JN.1 COVID Variant Symptoms vs. Allergy Symptoms

The JN.1 COVID variant emerged in the U.S. in November of 2023 and quickly started gaining steam in the country. Now, it’s responsible for nearly 84% of COVID-19 cases in the U.S.—and that dominance is coinciding with peak allergy season.

Data currently suggest that COVID-19 severity indicators, including hospitalizations and deaths, are on the decline right now. But knowing if and how you can differentiate COVID from allergies is important to prevent further spread of the disease. Here’s what infectious disease doctors want you to know.

JN.1 Is an Offshoot of Omicron

The JN.1 COVID variant descended from BA.2.86, a variant that was first sequenced in July 2023, Thomas Russo, MD, professor and chief of infectious diseases at the University at Buffalo in New York, told Verywell. “JN.1 is an Omicron variant,” he said.

BA.2.86 has 20 differences in its spike protein from previous Omicron variants, Russo explained, noting that the spike protein is what SARS-CoV-2, the virus that causes COVID-19, uses to infect you. “JN.1 has an additional mutation on its spike protein,” he said.  

JN.1 “is very, very contagious, but it does not appear to produce more severe disease,” William Schaffner, MD, a professor at the Vanderbilt University School of Medicine, told Verywell.

Symptoms of the JN.1 Variant

The Centers for Disease Control and Prevention (CDC)’s list of COVID-19 symptoms has been consistent for months, despite several variants coming and going. Those symptoms include:

• Fever or chills
• Cough
• Shortness of breath or difficulty breathing
• Fatigue
• Muscle or body aches
• Headache
• New loss of taste or smell
• Sore throat
• Congestion or runny nose
• Nausea or vomiting
• Diarrhea

Schaffner said that there aren’t “striking differences” between the symptoms of previous COVID-19 variants and JN.1, but there are a few small changes.

“Sore throat is more common, as is nausea,” he said. “Diarrhea might be a bit more common with this variant.”

There is also less of a chance of having a loss of taste and smell with JN.1 than past variants, he said.

“The latest variants have been mimicking the common cold,” Russo said. “We’re seeing milder symptoms as a general rule. However, if you’re in a high-risk group, COVID-19 can still cause serious disease and is potentially lethal.”

How to Tell JN.1 Variant Symptoms From Seasonal Allergies

Russo said that it can be tricky to tell symptoms of JN.1 from seasonal allergies, but there are a few hints you may be dealing with one over the other.

“Certainly, seasonal allergies can give you a runny nose and clog your sinuses, but it will not give you a fever,” he said. “Shortness of breath would not be due to seasonal allergies.”

Seasonal allergies are also unlikely to cause a cough or congestion that is deep in your chest, Schaffner said. “You should also not get diarrhea,” he said. “Those are symptoms that are more likely to indicate a viral infection.”

If you have seasonal allergies and experience symptoms around the same time every year—including this year—that may indicate that your current illness is due to allergies, Russo said. “But the best way to differentiate COVID-19 from seasonal allergies is to test for COVID-19,” he added.

Schaffner said that having symptoms of a respiratory virus right now makes it more likely that you have COVID-19 compared to the flu or RSV. “The flu and RSV have pretty much returned to low baseline levels,” he said.

Still, he said you should test yourself for COVID-19 if you’re not sure what illness you have.

The information in this article is current as of the date listed, which means newer information may be available when you read this. For the most recent updates on COVID-19, visit our coronavirus news page.