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What to know about JN.1, the dominant COVID-19 variant in US: Symptoms and more

A highly mutated COVID-19 variant, JN.1, is the dominant strain in the U.S., the CDC says. What to know about symptoms, transmission and vaccines.

Nearly all COVID-19 cases in the United States right now are being caused by one, highly contagious variant called JN.1. The fast-spreading omicron subvariant currently accounts for over 93% of cases nationwide and the majority of infections globally.

JN.1 is a direct descendant of the BA.2.86 variant, or “Pirola," which has been circulating since last summer. Compared to its parental strain, JN.1 has an additional mutation that affects its ability to evade immunity, according to experts.

In December, JN.1 overtook other highly transmissible variants — including HV.1 and EG.5 or Eris — to become the dominant strain in the U.S. By January, JN.1 was the most prevalent strain worldwide.

The JN.1 variant is currently considered the fastest-growing variant in the country, according to the U.S. Centers for Disease Control and Prevention.

During a two-week period ending Feb. 3, JN.1 made up 93.1% of cases in the U.S., up from 87% during the previous two-week period ending on Jan. 20, according to the CDC. This was a steep increase from 62% during the two-week period ending on Jan. 6 and 44% during the two-week period ending on Dec. 23.

As JN.1 swept across the country in the last two months, COVID-19 infections and hospitalizations also rose steadily. According to data models, the U.S. just faced its second-largest COVID wave, smaller than only the original omicron surge in late 2021 and early 2022.

The JN.1 variant may be "intensifying the spread of COVID-19 this winter," the CDC said in an update on Jan. 5. Waning immunity, low COVID-19 vaccine uptake, and holiday gatherings likely also fueled the recent wave of cases.

Although COVID-19 cases and hospitalizations have started to decline in the U.S., respiratory virus season isn't over yet. As JN.1 continues to circulate, RSV and influenza activity remains high in many parts of the country.

What are the symptoms of JN.1, is it more transmissible than previous strains, and does it affect testing or vaccines? Here's what experts know about JN.1 so far.

What is JN.1, the new COVID-19 variant?

JN.1 was first reported in August 2023, according to the World Health Organization. On Dec. 18, the WHO classified JN.1 as a “variant of interest” due to its rapid spread worldwide.

Just like other COVID-19 strains that gained dominance in the last year, JN.1 is part of the omicron family, which emerged in late 2021.

"Think of (the variants) as children and grandchildren of omicron. They're part of the same extended family, but they each have their own distinctive personalities," Dr. William Schaffner, professor of infectious diseases at Vanderbilt University Medical Center, tells TODAY.com.

JN.1 descended from BA.2.86, which is a sublineage of the omicron BA.2 variant, TODAY.com previously reported — that's what sets JN.1 and BA.2.86 apart from the other prevailing variants like HV.1 and EG.5, which descended from omicron XBB.

BA.2.86 has more than 30 mutations compared to the omicron XBB.1.5 variant, the dominant strain for most of 2023 and the variant targeted in the updated COVID-19 vaccine, TODAY.com previously reported.

“When its parent BA.2.86 emerged, everybody was worried because it had a lot of mutations and looked like it was going to evade a lot of the immunity from vaccines and infection in the population,” Andrew Pekosz, Ph.D., professor and vice chair in the Department of Molecular Microbiology and Immunology at the Johns Hopkins Bloomberg School of Public Health, tells TODAY.com. “But (BA.2.86) sort of fizzled out,” he adds.

Laboratory data suggest that Pirola is less contagious and immune-evasive than scientists once feared, NBC News reported.

JN.1, however, picked up an additional mutation in its spike protein, says Pekosz. Spike proteins help the virus latch onto human cells and play a crucial role in helping SARS-CoV-2 infect people, per the CDC. This mutation may affect JN.1's immune escape properties, says Pekosz.

"Now it's circulating and growing at a really fast rate compared to other variants, as well as the parent it’s derived from (BA.2.86),” says Pekosz.

In early November, JN.1 accounted for fewer than 1% of COVID-19 cases in the U.S. Several weeks later, it was driving over 20% of cases, Dr. Michael Phillips, chief epidemiologist at NYU Langone Health, tells TODAY.com. Now, only two months later, it's causing nearly all cases nationwide.

However, JN.1 does not pose an increased public health risk compared to other variants in circulation, the CDC and WHO said.

What are the symptoms of JN.1?

It’s not known whether JN.1 causes different symptoms from other variants, according the CDC.

“Right now, there’s nothing that says that JN.1 infection is any different from previous COVID variants in terms of disease severity or symptoms, but we’re paying close attention,” says Pekosz.

The symptoms of JN.1 appear to be similar to those caused by other strains, which include:

  • Sore throat
  • Congestion
  • Runny nose
  • Cough
  • Fatigue
  • Headache
  • Muscle aches
  • Fever or chills
  • Loss of sense of taste or smell
  • Shortness of breath or difficulty breathing
  • Nausea or vomiting
  • Diarrhea

According to the CDC, the type and severity of symptoms a person experiences usually depends more on a person’s underlying health and immunity rather than the variant which caused infection.

While severe infections do still occur, overall “(COVID-19) is causing a lot of milder illness,” says Schaffner.

Some doctors have reported that upper respiratory symptoms seem to follow a pattern of starting with a sore throat, followed by congestion and a cough, NBC News previously reported.

“The virus is adapting. ... I think it’s getting better at infecting humans and evading pre-existing immunity in the population ... but it’s not changing symptomology too much,” says Pekosz.

At this time, there’s no evidence that JN.1 causes more severe infection, the experts note.

Is JN.1 more transmissible?

“One of the things these (omicron variants) have in common is that they are highly contagious, and as new variants crop up, they seem to be as contagious or even more contagious than the previous variants,” says Schaffner.

According to the CDC, the continued growth of JN.1 suggests that the variant is either more transmissible or better at evading our immune systems.

JN.1 is likely more transmissible than its parental virus because "we’ve seen an increase in case numbers that we didn’t with (BA.2.86),” says Pekosz.

Many of the newer variants, including JN.1, have another mutation that affects how strongly the spike protein binds to cells in the respiratory tract, says Pekosz. “We know that it’s probably helping the virus become better at replicating and helping the virus evade more of that pre-existing immune response,” he adds.

Over 97% of people have natural or vaccine-induced antibodies against the the SARS-CoV-2 virus, the CDC said, but this immune protection fades over time.

It’s too early to tell exactly how JN.1’s transmissibility or immune escape properties compare to other omicron variants, but it's clear that JN.1 is very virulent, experts say.

“The current strain right now seems to be packing a meaner punch than the prior strains,” Dr. Joseph Khabbaza, a pulmonary and critical care specialist at the Cleveland Clinic, previously told TODAY.com.

Did JN.1 cause a surge?

In December, JN.1 caused a growing percentage of COVID-19 cases, an also seemed to lead to an increase in total cases, Pekosz told TODAY.com at the time.

Test positivity, an early indicator of case levels, rose steadily in December and January, reaching 12% in mid-January, per the CDC. As of Jan. 27, the rate had fallen to 6.8%. (The CDC no longer tracks the total number of cases in the U.S.).

Wastewater data published by the CDC show that the viral activity level for COVID-19 is currently considered "high" — it was considered "very high" for most of last month.

“Now, because it is more widespread, it’s also reaching older people, people with chronic underlying conditions, those who are immune compromised, and sometimes the very young, and those are the most vulnerable,” says Schaffner.

Hospitalizations and intensive care unit admissions were also up in December and January. But in the last two weeks, they've fallen by 22% and 14%, respectively, according to an NBC News analysis.

Some experts say the recent wave in cases fueled by JN.1 was the second-largest wave of COVID-19 in the U.S. since the pandemic began, TODAY.com previously reported.

According to Schaffner, these COVID-19 trends are not indicative of a massive surge, but rather, expected seasonal increases.

Many experts anticipated COVID-19 activity to rise around this time as the U.S. entered its winter and respiratory virus season. In recent years, COVID-19 has followed a pattern of increasing and peaking around new year, according to the CDC.

It's unclear how this latest wave driven by JN.1 will pan out in the coming months, but at the present time, "it's nothing like what COVID-19 has done to us in previous years,” says Schaffner.

Do COVID-19 tests detect JN.1?

All COVID-19 diagnostic tests — including rapid antigen tests and PCR tests — are expected to be effective at detecting JN.1, as well as other variants, according to the CDC.

Testing is an important tool to protect yourself and others from COVID-19, especially ahead of indoor gatherings, says Schaffner.

The symptoms of COVID-19 are often indistinguishable from those caused by other viruses spreading right now, the experts note. These include respiratory syncytial virus (RSV), influenza and rhinovirus, which causes the common cold.

The experts urge anyone who becomes ill or is exposed to COVID-19 to take a test, especially people at higher risk of severe disease, such as people over the age of 65, who are immunocompromised and who have underlying health conditions.

Every American can order four free at-home COVID-19 tests from the government, which will be delivered by mail via the U.S. Postal Service. To order your free tests, go to COVIDTests.gov.

"Get tested because, whether it's COVID or flu, we have treatment available," says Schaffner. Current treatments are also expected to be effective against JN.1, the CDC said.

"JN.1 should be just as sensitive to the antivirals available as any other variants," says Pekosz, adding that antivirals like Paxlovid are most effective when taken within the first few days after infection.

Does the new COVID vaccine protect against JN.1?

The new, updated COVID-19 vaccines, recommended for everyone 6 months and older, are expected to increase protection against JN.1, as well as other variants, the CDC said.

Although the shots target omicron XBB.1.5, which has since been overtaken by HV.1, JN.1, EG.5 and others, there is still evidence that it will protect against new strains circulating this winter, TODAY.com previously reported.

Data from laboratory studies show that the vaccine appears to generate a strong immune response against JN.1's parent strain, BA.2.86, Schaffner notes.

The new vaccines also protect against severe disease, hospitalization and death, the experts emphasize. So even if you get COVID-19 after vaccination, the infection will likely be milder and it can keep you out of the hospital, Phillips adds.

However, uptake of the new booster among the U.S. population has been low so far, the experts say. As of Feb. 2, only about 21% of adults and 11% of children in the country have gotten the updated vaccine, according to the latest CDC data on vaccination trends.

In December, CDC officials issued an alert to warn about low vaccination rates against COVID-19, flu, and RSV.

It's still not too late to get vaccinated if you haven't already, the experts say. "The sooner you get vaccinated, the sooner you'll be protected and it does take seven to 10 days for protection to build up to the maximum," says Schaffner.

Phillips recommends everyone, especially high-risk individuals, to get the seasonal influenza shot, as well. Hospitalizations for flu increased 200% over the past month, according to the CDC's Dec. 14 warning.

"Getting vaccinated is the best present you can give yourself and your family," Schaffner adds.

How to protect yourself from JN.1

Every day, but especially during respiratory virus season, people can take steps to protect themselves and others from COVID-19.

The experts encourage everyone to:

  • Stay up to date with COVID-19 vaccines.
  • Test if you have symptoms.
  • Isolate if you have COVID-19.
  • Avoid contact with sick people.
  • Improve ventilation.
  • Wear a mask in crowded, indoor spaces.
  • Wash your hands with soap and water.