Genomic surveillance of SARS-CoV-2 and emergence of JN.1 variant in Rajasthan

Objectives JN.1 was initially identified as a variant of Interest (VOI) by the World Health Organization (WHO), and was later recognized as a distinct VOI, after which the government of India issued an advisory to states for genome sequencing of COVID positive samples. Material and Methods A total of 335 throat/nasopharyngeal swabs of SARS-CoV-2 positive patients were received at Sawai Man Singh Medical College (SMSMC), Jaipur, from 19-12-23 till 18-04-24 for whole genome sequencing, of which 223 samples that were found positive for SARS-CoV-2 and having a Ct value <25 were further processed for sequencing. Results Out of 206 lineages identified, 62.14% (128) were JN.1 and 37.86%(78) were other lineages. Among the total 128 JN.1 cases identified, 60.16% were males and 39.84% were females. 14.84% were <18 years, 57.03% were in the age group 19-59 years, and 28.13% were ≥60 years of age. 22.65% cases were asymptomatic, while 77.34% cases were symptomatic. Re-infection was found in 23.44% (30) of cases. The maximum positive cases were from the Jaipur district. The majority (81.25%,104) of the JN.1 infected cases were already vaccinated, 3.91% (5) were unvaccinated, while 14.84% (19) were not eligible for vaccination. Co-morbidities/other conditions were present in 23.44% (30) of patients. Hospitalization was required in 18.75% (24) of cases. Only one patient had a history of international travel. Death due to COVID was reported in 2 cases. Conclusion Rapid spread of JN.1 variant implicates continuous evolution of the virus and emphasizes continuous monitoring for timely detection of new variants.