Rapid replacement of prevailing genotype of human respiratory syncytial virus by genotype ON1 in Beijing, 2012-2014

- A PCR method was developed to identify the novel genotype ON1 of HRSV.
- Rapid replacement of prevailing genotype by ON1 was found in Beijing, 2012-2014.
- The evolutionary rate of the global ON1 strains was higher than previously estimated.
- The time of most recent common ancestor of ON1 strains dated back to June 2009.

Human respiratory syncytial virus (HRSV) is the most common viral pathogen causing lower respiratory infections in infants and young children worldwide. HRSV ON1 genotype in subgroup A with a characteristic of a 72 nucleotide duplication in the second highly variable region of attachment glycoprotein gene, has been reported in some countries since it was first detected in clinical samples collected in Canada in 2010. In this study, 557 HRSV antigen-positive nasopharyngeal aspirates were randomly selected during 2012/2013 to 2013/2014 HRSV seasons in Beijing for subgroup typing and for ON1 genotype screening by using a PCR based method developed for easily identifying genotype ON1 out of strains of subtype A. It was found that subgroup B was dominant in the 2012/2013 season and sudden shift of subgroup dominance from B to A and rapid replacement of previously prevailing NA1 genotype by ON1 genotype occurred in the 2013/2014 season. Reversible amino acid replacement in the G protein gene was found in a new branch of ON1 genotype. The evolutionary rate of the 351 global ON1 sequences was estimated to 7.34 × 10−3 nucleotide substitutions per site per year (95% highest probability density intervals, HPD, 5.71 × 10−3 to 9.04 × 10−3), with the time of most recent common ancestor dating back to June 2009.