Public Health

JN.1 Omicron subvariant: Questions patients may have

Sara Berg, MS , News Editor

Amid the peak of respiratory virus season in the U.S., a highly mutated form of SARS-CoV-2 is spreading and contributing to rising cases nationwide: JN.1.

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When JN.1 (BA. first emerged in September, it had been classified with BA.2.86 because it descended from that lineage. The Omicron subvariant BA.2.86 emerged during the summer and promptly drew attention from health officials due to its extensive mutations. But as the weeks passed, BA.2.86 did not exhibit a significant surge and researchers determined that it shared similarities with previous strains of SARS-CoV-2. Several months later, though, BA.2.86 gained traction and accounted for between 5% and 15% of circulating variants in the U.S.

Now, though, JN.1 accounts for more than 20% of all cases in the U.S. and could be more transmissible and better at slipping past people’s immune systems.

Here are some questions patients might have about the JN.1 COVID-19 Omicron subvariant, along with the answers that physicians should be ready to share.

The Centers for Disease Control and Prevention (CDC) first referenced the JN.1 subvariant back in September. By the end of October, JN.1 made up less than 0.1% of SARS-CoV-2 viruses while BA.2.86 grew in prevalence.

But now, BA.2.86 only accounts for about 1.6% of variants circulating in the United States. BA.2.86 is now replaced by its close relative JN.1, which likely accounts for 15% to 29% of circulating variants in the U.S. JN.1 is currently the fastest growing variant in the U.S., according to the CDC.

BA.2.86 comes from the BA.2 lineage and is a subvariant of Omicron, which dominated COVID-19 cases two years ago and has mutated into different subvariants. It features more than 30 mutations compared to the XBB.1.5 Omicron subvariant, which was the dominant strain for most of 2023. And there is only one change between JN.1 and BA.2.86 in the spike protein, says the CDC.

At this time, the expected public health risk of JN.1 and BA.2.86 variants, according to the CDC, remains low for severe illness compared with other variants. But this winter and holiday season, there are more opportunities for the virus to spread as it has during the last couple of years.  The CDC will continue to track the JN.1 subvariant.

While JN.1 is reportedly more transmissible than other circulating variants, it is unlikely that this subvariant will reach levels of the first COVID-19 outbreak in spring 2020 or that of the Omicron variant. At this article’s deadline, the HV.1 subvariant is still the dominant strain the U.S., accounting for 21.4% of cases. After HV.1, the next most common COVID-19 variant is JN.1, which made up about 21% of cases followed by EG.5 with 8.8%.

The proportion of cases caused by JN.1 is going up, but it does not appear to be driving increases in hospitalizations. Yet BA.2.86, a close relative to JN.1, set off alarms when it first emerged  due to its high number of mutations, which experts feared may make it  more capable of bypassing existing immunity from COVID-19 vaccines or prior infection.

Due to the rapid growth of JN.1 compared with other variants, it does raise the question of whether it may drive an increase in infections. But there is no evidence that it causes more severe illness.

At this time, it is not possible to know whether JN.1 or BA.2.86 produce different symptoms than other Omicron subvariants or COVID-19 variants. Generally, though, there have been similar symptoms across COVID-19 variants. The common symptoms of other COVID-19 variants and subvariants include:

  • Cough.
  • Sore throat.
  • Congestion.
  • Runny nose.
  • Sneezing.
  • Fatigue.
  • Headache.
  • Muscle aches.
  • Altered sense of smell.

Ultimately, symptoms and how severe they are will depend in part on a person’s individual immunity from vaccination and previous infection.

The recipe for protection is one everyone should be familiar with. Patients should ensure they are up to date with their COVID-19 vaccinations for protection from severe disease, hospitalization and death. It is also helpful to wear a medical-grade face mask or respirator—such as a N95 or KN95—when in crowded places. Handwashing also remains an important preventive measure.

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The updated COVID-19 vaccines are expected to increase protection against JN.1 and BA.2.86. But the problem is there are lagging vaccination rates for not only COVID-19, but the flu and respiratory syncytial virus (RSV) too. Health officials and physicians continue to urge vaccinations for COVID-19, the flu and RSV to head off another severe respiratory virus season as was experienced last year.

Getting vaccinated against COVID-19 also helps protect against reinfection, severity and duration of symptoms. In turn, preventing COVID-19 reinfection can also help reduce your risk of long COVID.

Those who are 6 months or older are eligible to receive the vaccine and should get it as soon as possible. This is a universal recommendation, similar to the flu vaccine.

Visit to find a COVID-19, flu or RSV vaccine near you.

While a COVID-19 test will not tell you which variant of SARS-CoV-2 caused your infection, it is important to get tested if you have been exposed or are experiencing symptoms. The COVID-19 testing will tell you whether you have or have had a recent infection. Nucleic acid amplification tests and antigen tests can both be used.

But at-home tests are also available for rapid results. If an at-home test is positive, isolate and speak with your physician for further guidance. Testing can also differentiate between COVID-19, the cold, flu and RSV as well as help discern what treatments to follow.

The short answer is yes. With each COVID-19 variant, the risk of long COVID or post-COVID conditions remains. This can include a wide range of ongoing health problems that can last for weeks, months or longer.

While long COVID has been reported more often in people who have had severe illness, it can impact anyone who has been infected with SARS-CoV-2, even people who had mild illness or no symptoms. Although, new research has shown that for those with mild illness, long COVID symptoms clear after a year.

But the good news is that getting vaccinated against COVID-19 may cut your risk of long COVID.

After examining the mutation profile of the Omicron subvariant BA.2.86, the CDC suggests that currently available COVID-19 treatments will still be effective. This includes COVID-19 oral antivirals Paxlovid, molnupiravir (Lagevrio) and remdesivir (Veklury), according to the CDC. With ongoing monitoring, the CDC will update treatment options as more data on the impact of JN.1 and BA.2.86 is known.