What to Know About JN.1, the Latest Omicron Variant
Vaccines, tests, and antivirals are still effective tools in the latest COVID surge.
January 09, 2024
In early November 2023, the JN.1 variant caused less than 5% of COVID-19 cases in the U.S. Now it is estimated to cause more than 60% of them. Virologists including Andy Pekosz, PhD, a professor in Molecular Microbiology and Immunology, are paying attention.
Here, Pekosz explains what virologists are seeing, what this new variant means for case rates and treatments, and why it’s so important for more people to get the updated COVID-19 vaccine rolled out this fall.
What is JN.1?
A SARS-CoV-2 variant called BA.2.86 emerged a few months ago and caught virologists’ attention because it contains many more mutations—about 30 of them—to evade immunity than any other variant circulating at that time. However, the BA.2.86 variant never came to dominate among the group of SARS-CoV-2 variants that were circulating in the late summer/early fall of 2023. The JN.1 variant is a descendant of BA.2.86 that has acquired the ability to transmit efficiently through an additional one or two mutations. It has the immune evasion of its parent but has now mutated to transmit more efficiently.
What’s happening now with this variant?
The increase in the number of cases caused by JN.1 corresponds to an overall increase in COVID-19 cases. Symptoms of JN.1 infection are very similar to those of previous omicron variants, and it doesn’t seem to cause more severe disease, either. There is some suggestion that JN.1 may be causing more diarrhea than previous variants, but we don’t have any firm data supporting that yet.
What’s most important to understand about this variant?
This latest variant should be a reminder that we have tools to fight off COVID infection and minimize severe disease: Tests detect JN.1, the new vaccinesprotect against severe disease, and antivirals are still capable of treating infection from JN.1. We just have to use these tools more effectively than we have over the last six months.
So far, only 8% of children and 19% of adults have received the latest vaccine, so a lot of people are missing out on protection from this virus.
What does the transmission timeline look like for JN.1?
The period of infectiousness for JN.1 is very similar to that of the other omicron variants that have been circulating over the past year: You are contagious one to two days before your symptoms begin, and you are still contagious for at least two to three days after your symptoms begin—though some people can continue to have the detectable live virus for up to a week after symptom onset. After exposure, it may take five days or more before you begin to develop symptoms.
Are people who had an older vaccine or who’ve had COVID from another variant likely to be reinfected by JN.1?
The older vaccines were based on SARS-CoV-2 variants that are very different from variants circulating now. That, combined with the fact that your immunity from vaccination or infection tends to drop off over time, means that you won’t get a lot of protection from COVID-19 if you are relying on the vaccines you received nearly a year ago. It’s very similar to why we have annual influenza vaccines: The virus is changing, so we have to change the vaccine to make sure it is a good match with the virus variants that are causing infection right now.
Do we know yet how well this fall’s COVID-19 vaccines work against this variant?
While the JN.1 variant does have a number of mutations that help it avoid immunity, laboratory studies suggest that the updated COVID-19 vaccine does increase the amount of antibodies that can recognize JN.1, and it is still effective in protecting against severe disease. You really need the newest COVID-19 vaccine formulation to be protected from severe illness from JN.1 and other recent variants.
COVID numbers have been rising for a few weeks now. Is it too late to get the vaccine?
No. Getting vaccinated now can provide protection during this surge. Don’t wait. This is particularly important for those in high-risk groups, but it goes for all eligible individuals.
Is Paxlovid effective against JN.1?
Paxlovid is still working very well, particularly in high-risk populations, but it’s not being prescribed as frequently as it should be. It’s important to remember that Paxlovid needs to be taken as soon as possible after symptoms begin, within five days of symptom onset is the guidance, but the earlier, the better. This means it is particularly important to test when you start feeling sick and then get a prescription if you test positive.
What might we expect in terms of case rates over the next few weeks?
Case rates will likely go up. We’re coming out of a period when we already expected transmission to go up, due to increased travel and holiday gatherings. For the rest of January and into February, we will continue to have a high amount of respiratory virus activity that includes COVID-19 cases. Now is the time to get vaccinated if you haven’t already, get some COVID-19 tests available for free from the U.S. government, and make sure your local pharmacy can fill a COVID-19 antiviral prescription if you do end up testing positive.
Aliza Rosen is a digital content strategist at the Johns Hopkins Bloomberg School of Public Health.
Melissa Hartman is the managing editor of Hopkins Bloomberg Public Health magazine and associate director of editorial at the Bloomberg School.
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Blog Editor15 January 2024
With the emergence at the end of last year of COVID-19 variant JN.1, there are questions about how it compares to the many other variants that have been identified.
JN.1 descends from variant BA.2.86 and has an additional mutation in the spike protein. It has recently become the most widely circulating variant in the US as well as in France. As of January 2024, approximately 60% of English cases are caused by JN.1.
UKHSA is continuing to monitor data relating to variants both in the UK and internationally, including close monitoring of the JN.1 variant, and assessment of severity and vaccine effectiveness. There is no change to the wider public health advice at this time.
There are no reports of people becoming more ill with this COVID-19 variant than with previous ones.
It is important to note that we will need more data to draw any conclusions about the effect of these mutations on transmissibility and severity of the variant. In this blog post we’ll outline what we know so far and what action we are taking.
It’s normal for viruses to mutate and change, and more widely we’re still getting to grips with how the healthcare system responds to the ebb and flow of seasonal cases. As more data becomes available on this variant, we’ll have a better understanding of how it interacts with our immune systems and how to optimise our protection and as well as actions we can take to keep the most vulnerable safe and live our lives as normally as possible.
If people become unwell, and are unsure if they have COVID-19, what should they do?
If you have symptoms of a respiratory infection, such as COVID-19, and you have a high temperature or do not feel well enough to go to work or carry out normal activities, you should avoid contact with vulnerable people and stay at home if possible.
For those of us who absolutely can’t stay at home, our Living with COVID guidance is unchanged, and outlines how to prevent transmission to others.
Why should people come forward for their vaccine?
Vaccines remain our best defence against severe disease and hospitalisation from flu and COVID-19. That’s why we’re asking over-65s, anyone in a clinical risk group, and anyone living in a household with someone who is in a clinical risk group, to come forward for their vaccination. Their protection since their last vaccination will have waned and they remain at increased risk from a respiratory infection this winter. It’s also important to note that COVID-19 isn’t a special case; respiratory infections can be unpredictable, and we’re asking similar groups to get vaccinated against flu.
The last date that the seasonal COVID-19 vaccination will be available is 31 January 2024.
What surveillance systems are in place?
We publish the latest surveillance data for COVID-19 and other respiratory illnesses weekly, to the UKHSA data dashboard. We’re also getting vital data from those who are admitted to hospital with symptoms, and we are utilising genome sequencing to understand which variants people are most vulnerable to.
There are also specific surveillance programmes in place, where small sample groups are tested regularly. These allow us to monitor trends in the wider community.
Hospital is where we will see the more severe cases, and we will be monitoring the numbers of people attending with COVID-19 symptoms very carefully. This will help us understand the growth rate and transmission potential of the new variant.
We continue to collaborate globally with health organisations in other countries, the World Health Organisation and initiatives such as the Global Influenza Surveillance & Response System (GISAID) to ensure that we have the most current data.
What is the UKHSA doing to tackle the new variant?
When a new variant appears on our radar, at the initial stages it is often quite difficult to know whether the mutations provide any advantages to the virus. Genetic mutations happen all the time, and in some cases have been known to make a virus less transmissible or cause a milder reaction in people.
At these early stages our scientists at the Vaccine Development and Evaluation Centre (VDEC) are busy growing a stock of the JN.1 variant in our high containment facilities, so that we can begin testing.
At the same time, scientists in our COVID-19 Vaccine Unit work hand in glove with vaccine developers to get samples of new, as yet unlicensed, vaccines to assess whether they will give better protection against the virus.
Vaccinations for flu and COVID-19 help to keep vulnerable people out of hospital and carrying on with their day-to-day lives, as well as reduce pressure on our NHS which is always critical in the winter. If you’re eligible for the jabs, please don’t hesitate, book your vaccine and get winter strong.