Molecular characterization of human respiratory syncytial virus NA1 and GA5 genotypes detected in Assam in northeast India, 2009-2012.

A significant number of children die each year from acute respiratory tract infections especially in developing countries. Human respiratory syncytial virus (RSV) is the most common virus identified in such cases. Genetic characterization and the circulation pattern of RSV is important for future selection of appropriate vaccine strains. Limited information is available on the circulation of RSV in developing countries including India. The present study aimed to provide baseline information on the genetic variability of RSV in the Dibrugarh district of Assam, northeast India. Clinical specimens collected from children aged ≤6 years for routine influenza surveillance in the Dibrugarh district of Assam during the period 2009-2012, were screened for RSV by real-time reverse transcription-polymerase chain reaction. Genotyping was based on partial sequencing of the RSV attachment glycoprotein gene. RSV was detected in 7.9% (39/493) of cases. Only RSV group A viruses were detected during the study period with predominance of NA1 genotypes (89%). Two RSV GA5 genotypes were found to be co-circulating during 2012. The specific amino acid substitutions characteristics of the NA1 genotypes were distinct from RSV strains reported from the rest of India. It is concluded that the circulating genotypes of RSV in Assam, northeast India are NA1 and GA5. To our knowledge this is the first report of circulation of the NA1 genotype in India.