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By this stage of the pandemic, taking an at-home COVID antigen test has become routine for many. (Beth LaBerge/KQED)

The JN.1 COVID Variant: Symptoms, Incubation Period and When to Test

The JN.1 COVID Variant: Symptoms, Incubation Period and When to Test

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If it feels like many people you know are getting COVID-19 again … you’re not alone.

Fueled by a new subvariant called JN.1, COVID-19 rates are way up for the start of 2024, as part of a sharp rise that began back in November.

So, what do you need to know about the symptoms of JN.1? Is there an updated incubation period to know about for COVID-19 in 2024, and where can you even find a free COVID-19 test now? Keep reading for everything you need to know, or jump straight to:

And remember, the new COVID-19 vaccines from Moderna and Pfizer — and most recently Novavax — are available across California. The new shots are free for everyone, with or without health insurance, and are formulated to target strains like these latest subvariants. Read where to find the new COVID-19 vaccine near you.

What is JN.1, and why is it spreading so much?

Right now, JN.1 is the most prevalent COVID-19 subvariant in the United States, which the Centers for Disease Control and Prevention (CDC) estimates currently makes up almost 62% of cases nationwide. Behind it is the previous top variant, HV.1, which now only makes up 14.8% of cases across the country.

COVID Is Still With Us

(If you’re losing track of all these subvariants of the omicron variant by this stage of the pandemic, that’s understandable. To recap: The swell of COVID-19 cases in summer 2023 was fueled by EG.5, unofficially nicknamed “Eris” by some online just as XBB.1.16 before it was nicknamed “Arcturus” — even though the World Health Organization has revised its naming conventions to reserve “Greek labels” only for “variants of concern.” After the summer of EG.5, HV.1 rose to national prominence, followed now by JN.1.)

Whereas HV.1 was a part of the XBB sublineage of the omicron variant, JN.1 is closely related to the BA.2.86 strain, the CDC said in an announcement declaring JN.1 “a variant of interest” back in December. And when you’re dealing with descendants like JN.1 and HV.1 before it, it’s important to remember that each new subvariant is more easily transmitted, said Dr. Peter Chin-Hong, an infectious disease expert at UCSF.

“Every time something rises up the charts in the ‘tree of COVID life,’ by essence it had to have a superpower that makes them more powerful than the rest,” Chin-Hong said. “And that superpower is generally transmissibility.”

JN.1’s infectiousness means that the “strategies people could use to escape infection over the summer during our surge are probably not working right now,” Chin-Hong said — added to the fact that winter holidays like Christmas, Hanukkah and New Year prompted travel and brought many people together in crowded gatherings. All of this means that “we all get together, we mix risks from all over the country [and] we don’t have much time to recover before being exposed and exposing others,” Chin-Hong said.

Aside from its infectiousness, the CDC said in its Dec. 8 briefing that there’s “no evidence that JN.1 presents an increased risk to public health relative to other currently circulating variant,” and “no indication of increased severity from JN.1 at this time.”

But, Chin-Hong stressed, JN.1’s increased transmissibility still means that “more people will get infected, which means that our hospitals will be fuller, and that will limit our ability to care for those who have other illnesses.”

What are the symptoms of JN.1?

Chin-Hong confirms that no surprising wild card symptoms have yet been reported for JN.1, or HV.1 before it — they’re the same COVID-19 symptoms you’re used to hearing about from previous variants. Or at least, that’s how it looks right now.

“Like the other omicron flavors,” Chin-Hong said, “many [cases] start with a sore throat,” followed by congestion and a dry cough. From there, “the other symptoms — headache, runny nose, muscle aches, diarrhea or upset stomach, fever, loss of smell— may also join in,” he said.

“The characteristics of the person becoming infected can also shape what symptoms are experienced,” Chin-Hong said, noting that a person age 75 or over or an immunocompromised person who didn’t receive the new COVID-19 vaccine “may experience shortness of breath or difficulty breathing.”

According to the CDC, this is the full list of the possible symptoms of COVID-19:

  • 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.

Remember, you might have a combination of these symptoms or just one. They might be mild or feel more severe. But if you’re experiencing any of these, take a COVID-19 test (more on this below).

What are the current COVID-19 cases in the Bay Area right now?

“COVID cases” — that is, positive test results — are not tracked in the way they once were. There’s more on that below, but in the absence of up-to-date widespread data on positive COVID-19 test results, watching for the presence of the coronavirus in human sewage has become increasingly important instead for gauging the levels of COVID-19 spread in a particular area.

Stanford University’s WastewaterSCAN project monitors the presence of COVID-19 — as well as other viruses — in wastewater across the U.S. (For example, you can see the concentration of COVID-19 in wastewater collected from the Oceanside San Francisco watershed.)

And when it comes to COVID-19 in Bay Area sewage, after numbers came down after that summer swell, WastewaterSCAN’s Ali Boehm told KQED by email on Jan. 8 that those levels of COVID-19 are unfortunately “high and increasing” right now. In the chart below, which shows a trend line aggregated from the Bay Area wastewater sites, you can see how the current rise compares to the highest spike visible, which is the initial omicron surge of winter 2021-22.

A chart showing COVID-19 levels collected from across Bay Area wastewater sites. (WastewaterSCAN)

As for other winter respiratory viruses, levels of RSV in Bay Area wastewater are “still quite high and have not clearly started decreasing,” Boehm said. One bit of good news: Boehm said that local wastewater shows that the flu is “not circulating now like it did at this time last year.” Read more about the different symptoms of RSV and flu in relation to COVID-19.

Statewide, COVID-19 metrics are also back on the upswing after a lull. The state’s 7-day COVID-19 positivity test rate tracks the average percentage of people in California each week who get a positive diagnostic test result from a lab after taking a PCR test. The statewide positivity rate reached its highest point for the entire year back on Sept. 2, at 17.4%.

But after falling to a low of 6.1% on Nov. 3, the weekly average positivity rate has climbed again to 12.3% as of the most recently available data, collected on Jan. 1. (It’s worth noting that many people who suspect they have COVID-19 in 2023 test themselves at home with an antigen test kit, not a PCR test — so this tracking from the California Department of Public Health doesn’t represent the full picture of COVID-19 positivity around the state.)

After a lull following the 2023 summer swell, the number of people hospitalized with COVID-19 in California began climbing again in November and peaked on Dec. 22 with a 7-day average of 2,339 people hospitalized statewide. The most recent available data, from Dec. 31, shows a drop to a 7-day average of 1,990 patients.

Why don’t we have firmer numbers on how many people are actually testing positive for COVID-19 right now? Earlier in the pandemic, most people were getting diagnostic PCR tests through official sites, which were then tracked through their laboratory processing and had their numbers reported — the way the state’s official test positivity rate is still tracked.

However, the arrival of widespread antigen tests has now given more people a way to test themselves for COVID-19 at home without having to find a PCR test (albeit in a manner different from how a PCR test “detects” the virus). But while public officials have urged at-home testers to report positive results to their local health authority, very few people still do so.

All of this goes some way to explain why the “true” number of people who currently have COVID-19 in 2023 is a very difficult number to report — and why any official number from PCR testing almost certainly represents a big undercount.

In this photo illustration, a COVID-19 self-test package is seen on a dark table.
When COVID-19 cases rise, strongly consider rising up — and testing if you feel symptoms. (Photo Illustration by Michael Ho Wai Lee/SOPA Images/LightRocket via Getty Images)

Is the new COVID-19 vaccine still effective against JN.1 and HV.1?

Yes: The new COVID-19 vaccine that’s now available across California is formulated to target the XBB sublineage, from which HV.1 is descended. And that same vaccine is “still effective against JN.1,” too, Chin-Hong said, despite this latest subvariant having more than “30 more mutations than XBB.1.5, which the vaccine is based on.”

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I think I was exposed, or have symptoms. When should I take a COVID-19 test?

Step 1: Know about updated incubation times for JN.1

If you’ve heard that incubation times for the virus are getting shorter — that is, the amount of time between getting exposed to COVID-19 and testing positive for COVID-19 — it’s true. People are testing positive for COVID-19 more quickly than they were in 2020 when the average incubation period was five days because the incubation period has changed with each new variant, confirms Chin-Hong.

While “we don’t have a ton” of up-to-date information on incubation times at this stage of the pandemic, notes Chin-Hong, given this general trend, it makes sense to take a COVID-19 test as early as two days after exposure if you’re already having symptoms. But there’s a crucial update for 2024…

Step 2: Don’t trust a negative early COVID-19 test

If your first test is negative, you should absolutely test again the next day if symptoms persist — and again after that if you’re still negative.

Here’s why you can’t necessarily trust a negative at-home COVID-19 test in 2024: While incubation times have gotten shorter, “paradoxically, we’re seeing people take longer to get a positive test,” Chin-Hong said.

Why? Chin-Hong said that the hypothesis that makes sense to him is less about the efficacy of the antigen tests themselves and way more about how much quicker someone with COVID-19 might develop symptoms in 2024 than they would have done in 2020.

As a reminder, those symptoms are the sign that your body’s immune system is mounting a response to an invading virus — and back at the start of the pandemic, by the time you developed COVID-19 symptoms and took a test it would probably already be positive, Chin-Hong said.

But at this stage of the pandemic, most of us now have “a lot of immune experience,” Chin-Hong said — and the average person’s immune system is increasingly “on guard” and “activated more than in 2020,” he said. So when your body detects a burgeoning coronavirus infection now, “your whole immune system just gets agitated and active, and you begin to get sick sooner, but you actually don’t have as much virus in your blood yet,” Chin-Hong said. Dr. Abraar Karan, an infectious disease physician and researcher at Stanford University, also put it this way for NPR: “With our immune systems primed, the body’s response [now] comes much more quickly than it would have back in 2020 when SARS-CoV-2 was a novel pathogen.”

And because many of us take a COVID-19 test when we start to feel sick, we might actually be testing way too early at that time for an at-home antigen kit to successfully detect enough virus inside us. This mismatch between when your symptoms start and when you’ve got enough virus present in your body to result in a positive COVID-19 test “was started to be observed in early omicron, but I think it just seems more accentuated now,” Chin-Hong said.

Dr. Elizabeth Hudson, regional chief of infectious diseases at Kaiser Permanente Southern California, told the Los Angeles Times that for her part, she attributes this delay we’re seeing in accurate test results to people acquiring accumulated immunity from COVID-19 over the years, either from getting infected or vaccinated.

“It’s actually pushing back the time that people’s COVID tests are coming up positive,” Hudson said. “So some people are testing at Day 1 and Day 2 … If they probably tested themselves a couple of days later, there’s a pretty good chance that it actually would turn out to be COVID.”

The bottom line is: If you’re testing because you’ve started feeling unwell, don’t assume a negative result means you don’t actually have COVID-19. Play it safe, stay home as much as you can and wear a well-fitted mask if you can’t, and take another antigen test 48 hours later, Chin-Hong said. You can also seek out a PCR test, which are more sensitive.

Step 3: Make sure your COVID-19 test hasn’t expired

Many of the COVID-19 tests being made available right now (for example, at your local public library) may be approaching their expiration date if they haven’t already passed it. And an expired test could give you an unreliable result.

You can check the FDA’s list of antigen test types to see whether the box you’re holding has had its shelf life extended by the manufacturer. The FDA said that if a test’s shelf life has been extended, it’s because the manufacturer has given the agency enough “data showing that the shelf-life is longer than was known when the test was first authorized.” (In other words, it’s still OK to use that test.)

Should I be altering my behavior right now?

With the onset of winter respiratory virus season, everyone should consider taking extra or new steps to protect themselves from COVID-19 infection during a rise in level, even if it feels like “a step backward” for you, at this stage of the pandemic.

This might include bringing a well-fitting N95 mask along to indoor spaces that you know could be crowded, like the grocery store. Or if you’re hosting people indoors in your home, ensure the space has good ventilation by taking measures like opening windows.

If the weather allows, you might also consider favoring outdoor hangouts and meetups with friends and family at this current time, to help reduce the potential risks of COVID-19 transmission. The chances are good that the folks you’re meeting up with could also be feeling a little anxious about the recent rise in cases but might not feel able to articulate it for fear of killing the social vibe. Consider doing the quieter folks in your circle a favor and being the person who raises the issue first to keep everyone safer. Remember: It’s not weird to not want to get COVID-19.

If you’re at higher risk for serious illness or hospitalization from COVID-19, it’s an especially good idea to take extra precautions against the virus right now. These groups can include older people, immunocompromised and disabled folks, and people who “haven’t been recently vaccinated, in the last six months or so,” advises Chin-Hong.

Another reason you might consider being extra cautious about COVID-19 right now is if you’ve got upcoming travel plans (for example, for the holidays).

Even if your symptoms are mild, a COVID-19 infection can require isolation from other people for well over a week — and you can double that timeline if you get a rebound (i.e., second) infection, which is surprisingly common even in people who don’t take the antiviral treatment, Paxlovid.

Where can I still find a free COVID-19 test?

Good question. Finding a quick, free COVID-19 test — whether an at-home antigen test or a PCR test — has gotten progressively harder at this stage of the pandemic as more sites and services have been shuttered.

The federal government has, at least, restarted its free at-home COVID-test-ordering service through USPS, meaning you can once again order another four free antigen tests to be delivered to your door for a future time.

A person with long hair inserts a long cottonswab in her nostril while standing in the doorway of her home.
Janet Franco-Orona swabs her nose for a COVID-19 test at her home in San José on Feb. 3, 2021. (Beth LaBerge/KQED)

But what do you do now if you don’t already have a supply of antigen tests for COVID-19 at home right now? Try the following:

Purchase a COVID-19 at-home antigen test at a pharmacy near you

The quickest option will also be one of the most expensive up-front: Purchasing an at-home antigen test at a nearby pharmacy. (Ideally, ask someone to purchase one for you so you don’t potentially expose other people at the pharmacy — and if you really have to go yourself, wear a well-fitted N95 mask to help lower the risk you pose to others.) These at-home test kits are usually around $20 for a pack of two antigen tests.

If you have health insurance, you can request reimbursement from your health insurer for the cost of up to eight at-home tests per month, so don’t throw away your receipts.

Find a COVID-19 PCR testing site near you

PCR testing is more accurate than an antigen test — because it’s more sensitive at picking up traces of the coronavirus in your body — but it may take longer to get your results than with an at-home test.

Currently, there are still some sites offering free COVID-19 testing around the state. Try using:

If you have health insurance, you may be able to get a PCR test ordered by your health care provider with the costs covered. Having a test ordered by a provider is — usually — the only way to get your testing costs covered if you have Medicare, too.

Try your local public library

Free COVID-19 tests may also be available for pick-up at your local Bay Area public library this winter.

For more information, read our new guide to which Bay Area public libraries are giving away free at-home antigen tests.

If you have health insurance, contact your provider

If you are insured with major Bay Area providers, such as Kaiser Permanente or Sutter Health, the easiest option to secure a COVID-19 test may be to make an appointment through your particular provider. Most providers offer sign-ups online through a member’s login, and appointments can also be made by phone.

For more ideas on how to find a free or low-cost COVID-19 test near you, see the KQED guide, which includes finding a test through your Bay Area county’s public health department or at a private testing site.

You can also read our guide to using at-home antigen tests in 2023 and how effective they are.

Tested positive for COVID-19? Consider asking for a Paxlovid prescription

Paxlovid (pronounced “pax-LOH-vid” or sometimes “PAX-loh-vid”) is a highly effective antiviral treatment for COVID-19, available free by prescription in California.

The treatment is fairly simple and entails taking a pill orally twice a day for five days. There’s evidence that it could help lower your risks of developing long COVID-19, and as well as helping to reduce your risks of severe illness or hospitalization, it can also help ease symptoms during an infection.

Because of good supply, the drug is no longer reserved for people most at risk of severe illness from COVID-19, and everyone is encouraged to contact a health care provider to see whether they qualify.

As of February 2023, you no longer need proof of a positive COVID-19 test to get a prescription for Paxlovid either. But for it to be effective, health officials recommend starting a course of Paxlovid within five days of a positive test. This means that taking a test as soon as you suspect you have COVID-19 is still very important.

If you took Paxlovid for a previous COVID-19 infection, can you retake it for a new infection? Yes, it’s “definitely OK” to do so, said UCSF’s Chin-Hong if it’s a new, “distinct episode of COVID”. The only time it wouldn’t make sense to take Paxlovid a second time, Chin-Hong said, is for the same infection — because you “will likely not benefit in taking another course even if you still test positive.”

If you’re seeking a prescription, be aware that as of November there have been some changes to how Paxlovid is funded, meaning people with health insurance should make sure they’re requesting Paxlovid “in-network” to avoid an unexpected bill. 

Read more on how to request a prescription for Paxlovid, with or without health insurance.

Tell us: What else do you need information about?

At KQED News, we know that it can sometimes be hard to track down the answers to navigate life in the Bay Area. We’ve published clear, practical explainers and guides about COVID-19, how to cope with intense winter weather, and how to exercise your right to protest safely.

So tell us: What do you need to know more about? Tell us, and you could see your question answered online or on social media. What you submit will make our reporting stronger and help us decide what to cover here on our site and on KQED Public Radio, too.

An earlier version of this story was originally published on Nov. 22. KQED’s Lesley McClurg, Alexander Gonzalez and Brian Watt contributed reporting to this story.

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