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New COVID Variant JN.1: All We Need to Know

M3 India Newsdesk Dec 21, 2023

Global concerns rise as the JN.1 COVID variant with unique spike protein mutations sparks worry worldwide. Explore through this article, the symptoms, vaccine updates, and the CDC's response to this evolving threat.

A new COVID-19 variation has scientists on high alert because it has the potential to be more contagious than earlier versions. The JN.1 variant of coronavirus has just been identified in Kerala.

The case was identified in a sample from Karakulam in Thiruvananthapuram district of the southern state on December 8, using the RT-PCR test.

The septuagenarian lady had moderate symptoms of influenza-like illness (ILI) and has subsequently recuperated from COVID-19. This particular strain is leading to a significant increase in illnesses on a global scale once again, which is creating concern among health officials.

What are the latest updates on the COVID-19 virus variant JN.1?


JN.1 is a unique iteration of the Omicron sub-variant BA.2.86, distinguished by an extra mutation on its spike protein. This particular strain had the capacity to quickly propagate and elude immunity, underscoring the need for ongoing surveillance and prudence in India.

Global presence

The COVID JN.1 variation is believed to represent the Omicron sub-variant BA.2.86, also referred to as Pirola. The case was first identified in the United States in September of the current year. News reported that on December 15, seven instances of the particular sub-variant were detected in China. The CDC said in a recent update that despite the distinct nomenclature of BA.2.86 and JN.1 variations, they only vary by a single alteration in the spike protein.

Vaccine updates

The spike protein, named for its resemblance to tiny protrusions on the surface of the virus, plays a crucial role in the virus's capacity to infect people. As to the CDC, immunisations that specifically target the spike protein of a virus should also be effective against JN.1 and BA.2.86.

How does the novel COVID-19 virus JN.1 manifest its symptoms?

The symptoms of COVID-19 induced by the JN.1 variation are comparable to those seen by other forms. Reported symptoms include fever, rhinorrhea, pharyngitis, cephalalgia, and minor gastrointestinal manifestations. Nevertheless, it remains uncertain if JN.1 displays discernible symptoms in contrast to earlier variations.

New Coronavirus JN.1: Is it cause for concern?

CDC warning

JN.1 may be more immune system evading than previously thought, raising questions about its transmissibility, according to a warning from the Centres for Disease Control and Prevention (CDC).

WHO guidance

The World Health Organisation (WHO) has asked member nations to continue stringent monitoring and exchange sequencing data in response to the spike in cases.

Union Health Ministry's directive

The Union Health Ministry has written to states and Union Territories, requesting that they keep an eye out for influenza-like infections, undertake sufficient testing, and submit all positive samples for whole genome sequencing. This is in response to the rising number of COVID-19 cases in Kerala.

According to sources acquainted with the situation, tests from Goa revealed the detection of an additional 15 cases of the JN.1 strain.

What are our current understandings about JN.1?

The less-than-variant JN.1 is not very new; it is a descendant of the BA.2.86 variation, sometimes known as Pirola. The first instances of this variety were found in the United States in September, and as early as January of this year, the first case was found worldwide.

Even though JN.1 only has one more spike protein mutation when compared to Pirola, researchers have been keeping an eye on it since Pirola has more than thirty mutations. Because the Sars-CoV-2 spike protein binds to receptors on human cells and enables the virus to enter them, mutations on the protein are important.

Does the JN.1 COVID variant pose a higher risk of transmission and severity?

There is no proof that JN.1 can spread more quickly than the current versions in circulation or produce severe symptoms. At first, there were worries that Pirola might spread quickly and avoid immune response more readily because of the large number of mutations. But it hasn't really occurred.

In fact, serum from people who had both the illness and the immunisation successfully neutralised both JN.1 and Pirola, according to an evaluation by the WHO Technical Advisory Group on COVID-19 Vaccine Composition.

Although Pirola and JN.1 are regarded as Variants of Interest (variants that have the potential to spread and are less effectively neutralised in labs by antibodies from infection or vaccination), they have not been classified as Variants of Concern (variants that increase the risk of transmission, cause severe illness that requires hospitalisation, and decrease the effectiveness of vaccines).

Causes of present concerns?

Worldwide, Pirola and its closely related JN.1 are undoubtedly causing a greater number of cases. There have been cases found in the United States, China, Singapore, and a few European nations.

According to a WHO announcement, 17% of the Sars-CoV-2 sequences uploaded to the worldwide database Initiative on Sharing All Influenza Data (GISAID) were attributed to Pirola and its offspring. More than half of these sequences were JN.1 at the start of December. Between 15% and 29% of the COVID-19 variations in circulation in the US were JN.1.

From December 4 to December 10, an estimated 56,043 cases were reported in Singapore. Additionally, there was a rise in hospital admissions, mostly for those over 60. "JN.1, a sublineage of BA.2.86, is presently responsible for the great majority of COVID-19 cases in Singapore." The Singapore Ministry of Health said, "There is currently no clear indication that BA.2.86 or JN.1 are more transmissible or cause more severe disease than other circulating variants based on the available international and local data."

In terms of variation, it seems to be multiplying almost twice as quickly as recent variations, and the fraction of isolates found in the US within the last two weeks has more than doubled. The symptoms of this most recent variation, according to the CDC, differ based on an individual's immunity and health.

Are further shots required?

Although Singaporean data indicates that individuals who received their last dose of the COVID-19 vaccine more than a year ago had a 1.6-fold increased risk of hospitalisation, experts noted that India's high vaccination rate and subsequent non-symptomatic infections are likely to have contributed to a high level of protection.

The majority of Indians have gotten at least two doses of the vaccination and have been exposed to COVID-19 at least twice, if not three times. In India, specialists from WHO's Technical Advisory Group on Sars-CoV-2 Virus Evolution said that new vaccinations are not actually required since the country's population has a high degree of immunity, which may avoid serious sickness.

In what ways can you safeguard yourself?

Experts predict that while Sars-CoV-2 variations will continue to emerge, preventative methods against respiratory viruses will not change. If the number of cases is growing locally, experts advise masking up in busy settings, particularly enclosed ones. Staying in areas with good ventilation slows the infection's spread. Additionally, regular hand washing helps to avoid infection.

Understanding JN.1

  • Variant propagation: The COVID-19 virus is dynamic. It changes with time. New varieties may sometimes spread more rapidly or successfully as a result of these modifications. If that happens, the new version could spread more widely than the existing variants that are already in use.
  • How common: According to CDC projections, the fraction of JN.1 SARS-CoV-2 genomic sequences will keep rising. In the US, it is now the variety that is expanding the quickest.
  • History: The CDC has been monitoring the variation BA.2.86 since August, and JN.1 is closely connected to it.
  • The spike protein only differs by one alteration between JN.1 and BA.2.86, despite the fact that their names make them seem highly distinct.
  • Impact: JN.1's continuous expansion implies that it is either more contagious or more adept at eluding human immune systems. already, there is no proof that JN.1 poses a greater danger to public health than the other versions that are already in circulation.
  • At this point, there is no sign that JN.1 is becoming more severe.
  • As with previous variations, updated COVID-19 vaccinations might improve protection against JN.1.
  • COVID-19 testing and treatments are anticipated to be effective against JN.1, as previously reported in updates.
  • The issue of whether JN.1 may cause an incremental rise in infections is raised by the variant's quick proliferation when compared to other variations.
  • Right now, COVID-19 activity is rising.
  • We currently don't know how much JN.1 could be influencing these increases or potential increases that might occur during the remainder of December, similar to those seen in prior years. The CDC will keep a careful eye on JN.1 transmission and COVID-19 activity.
  • Symptoms: Whether JN.1 infection causes distinct symptoms from other variations is not yet understood. COVID-19 symptoms are generally consistent between variations. Rather than the specific variation that causes the infection, a person's immunity and general health are more likely to determine the kinds of symptoms and how severe they are.
  • What lies ahead: It is anticipated that COVID-19 activity will rise in the next month. You may maintain your protection against JN.1 and other variations by getting an updated COVID-19 vaccination. If you haven't had a vaccination this autumn, now is an excellent opportunity to do so.

The efficacy of vaccinations against JN.1 and other novel variants

Researchers found that the novel XBB.1.5 monovalent vaccination not only offers protection against JN.1 and other "emergent" viruses but also against another Omicron subvariant, XBB.1.5. The article was published on bioRxiv on November 26 but has not yet undergone peer review certification.

According to the researchers, the revised vaccination increased antibodies against JN.1 and other emerging viruses by 13–27 times and against XBB.1.5 by roughly 27-fold when administered to uninfected individuals.

The new JN.1 subvariant will probably be protected against by the COVID vaccination even after the first doses, but "if you got the XBB.1.5 booster, it is going to be protecting you better against this new variant."

Statement from the WHO on the antigens in COVID-19 vaccines

Key points:

  1. The spike protein has undergone significant genetic and antigenic evolution as SARS-CoV-2 spreads and changes.
  2. Vaccines against circulating SARS-CoV-2 variants that are monovalent (XBB.1.5) induce widely cross-reactive neutralising antibody responses when administered on various platforms.
  3. The TAG-CO-VAC recommends sticking with the present COVID-19 vaccine antigen composition, that is, using a monovalent XBB.1.5 as the COVID-19 vaccine antigen, given the current SARS-CoV-2 evolution and the breadth of immune responses exhibited by monovalent XBB.1.5 vaccinations against circulating variants.
  4. Monovalent XBB.1.5 vaccinations produced neutralising antibodies in naïve mice that interacted effectively with XBB descendant lineages (EG.5, HV.1, HK.3). But BA.2.86 and JN.1 did not neutralise as well, suggesting that in this model, BA.2.86 and JN.1 can be distinguished from XBB.1.5 antigenically.
  5. On the other hand, sera from people who had monovalent XBB.1.5 vaccinations, whether or whether they had recently contracted an illness, neutralised XBB descendant lineages such as EG.5, HK.3, HV.1, BA.2.86, and JN.1. On the other hand, the information on JN.1 cross neutralisation is scarce.


Disclaimer- The views and opinions expressed in this article are those of the author and do not necessarily reflect the official policy or position of M3 India.

About the author of this article: Dr Monish Raut is a practising super specialist from New Delhi.

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