Molecular epidemiology of human rhinovirus from clinical cases of Dibrugarh, Assam, India

PURPOSE: Human rhinovirus (HRV), a member of the Enterovirus genus of the Picornaviridae family is a major respiratory pathogen and the leading cause of upper respiratory tract infections. Given the limited information on HRV prevalence and molecular epidemiology in Northeast India, this study investigated circulating HRV strains in the region from 2015 to 2018. METHODS: Nasopharyngeal and throat swab samples were collected and RNA was extracted for HRV detection using qRT-PCR. HRV-positive samples were subjected to bidirectional Sanger sequencing targeting the 549 bp VP4/VP2 region. Obtained sequences were aligned and analyzed phylogenetically using bioinformatics tools to determine genotype distribution and genetic diversity. RESULTS: Among 2642 cases, 354 (13.3 %) tested positive for HRV. HRV-C was the predominant species (48.7 %), followed by HRV-A (38.4 %) and HRV-B (7.6 %). HRV infection was significantly associated with lower respiratory symptoms such as cough (p < 0.001) and breathlessness (p < 0.026). The study identified 27 different HRV genotypes in the 39 sequenced samples, with HRV-C15 being the most common (9/39) overall and associated with disease severity (p = 0.003). Seasonality analysis indicated peak HRV circulation between August and November (48.8 %, 173/354), with the lowest detected in June-July (14.1 %). HRV-C was more frequently observed in severe acute respiratory infection (SARI) cases and demonstrated the highest heterogeneity, with an intra-species nucleotide mean p-distance of 24.0 %. CONCLUSION: In conclusion, this study presents the first report on the prevalence of human rhinovirus (HRV) among influenza-like illness (ILI) cases in Dibrugarh, Assam, India. HRV-C exhibited distinct epidemiological characteristics compared to HRV-A and HRV-B strains. Molecular epidemiological analysis revealed notable nucleotide variation in the VP4/VP2 region, with HRV-C15 emerging as the predominant genotype associated with increased disease severity. Further research involving larger sample sizes and detailed clinical follow-up is essential to better understand the genotype distribution and genetic diversity of HRV strains circulating in the region.