COVID again: All you need to know about JN.1, the latest coronavirus strain

Even as another COVID-causing coronavirus strain has been reported in India as of May 2025 is the JN.1 variant, a descendant of the Omicron BA.2.86 lineage, along with its sub-lineages LF.7 and NB.1.8.1, many will be surprised to know that the virus that caused a worldwide pandemic in 1918-20, the Spanish flu, might still be 'in the air'. Well, not quite, but it's there.

The following is what scientists have come to know about the origin and evolution of the latest strain of the pathogen that killed thousands across the world in 2020-21 through COVID-19 and questions related to the nature of such viruses.

Mutation from Omicron

JN.1 is not a completely new strain but a further mutation of the Omicron variant, specifically from the BA.2.86 sub-lineage (sometimes referred to as “Pirola”). It emerged due to additional mutations in the spike protein, which enhance its transmissibility compared to earlier Omicron sub-variants. These mutations likely occurred through natural viral evolution in human populations, as coronaviruses continuously mutate during replication.

Geographic origin

The exact geographic origin of JN.1 is not pinpointed to a single location, as it has been detected globally. It was first identified in late 2023 in multiple countries, including the United States and Europe, and by December 2023, it was classified as a variant of interest by the World Health Organisation (WHO).

In India, JN.1 was first detected in Kerala in December 2023, but this does not mean it originated there. Its global spread suggests it likely emerged in a region with high viral transmission, possibly where surveillance was less robust, allowing mutations to accumulate.

No definitive evidence points to a specific “ground zero” like Wuhan in China was for the original SARS-CoV-2 in 2019.

Relation to Delta and Omicron

The Delta variant (B.1.617.2) and Omicron variant (B.1.1.529) were distinct lineages that emerged in 2021 and late 2021, respectively. JN.1 is a direct descendant of Omicron, not Delta. It represents ongoing evolution within the Omicron family.

Delta is no longer a dominant strain globally, having been outcompeted by Omicron and its sub-variants due to their higher transmissibility.

Evolution

Genomic sequencing data from the Indian SARS-CoV-2 Genomics Consortium (INSACOG) and global databases like GISAID confirm that JN.1 evolved from BA.2.86 through mutations that improved its ability to evade immunity and spread. This is a typical process for RNA viruses like SARS-CoV-2, which mutate rapidly due to errors in replication. There’s no evidence suggesting JN.1 originated from a lab leak or deliberate release; it’s a natural progression of the virus.

The JN.1 variant is a mutation within the Omicron lineage, not a new strain from a single origin point like Wuhan in 2019. It likely emerged globally through natural viral evolution, with no specific country identified as the source. It’s a continuation of Omicron’s dominance, not a resurgence of Delta or an entirely new lineage.

FAQ

Can disease-causing vectors be eliminated? Is the Spanish flu virus still present?

Some science journals say it’s technically impossible to eliminate a disease-causing vector and that the Spanish flu virus from 1918–1920 is still present with reduced potency. In this context, two technical terms are often used: Vector and pathogen.

In epidemiology, a “vector” typically refers to an organism (e.g., mosquitoes for malaria) that transmits a pathogen. The pathogen is the virus causing a disease; in the case of some diseases, the pathogen may be a bacterium; in some others, it's a fungus that may grow inside the body of the host as a parasite.

Can a pathogen be eliminated?

Smallpox, caused by the variola virus, is the only human infectious disease fully eradicated (declared so by the WHO in 1980). This was possible due to an effective vaccine, global cooperation and the virus’s lack of an animal reservoir, meaning it only infected humans.

Eliminating a virus like SARS-CoV-2 or influenza is much harder because:

Animal reservoirs: Coronaviruses and influenza viruses can infect animals (e.g., bats, birds, pigs), which act as reservoirs, allowing the virus to persist and potentially spill back into humans.

High mutation rates: RNA viruses like SARS-CoV-2 and influenza mutate rapidly, creating new variants that can evade immunity. This makes "zero COVID" or complete elimination nearly impossible without global, sustained efforts.

Human behaviour and global spread: Incomplete vaccination coverage, asymptomatic transmission and global travel facilitate ongoing spread, as seen with SARS-CoV-2 variants like JN.1.

Endemicity: Many experts believe SARS-CoV-2 is now endemic, meaning it circulates at low levels and causes periodic outbreaks, much like seasonal influenza. Complete elimination is unlikely without a sterilising vaccine (one that prevents infection entirely) or unprecedented global coordination.

Eliminating even biological vectors (e.g., mosquitoes for dengue or ticks for Lyme disease) is challenging too, as techniques like sterilisation (e.g., releasing sterile mosquitoes) or genetic modification (e.g., CRISPR-based gene drives) can reduce vector populations but face ecological, ethical and practical hurdles.

Complete elimination of a vector species is rare and could disrupt ecosystems as, for example, there are mosquito breeds that help in pollination, which should not be wiped out from the face of the earth.

While eradication is technically possible for some pathogens (e.g., smallpox), it’s extremely difficult for viruses with animal reservoirs, high mutation rates or widespread human transmission. SARS-CoV-2, for instance, is likely to remain endemic due to these factors, as supported by studies in journals like Nature and The Lancet.

Is the Spanish flu virus still present?

The 1918 influenza pandemic was caused by an H1N1 influenza A virus. It killed an estimated 50 million people globally. The claim that it’s “still in the air” with reduced potency needs clarification.

The 1918 H1N1 virus did not disappear but evolved into seasonal influenza strains. Genetic studies (e.g., published in Science in 2005) show that descendants of the 1918 H1N1 virus circulated for decades, contributing to seasonal flu. The 2009 H1N1 “swine flu” pandemic was caused by a related H1N1 strain, which shares some genetic features with the 1918 virus but is far less virulent.

The 1918 virus’s descendants have reduced virulence due to several factors:

Human immunity: Repeated exposure to H1N1 strains over generations has built partial immunity in human populations.

Viral evolution: Influenza viruses evolve to balance transmissibility and virulence. Highly lethal strains may “burn out” by killing hosts too quickly, while less lethal strains persist by allowing hosts to survive and spread the virus.

Modern medicine: Vaccines, antivirals (e.g., Tamiflu), and improved healthcare have mitigated the impact of H1N1 and other flu strains compared to 1918, when medical interventions were limited.

The claim that the Spanish flu virus is “still in the air” is likely a metaphor for its genetic legacy in circulating influenza strains. The original 1918 virus is not actively circulating in its exact form but exists in evolved forms within seasonal flu. It’s also preserved in laboratory samples (e.g., reconstructed from permafrost-preserved tissue for research) and could theoretically persist in frozen environments, but there’s no evidence it’s actively infecting people in its original form.

Studies, such as those in the Journal of Virology and Nature Reviews Microbiology, confirm that H1N1 strains related to the 1918 virus continue to circulate as part of seasonal influenza, with reduced potency due to immunity and viral evolution. The WHO and CDC monitor these strains through global influenza surveillance networks.

The claim is partially true. The Spanish flu virus’s genetic legacy persists in modern H1N1 influenza strains, which are far less deadly due to immunity, viral evolution, and medical advances. However, the original 1918 virus is not actively circulating in the environment; it exists in evolved, less potent forms. Eliminating disease-causing pathogens or vectors is technically challenging and often impossible for viruses like influenza or SARS-CoV-2 due to reservoirs, mutations, and global spread.

Crux

To sum up, the JN.1 variant is a mutation of the Omicron BA.2.86 lineage, not a new strain from a single origin like Wuhan. It likely emerged globally through natural evolution, with no specific source country identified.

It’s extremely difficult to eliminate viruses like SARS-CoV-2 or influenza due to reservoirs, mutations, and human factors. The Spanish flu virus’s descendants persist in modern H1N1 strains with reduced potency, not as the original 1918 virus, supporting the claim that it’s “still around” in an evolved, less harmful form.