JN.1 Covid variant: Should we worry?

A 78-year-old Kerala woman on Saturday became the first person in India confirmed to be infected with JN.1 variant of Sars-CoV-2 — the latest sub-variant of the virus that is behind a spike of infections in several countries across the world and has also prompted the World Health Organization (WHO) to warn nations to continue with strong surveillance and sequence sharing.

While the patient in Kerala reported mild symptoms and has even recovered from her infection since, the Union health ministry, keeping in mind how this sub-variant has led to a resurgence in cases and become the dominant strain in several nations, asked states on Monday to step up Covid surveillance as a matter of abundant precaution.

Here, we take a look at why this strain has given many countries reason to step up their battle against Covid-19 again, with nations like Singapore deciding to reinforce a public masking mandate, but just as importantly, why it is not yet a reason for panic.

What is the JN.1 variant?

The JN.1 sub-variant a new sub-lineage of the BA.2.86 (also known as Pirola) — by itself an off-shoot of the widely circulating Omicron variant — which experts have warned appears to be more immune evasive, and has been identified in November by WHO scientists as a Variant of Interest (VOI).

It was first reported in Denmark and Israel, according to GISAID, a global science initiative that provides access to genomic data of influenza viruses. So far, according to GISAID data, more than 6,600 samples of BA.2.86 and its sub-lineages (including JN.1) have been sequenced in several countries including China, the UK, Iceland, Spain, Portugal, and the Netherlands.

The JN.1 variant of BA.2.86, which was first detected by the US Centers for Disease Control and Prevention (CDC) in September 2023, has one additional substitution in the spike protein (L455S), and its continued growth suggests that it is either more transmissible or better at evading our immune systems, experts have suspected.

WHO’s technical lead Maria Van Kerkhove explained the reason for the recent surges, and what precautions can be taken. “Respiratory diseases are increasing around the world due to a number of pathogens incl Covid-19, flu, rhinovirus, mycoplasma pneumonia and others. SARS-CoV-2 continues to evolve. JN.1 (sub-variant of BA.2.86) is already a VOI and continues to increase in circulation,” she wrote on X.

To be sure, Sars-CoV-2 — the virus that causes Covid-19 — has seen a near-continuous series of mutations since it was detected in late 2019. Some of these new variants, such as the Delta variant that was circulating in early 2021 proved to be far more fatal than previously circulating variants, while others such as the Omicron variant that was circulating through most of 2022 ended up being highly infectious while still being mild in terms of fatalities. In the case of latter, the majority of population across the world had acquired some form of immunity, either through vaccines or previous infections — both factors that remain in play even now.

This means that while new variants crop up naturally with time and spread of a virus, it may not necessarily mean that the newer variants are more dangerous, even if they end up becoming the common, or dominant strains, relative to other variants in circulation in a region.

Where is it circulating, and how is it effecting the outbreak?

According to data compiled by GISAID, of the total 15,416 positive cases of Covid-19 sampled across 56 countries, 43% (6,682) samples have returned positive for BA.2.86 or its sub-variants including JN.1. At least 35 nations have so far reported to GISAID the presence of the variant. Among them, six regions — Spain, Singapore, Brazil, Belgium, Netherlands and Malaysia — have found the variant in more than 50% of positive samples they have sequenced, data shows. In Spain and Singapore, close to two-thirds of all samples sequenced have come back positive for this variant, data shows.

In the US, CDC projects that JN.1 will continue to increase as a proportion of Sars-CoV-2 genomic sequences. Currently, around a fourth of all positive samples being sequenced in the US are returning positive for JN.1, according to CDC data.

In Singapore, this variant is being attributed for a massive resurgence in Covid-19 cases. Average new infections in the city-state have jumped from 1,532 cases a day two weeks ago, to 8,006 new cases a day for the week ended December 9, according to government data. Keeping this in mind, Singapore on Monday reintroduced the mandatory use of masks in crowded places, particularly indoors.

India, meanwhile, has also seen a spike in infection numbers in the past few weeks. On average, 252 new infections were reported across the country in the week ended December 17, according to HT’s Covid-19 dashboard. This number was 125 a week ago, and was 59 the week before that. The number of average daily deaths, however, have remained stagnant.

Symptoms and severity

Despite the surge in cases, Singapore has yet to report a death attributed to Covid-19 since at least early November, according to global data compiled by Our World In Data. In the US, meanwhile, the seven-day average of daily deaths from Covid-19 has dropped from 177 for the week ended December 2, to 103 deaths for the week ended December 9 (the latest this data has been released). The numbers in other countries where JN.1 has been reported are similar.

In India, on average 0.9 deaths have been reported every day in the past week — this number was the same the week before that. While reading this figure, what should be kept in mind is India’s massive population, which gives context to how small this number truly is.

These early numbers are backed by authorities.

According to WHO, as things stand, there is no evidence that JN.1 presents an increased risk to public health relative to the other circulating variants. There is no indication of increased severity from JN.1 at this time; a pre-print study — Virological characteristics of the SARS-CoV-2 JN.1 variant — however, suggests that the variant has shown increased infectivity as compared to BA.2.86.

Scientists as US CDC have stressed that it is not currently known whether JN.1 infection produces different symptoms from other variants. In general, symptoms of Covid-19 tend to be similar across variants. The types of symptoms and how severe they are usually depend more on a person’s immunity and overall health rather than which variant causes the infection.

Vaccine efficacy

This is where the best news concerning the new variant lies. According to both WHO and CDC, updated vaccines are entirely effective against JN.1. According to WHO, sera from patients who had Omicron breakthrough infections (including XBB), exhibited robust neutralising activity against BA.2.86, suggesting that upcoming XBB.1.5 monovalent vaccines could confer added protection, by triggering the expansion of existing B cells that will enhance cross-protection against BA.2.86 and its descendant lineages (including JN.1). In addition, the existing Covid-19 tests and treatments are also expected to be effective against JN.1.