Tracing the emerging genotypes of human respiratory syncytial virus in Beijing by evolution analysis of the attachment glycoprotein (G) gene

Background: Emerging human respiratory syncytial virus (HRSV) genotypes, such as ON1 and BA9, are becoming the dominant genotypes prevailing worldwide. Objective To trace the emerging HRSV genotypes in Beijing. Methods: HRSV-positive specimens as determined by direct immunofluorescence, collected from children diagnosed with bronchiolitis from July 2006 to June 2016, were typed by real-time PCR, then genotyped by phylogenetic analyses of the full attachment glycoprotein (G) gene. A Bayesian skyline plot was constructed to analyze the population dynamics for identified HRSV strains, and selective pressure was analyzed. Results: The previous dominant HRSV A genotype, NA1, was replaced by ON1 in 2014. BA9 was the dominant HRSV B genotype for the duration of the study. The time to the most recent common ancestor (tMRCA) for HRSV A is since the 1943-1944 season; for the genotypes NA1 and ON1, since the 1999-2000 season and 2010-2011 season, respectively. The tMRCA for HRSV B is since the 1956-1957 season; for the genotypes BA and BA9, from the 1998-1999 season and 2005-2006 season, respectively. The mean evolutionary rate of HRSV A (3.65 x 10(-3 ) was faster than those of HRSV B (3.11 x 10(-3)), and the genotypes NA1 (2.01 x 10(-3)) and ON1 (1.66 x 10(-3)). The estimated effective population size (EPS) infected by HRSV A changed significantly from 2012 to 2013, which is consistent with the detection of ON1. Most positive selection sites were concentrated in the second highly variable region (HVR2) of the G gene. Conclusions: Over the 10-year period from 2006 to 2016, the dominant genotypes in Beijing were NA1, ON1, and BA9. The HRSV strains in Beijing may have their own unique phylogenetic characteristics.