India reports 21 cases of COVID sub-variant JN.1, now a WHO ‘variant of interest’

Rising COVID-19 cases have put authorities on high alert, with a focus on the COVID sub-variant JN.1. India’s case count of JN.1 reached 21 on December 20. Nineteen of these were traced to Goa. One each was detected in Kerala and Maharashtra.

“About 91 to 92 per cent of those infected are opting for home-based treatment,” NITI Aayog member (Health) VK Paul said, according to news agency Press Trust of India.

Union Health Minister Mansukh Mandaviya virtually chaired a high-level meeting with state health ministers on December 20 to assess the current status. He said states need to do a mock drill every three months.

“We need to be on the alert, but there is no need to panic. It is important to be prepared with mock drills of hospital preparedness, increased surveillance, and effective communication with people,” Mandaviya added.

COVID-19 data analyst NC Krishna Prasad had previously told Down to Earth (DTE) that India witnessed 19 COVID-19 deaths in December. Meanwhile, the media has reported 16 deaths so far this month.

On December 19, 614 fresh cases of COVID-19 were reported. This is the highest number of daily cases since May 20. Kerala reported 2,041 of 2,311 active cases, the highest number since June 11 and the highest in the state since May 24, Prasad told DTE. The rise in cases in Kerala has been attributed to a robust reporting system within the state.

In the wake of the surge, the World health Organization (WHO) is now closely monitoring the COVID sub-variant JN.1 and has classified it as a variant of interest (VOI).

“Based on the available evidence, the additional global public health risk posed by JN.1 is currently evaluated as ‘low’. Despite this, with the onset of winter in the Northern Hemisphere, JN.1 could increase the burden of respiratory infections in many countries,” WHO stated.

It was earlier clubbed together as a VOI as part of BA.2.86 sub-lineages.

What is a variant of interest?

In addition to JN.1, WHO is currently tracking four other VOIs: XBB.1.5, XBB.1.16, EG.5, and BA.2.86, all of which are descendants of omicron sub-variants.

“A VOI indicates that the country has to keep a close eye on three things: genomic surveillance, epidemiology (how a VOI spreads), and the variant’s clinical behaviour (its seriousness and increase in hospitalisations),” N K Arora, chief of the Indian SARS-COV-2 Genomics Consortium (INSACOG), told DTE. INSACOG is a network of genomic laboratories across India.

WHO updated its working definitions for variants of concern (VOCs), VOIs, and variants under monitoring (VUMs) in March 2023.

According to the definition, a VOI variant is considered a SARS-CoV-2 variant with genetic changes that are predicted or known to affect virus characteristics such as transmissibility, virulence, antibody evasion, susceptibility to therapeutics, and detectability.

Further, VOI variants are identified to have a growth advantage over other circulating variants in more than one WHO region, with increasing relative prevalence alongside an increasing number of cases over time. They should also have other apparent epidemiological impacts to suggest an emerging risk to global public health, the WHO states.

For declaring a variant as a potential VOI, WHO is required to review global epidemiology, monitor and track global spread, facilitate the sharing of virus isolates via WHO Biohub, and coordinate laboratory investigations with Member States and partners if needed.

After member states are alerted, countries are encouraged to submit complete genome sequences to a publicly available database such as the Global Initiative on Sharing All Influenza Data (GISAID), a genomic database of influenza viruses. India is the third largest contributor globally to GISAID.

WHO COVID-19 technical lead, Maria Van Kerkhove posted on X (formerly Twitter) saying, “As of 16 December 2023, 7,344 JN.1 sequences had been submitted to @GISAID from 41 countries, representing 27.1% of the globally available sequences in epidemiological week 48 (27 Nov to 3 Dec 2023).”

Countries also have to share virus isolates via WHO Biohub and/or other virus-sharing initiatives when alerted of a VOI.

The countries are required to perform field investigations to improve understanding of the potential impacts of the VOI on COVID-19 epidemiology, severity, effectiveness of public health and social measures, or other relevant characteristics, WHO says.

A higher level of monitoring is designated by the WHO for VOCs. After meeting the definition of VOI, the variant has to have at least one of the following characteristics to be classified as a VOC: 

• Detrimental change in clinical disease severity; 
• Change in COVID-19 epidemiology causing a substantial impact on the ability of health systems to provide care to patients with COVID-19 or other illnesses and therefore requiring major public health interventions;
• Significant decrease in the effectiveness of available vaccines in protecting against severe disease.

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