Appearance and Prevalence of JN.1 SARS-CoV-2 Variant in India and Its Clinical Profile in the State of Maharashtra

Rajesh P Karyakarte; Rashmita Das; Mansi V Rajmane; Sonali Dudhate; Jeanne Agarasen; Praveena Pillai; Priyanka M Chandankhede; Rutika S Labhshetwar; Yogita Gadiyal; Preeti P Kulkarni; Safanah Nizarudeen; Sushma Yanamandra; Nyabom Taji; Suvarna Joshi; Varsha Potdar

doi:10.7759/cureus.56718

Appearance and Prevalence of JN.1 SARS-CoV-2 Variant in India and Its Clinical Profile in the State of Maharashtra

Cureus. 2024 Mar 22;16(3):e56718. doi: 10.7759/cureus.56718. eCollection 2024 Mar.

Authors

Rajesh P Karyakarte^{1

2}, Rashmita Das^{1

2}, Mansi V Rajmane¹, Sonali Dudhate¹, Jeanne Agarasen¹, Praveena Pillai¹, Priyanka M Chandankhede¹, Rutika S Labhshetwar¹, Yogita Gadiyal¹, Preeti P Kulkarni¹, Safanah Nizarudeen¹, Sushma Yanamandra¹, Nyabom Taji¹, Suvarna Joshi¹, Varsha Potdar^{3

4}

Affiliations

¹ Microbiology, Byramjee Jeejeebhoy Government Medical College and Sassoon General Hospitals, Pune, IND.
² Microbiology, Byramjee Jeejeebhoy Government Medical College, Pune, IND.
³ Infectious Diseases, Indian Council of Medical Research, National Institute of Virology, Pune, IND.
⁴ Pediatrics, Byramjee Jeejeebhoy Government Medical College, Pune, IND.

Abstract

Background: In August 2023, the BA.2.86 SARS-CoV-2 variant, with over 30 spike protein mutations, emerged amidst the global dominance of XBB sub-lineages. It evolved into JN.1 by late 2023, spreading across 71 countries. JN.1, distinct for its L455S mutation, significantly dominated global sequences, raising concerns over its transmission and clinical impact. The study investigates JN.1's clinical severity and its effect on hospital admissions in Maharashtra, India.

Methodology: The present study involved 3,150 curated Indian SARS-CoV-2 whole genome sequences with collection dates between 1st August 2023 and 15th January 2024. Lineage and phylogenetic analysis of sequences was performed using Nextclade. Telephonic interviews were conducted to confirm the demographic details and obtain clinical information on the JN.1* (* indicates JN.1 and all its sub-lineages) cases. The obtained data were recorded and analyzed using Microsoft® Excel (Microsoft Corporation, Redmond, WA).

Results: Out of 3,150 sequences analyzed, JN.1* was the most common lineage (2377/3150, 75.46%), followed by XBB.2.3* (281/3150, 8.92%) and XBB.1.16* (187/3150, 5.94%). In India, it was first identified on 6th October 2023, in Kerala. The highest proportion of JN.1* sequences originated from Maharashtra (628/2377, 26.42%), followed by West Bengal (320/2377, 13.46%), Andhra Pradesh (293/2377, 12.33%), Kerala (288/2377, 12.12%), and Karnataka (285/2377, 11.99%). In Maharashtra, the JN.1* variant was first identified on 23rd November 2023. A total of 279 JN.1* cases were included in the clinical study. Of these, 95.34% (266/279) had symptomatic disease with mild symptoms; cold (187/279, 67.03%) being the most common symptom, followed by fever (156/279, 55.91%), cough (114/279, 40.86%), and headache (28/279, 15.64%). Of all the cases, 13.26% (37/279) required institutional quarantine or hospitalization, and the rest were isolated at home. Among the hospitalized patients, 54.05% (20/37) cases were given conservative treatment while 45.95% (17/37) cases required supplemental oxygen therapy. Regarding the vaccination status, 94.26% (263/279) of cases received at least one dose of the COVID-19 vaccine, while 5.02% (14/279) were not vaccinated, of which most were children aged zero to nine years (5/14, 35.71%). The overall recovery rate among JN.1* cases was 98.57% (275/279), with 1.43% (4/279) cases succumbing to the disease.

Conclusion: The JN.1* variant, the dominant variant in India, exhibits clinical features similar to previous circulating variants in Maharashtra without increased severity. Its notable transmissibility underscores the importance of studying the ongoing viral evolution. The pressing necessity for swift identification and the clinical features of new variants is essential for effective public health response.

Keywords: ba.2.86; ba.2.86.1.1; clinical characteristics; covid-19; covid-19 disease; jn.1; pirola; sars-cov-2; severe acute respiratory syndrome coronavirus 2.