Genetic characterization of respiratory syncytial virus highlights a new BA genotype and emergence of the ON1 genotype in Lyon, France, between 2010 and 2014

Background: Respiratory syncytial virus (RSV) is a well-recognized cause of respiratory tract infections. Based on G gene variations, 11 RSV-A and 36 RSV-B genotypes have been described to date. The ON1 genotype was detected in Ontario in 2010 and subsequently reported in several countries. Objectives: The objective of the present study was to investigate for the first time the RSV epidemiology and genotype diversity in France between 2010 and 2014. Study design: All respiratory samples received from patients with influenza-like illness or respiratory tract infection were screened for RSV infection by RT-PCR. The results were stratified according to winter season. Among the RSV-positive cases, 117 samples were further investigated for phylogenetic analysis out of 150 randomly selected for sequencing. Results: Among the 20,359 cases screened, 14% of the cases were RSV-positive. RSV-A was predominant during the four winter seasons. The first ON1 variant was detected during the 2010-2011 winter and reached 85% of all RSV-A-positive cases in 2013-2014. Most RSV-B was classified as BA9 and BA10 genotypes but a new genotype (BA-Ly) was described. Conclusion: As reported in different countries, ON1 variants were firstly detected in 2011 and became the predominant RSV-A genotype in Lyon. Among RSV-B, BA9 was predominant but detected alongside BA10 or a transient genotype (BA-Ly).