Genomic surveillance of SARS-CoV-2 and emergence of JN.1 variant in Rajasthan
Swati Gautam, Pratibha Sharma, Abhaya Sharma, Dinesh Parsoya, Farah Deeba, Nita Pal, Ruchi Singh, Himanshu Sharma, Neha Bhomia, Ravi Prakash Sharma, Varsha Potdar, Bharti MalhotraObjectives
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.