MOLECULAR EPIDEMIOLOGY OF RSV STRAINS CIRCULATING IN CHILDREN LESS THAN 5 YEARS IN KARACHI, PAKISTAN

Abstract

Intro: Human respiratory syncytial virus (HRSV) is the most important viral cause of severe acute respiratory tract infections in children worldwide. The disease burden of HRSV in low-income countries is poorly studied, but available data indicates that the virus is responsible for a high proportion of childhood acute respiratory tract infections. The aim of the current study was to elucidate the circulating genotypes of RSV strains in hospitalized children less than 5 years in Pakistan. Methods: A total of 1,121 children admitted with respiratory illness such as bronchiolitis and pneumonia were recruited in this study. Nasopharyngeal swabs were collected and real- time-PCR was performed. To genetically characterize the RSV, targeting Matrix gene of RSV from real- time PCR positive samples was amplified using nested rt-PCR and sequenced. The sequences were subsequently aligned with RSV genotype A and B reference sequences and phylogenetic relationship of RSV Matrix gene and its epidemic dynamics was analyzed through a Maximum Likelihood tree. Global pattern of RSV sequenced by utilizing publicly available data from 12 countries and analyzed through Neighbor Joining tree. Findings: Out of the 1,121 samples, 226 (20%) were found positive for RSV using real- time PCR while M gene was amplified only from 46/226 (20%) samples. All the samples clustered with genotype B reference sequences indicating genotype B to be the prevalent strain in the infected children. Majority of the sequence formed a monophyletic cluster, indicating that most of the infection was carried out by a ‘founder virus’ sharing similar genetic characteristics. Conclusion: The study data shows the high prevalence of RSV genotype B in children in Pakistan. Genetic analysis indicated that the RSV infection is carried out by phylogenetically similar genotype B strains evolving from a common founder virus (ancestor). This information can further be explored to understand the epidemic dynamics of RSV in children.