Genetic diversity and trends of influenza A (H3N2) virus in Puducherry, South India: Insights from the 2022–2023 season

PURPOSE: Influenza viruses are the most common causative agents of acute respiratory infections (ARIs), known for their frequent genomic changes, which necessitate close genetic monitoring to track emerging strains. This study aims to determine seasonal trends of H3N2 from 2019 to 2023 and to molecularly characterize H3N2 from August 2022 to March 2023 among ARI patients. METHODS: During the study, 7099 respiratory samples were tested for viruses such as Influenza A and Influenza B. Clinical samples that tested positive for influenza A (H3N2) by reverse transcriptase polymerase chain reaction (RT-PCR) and exhibited a cycle threshold (Ct) value ≤ 27, which is indicative of high viral load, were selected for HA gene sequencing. FluSurver was used to identify variations in amino acids. Categorical variables, such as positivity of influenza virus and its subtypes, were reported as percentages. RESULTS: Influenza A was the predominant causative agent, detected in 13.4% (950/7099) of all samples tested during the study period. The seasonality analysis revealed that H3N2 peaked from July to November of 2019 and September to November of 2021. Whereas in 2022 the peaks shifted to post November, extending upto March 2023. Among samples tested between January and March 2023 (n = 2900), H3N2 was the dominant subtype, accounting for 11.48% (333/2900) of cases. Most viral gene sequences (n = 20) clustered under clade 2a.3a.1, with two sequences in clade 2b and one in clade 2a.3. CONCLUSION: We observed a shift in the seasonality of H3N2 post-pandemic. This study explored the relationship between genetic and antigenic changes in H3N2 viruses. These findings underscore the need for genomic surveillance of evolving strains.