Tracking KP.2 SARS-CoV-2 Variant in India and the Clinical Profile of KP.2 Cases in Maharashtra, India

Following the emergence of the JN.1 SARS-CoV-2 variant, variants with key mutations in the spike protein, such as L455F, F456L, and R346T, were identified. In early January 2024, the KP.2 (JN.1.11.1.2) variant was first identified in clinical samples. Its increasing global prevalence has raised concerns over its transmission and clinical impact. The study investigates KP.2*'s (*indicates KP.2 and all its sub-lineages) spread and clinical severity in Maharashtra.

This study involved 5,173 Indian SARS-CoV-2 whole genome sequences with collection dates between November 1, 2023 and June 24, 2024. Lineage analysis of sequences was performed using Nextclade software (version 3.8.0). Telephonic interviews were conducted to confirm the demographic details and obtain clinical information on the KP.2* cases. The obtained data were recorded and analyzed using Microsoft® Excel (Microsoft Corporation, Redmond, WA).

Among the 5,173 sequences analyzed, JN.1* appeared as the predominant lineage (65.96%, 3412/5173), followed by KP.2* (7.83%, 405/5173) and KP.1* (3.27%, 169/5173). In India, KP.2* was first detected on December 2, 2023, in Odisha. The majority of KP.2* sequences were from Maharashtra (248/405, 61.23%), followed by West Bengal (38/405, 9.38%), Gujarat (27/405, 6.67%), and Rajasthan (24/405, 5.93%). Maharashtra reported its first KP.2* sequences on January 24, 2024. The clinical study included 160 cases of the KP.2* variant from Maharashtra. Of these, 95.63% (153/160) presented with mild symptoms, such as fever (108/160, 67.50%), cold (87/160, 54.38%), cough (80/160, 50%), sore throat (44/160, 27.5%), body ache (43/160, 26.88%), and fatigue (42/160, 26.25%). About 33.13% (53/160) of the cases required institutional quarantine or hospitalization, with the rest managed at home. Among those hospitalized, 50.94% (27/53) received conservative treatment, while 49.06% (26/53) needed supplemental oxygen, steroids, or antiviral therapy. Regarding the vaccination status, 89.38% (143/160) of the cases had received at least one dose of the COVID-19 vaccine, whereas 10% (16/160) were unvaccinated, with the majority of the unvaccinated being children aged zero to nine years (7/16, 43.75%). The overall recovery rate for KP.2* cases was 99.38% (159/160), with only 0.62% (1/160) succumbing to the disease.

The KP.2 variant has become the dominant SARS-CoV-2 variant in India and Maharashtra. Despite the affected individuals experiencing mild symptoms, studies have shown lower neutralization titers and high infectivity due to FLiRT mutations, suggesting KP.2's potential rise to global dominance.