Most changes in JN.1 sub-variant are found in the spike protein, which could lead to increased infectivity and immune evasion.
This latest Covid wave has been attributed to the new subvariant JN.1.
Kerala reported a sub-variant of Covid-19 — JN.1 — on 8 December.
A sample collected from a 79-year-old woman returned positive in an RT-PCR test on 18 November. She exhibited mild symptoms of influenza-like illnesses (ILI) and had recovered from Covid-19.
More than 90 percent of Covid-19 cases now in India are mild and the patients are in home isolation, sources said.
The JN.1 sub-variant — first identified in Luxembourg and since spreading to several countries — is a descendant of the Pirola variant (BA.2.86.1.1). The nomenclature conventions dictate changing alphabet letters when names become lengthy.
It contains a significant number of unique mutations, particularly in the spike protein, that may contribute to increased infectivity and immune evasion.
This sub-variant’s resemblance to earlier sub-strains with distinct spike proteins is also noteworthy.
Most changes in the JN.1 sub-variant are found in the spike protein, which likely correlates to increases in infectivity and immune evasion.
Globally, 3,608 cases of BA.2.86 and its sub-variants have been reported, mostly from Europe and North America.
The US Centers for Disease Control and Prevention (CDC), however, said initial data suggest that updated Covid-19 vaccines will help protect against JN.1 sub-strain.
It also said an analysis from the federal government’s SARS-CoV-2 Interagency Group suggested treatments and testing will be effective.
JN.1, identified as the rapidly spreading Covid variant globally, initially accounted for just one in 1,000 Covid infections in the US by late October. However, its prevalence surged in December, reaching one in five infections.
JN.1 evolved from BA2.86, a variant that gained attention globally over the past few months, due to its vast number of mutations. Several instances of BA2.86 were observed worldwide, drawing interest from scientists and the World Health Organization (WHO).
Speaking to South First, physician and Co-Chairman of the National Indian Medical Association Covid Task Force, Dr Rajeev Jayadevan said that the majority of sequences during the last surge in India in April 2023 belonged to the XBB lineage, a recombinant variant of Omicron.
XBB resulted from the genetic material mixing of two distinct Omicron sub-lineages in the same individual within the same cell, likely originating in the East Asian region.
“While BA2.86 appeared in the second half of 2023, it initially showed slow growth. In October, JN.1 emerged as a variant of BA2.86, distinguished by an additional spike mutation, the L455S mutation. This spike mutation is likely crucial, affecting the virus’s ability to evade human immune response and to enter cells, potentially conferring unique properties to JN.1 not present in BA2.86,” Dr Jayadevan said.
JN.1’s rapid global spread, including in India, is likely due to international travel. Asymptomatic carriers, coupled with limited testing, contribute to the virus’s dissemination.
“The rise of JN.1 in India is anticipated, with early reports from Kerala in the INSACOG database. More sequencing results are pending, akin to awaiting blood test results, and in the coming weeks, a clearer profile of JN.1’s prevalence is expected,” said
The pandemic situation in India, which had been relatively subdued since April, might thus change during this winter season.
Earlier, an Indian traveller was detected with JN.1 sub-variant in Singapore. The person was from Tamil Nadu’s Tiruchirapalli district and had travelled to Singapore on October 25.
No increase in cases was observed in Tiruchirapalli district or other places in Tamil Nadu following the strain being detected in them.
“No other case of JN.1 variant has been detected in India,” the source said.
So what if there is a surge in the JN.1 variant in the country? Will the vaccination which over a billion people have received in the past two years hold against the variant?
Health officials said initial data suggested that updated vaccines and treatments will still offer protection against JN.1 sub-strain.
The vaccines administered in India were developed based on the original version of the virus, which has undergone significant changes. These vaccines may have an immune response that was initially designed for the original variant.
“Using a metaphor, it’s like employing a spanner that might not be a perfect fit. While the antibodies generated by the vaccines may not perfectly match the evolved virus, there is still some level of cross-protection. The analogy highlights that although the response may not be an exact fit, the vaccines could still effectively work,” Dr Jayadevan said.
He added that the challenge lies in determining whether a perfect-fitting “spanner” (antibodies precisely tailored to the current virus) is necessary and, if so, how long such a fit would remain valid. The prospect of frequent adjustments raises concerns about practicality, costs, and potential side effects.
The rollout of the XBB 1.5 monovalent booster in the US showcased the ability to rapidly develop updated vaccines in response to virus evolution. However, the low uptake (17%) suggested a lack of public confidence about any incremental benefit in a person who is already vaccinated.
The fast evolution of the virus is a challenge for vaccine developers. For instance, JN.1 has already shown to be more resistant to the latest XBB.1.5 monovalent vaccine than other recent variants.
“Vulnerable individuals should exercise caution to avoid infection, considering the severity of recent cases, particularly among older populations. The observed rise in severe infections, oxygen requirements, and ICU admissions during the present surge emphasizes the ongoing threat,” Dr Jaydevan further stated.
He added that given the large population of older individuals in India, their susceptibility to the virus raises questions about the necessity of additional vaccine doses. The decision on whether to administer further vaccine doses requires complex consideration of factors such as incremental efficacy, safety, costs, and the rapidly evolving nature of the virus.
The first crucial point to understand is that the levels of immunity in India, Western nations, and basic human biology are essentially the same. Many people in India, much like in Western nations, have encountered the same virus through 1-3 infections plus a two-dose vaccine regimen, in total amounting to at least 3-4 immune encounters.
“Given this shared exposure, if a new variant like JN.1 is rapidly spreading in the West, it is likely to follow suit in India. Denial of this possibility is unproductive, but it’s equally important not to create panic,” Dr Jayadevan said.
He added that the next key consideration is to implement measures to reduce the intensity of the variant’s spread. Testing and sequencing play a crucial role, particularly during surges, in identifying clusters and unusual patterns. However, testing poses challenges in India, where there is reluctance, lack of financial resources, and limited availability of free tests compared to the West.
Monitoring and preparedness are essential, especially in high-travel zones like Kerala, Mumbai, Delhi, Goa, Bengaluru, and Hyderabad, where large populations move around globally, also contributing to the virus’s transmission.
“The paradox of wanting to test but facing financial constraints should be addressed, and efforts should be made to ensure that testing is accessible to all,” Dr Jayadevan opined.
He further added that amid these challenges, the top priority is to keep vulnerable populations safe. Every individual, regardless of age, has an equal right to live and remain healthy, and this principle should guide healthcare planning. With the emergence of the new variant, health officials should be prepared, acknowledging that the variant is already present and spreading globally.
India’s unique challenges, including a dense population, existing communicable diseases, and a high burden of non-communicable diseases (NCDs), further complicate the situation. Addressing the complexities of the healthcare system and maintaining a balance between treating the new variant with the respect it deserves and preventing a sense of hopelessness among the population are crucial aspects that require serious attention.
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