K.), across Asia (China, Australia, Japan, Singapore), Canada, and others. Dr. Eric Topol shared more references and details about these global patterns in an early-December issue of his newsletter.
The U.S. has been a couple of weeks behind Europe in its JN.1 surge, but this variant is quickly gaining dominance over other Omicron lineages. According to CDC estimates, JN.1 led to nearly half of new cases between December 9 and December 23 — about double the variant’s prevalence from the two weeks prior. JN.1’s rise has mirrored a sharp uptick in coronavirus spread, as seen in the U.S.’s wastewater. Thanks to this variant, combined with recent holiday travel and gatherings, we could be in for a very nasty January.
This year’s vaccines appear to work against JN.1
While JN.1 is spreading quickly, there is some good news: multiple lab studies have found that the latest Covid-19 vaccines, distributed this past fall, help bolster immune systems against this variant — even though the vaccines were designed for a very different strain. These include preprint studies from well-known scientists who have closely tracked SARS-CoV-2’s evolution: Yunlong Cao and his team at Peking University, David Ho and his team at Columbia, and David Veesler and his team at the University of Washington.
A recent study from Pfizer and Kaiser Permanente, shared as a preprint at the end of December, backed up the lab research with results from recent Covid-19 patients (i.e. infected October 11 through December 10) in the Kaiser healthcare system. Patients who had received this year’s Pfizer vaccine earlier in the fall were significantly less likely to be hospitalized or to require other healthcare visits, compared to those who weren’t recently vaccinated. The study supports that this year’s boosters reduce health risks for people infected with BA.2.86 or JN.1.
The recent Pfizer/Kaiser study also found that people who only received older vaccines — not the 2023 versions — didn’t have significantly lower risk of severe Covid-19 outcomes, compared to unvaccinated people. Or, in simpler terms: it is really important to stay up to date on these vaccines. Unfortunately, fewer than one in five U.S. adults had received a 2023 Covid-19 shot by Christmas, per the CDC.
Variants are getting harder to track — even as we keep encouraging them
While wastewater surveillance can show us when Covid-19 surges are happening, this type of disease monitoring doesn’t offer as much detail about illness as we got from case data. It’s now quite difficult to identify whether a particular variant is leading to different symptoms, less accurate rapid tests, or higher risk of hospitalization or Long Covid — all questions that frequently come up when a new lineage emerges. Mainstream media coverage of variants often emphasizes a lack of “more severe illness,” but really, we don’t know this for sure.
But we do know that JN.1 — and other variants that come after it — will follow an established pattern. When SARS-CoV-2 spreads widely, particularly at a time of year with unchecked travel and gatherings, humans essentially help the virus evolve. Variants don’t come out of nowhere; they come from our behavior. In particular, the latest variants (BA.2.86 and its descendant JN.1) may have emerged from a chronic infection in an individual who got sick with BA.2 nearly two years ago, as evolutionary biologist T. Ryan Gregory pointed out in a recent Tweet:
To reduce the chances of even worse variants evolving in the future, we must protect ourselves and our communities — especially the people at highest risk of chronic disease — from continued SARS-CoV-2 infections.
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