Molecular characterization of human respiratory syncytial virus, 2010-2011: identification of genotype ON1 and a new subgroup B genotype in Thailand

This study reports the molecular epidemiology and genetic characterization of human respiratory syncytial virus (RSV) samples collected in Thailand from January 2010 to December 2011. In total, 1,315 clinical samples were collected from Bangkok and Khon Kaen provinces and were screened by semi-nested PCR for RSV infection. We found 74 samples (27.7 %) and 71 samples (6.8 %) to be RSV positive for Bangkok and Khon Kaen, respectively, and we sequenced 122 of these samples. Phylogenetic analysis revealed that 100 of the RSV-A-positive samples clustered into either genotype NA1 or the recently discovered genotype ON1 strain, which has a 72-nucleotide duplication in the second variable region of its G protein. Moreover, 22 of the RSV-B-positive samples clustered into four genotypes; BA4, BA9, BA10 and genotype THB, first described here. The NA1 genotype was found to be the predominant strain in 2010 and 2011. The ON1 strain detected in this study first emerged in 2011 and is genetically similar to ON1 strains characterized in other counties. We also describe the THB genotype, which was first identified in 2005 and is genetically similar to the GB2 genotype. In conclusion, this study indicates the importance of molecular epidemiology and characterization of RSV in Thailand in order to better understand this virus. Further studies should be conducted to bolster the development of antiviral agents and a vaccine.