Predominance of ON1 and BA9 genotypes of respiratory syncytial virus (RSV) in Bulgaria, 2016‐2018

The objectives of this study were to investigate the prevalence of respiratory syncytial virus (RSV) infections in Bulgaria, to characterize the genetic diversity of the RSV strains, and to perform amino acid sequence analysis of the RSV G protein. Clinical, epidemiological data and nasopharyngeal swabs were prospectively collected from children aged less than 5 years presenting with acute respiratory infections from October 2016 to September 2018. Real‐time polymerase chain reaction for 12 respiratory viruses, and sequencing, phylogenetic, and amino acid analyses of the RSV G gene/protein were performed. Of the 875 children examined, 645 (73.7%) were positive for at least one viral respiratory pathogen. RSV was the most commonly detected virus (26.2%), followed by rhinoviruses (15%), influenza A (H3N2) (9.7%), adenoviruses (9%), bocaviruses (7.2%), human metapneumovirus (6.1%), parainfluenza viruses 1/2/3 (5.8%), influenza type B (5.5%), and A(H1N1)pdm09 (3.4%). The detection rate for RSV varied across two winter seasons (36.7% vs 20.3%). RSV‐B cases outnumbered those of the RSV‐A throughout the study period. RSV was the most common virus detected in patients with bronchiolitis (45.1%) and pneumonia (24%). Phylogenetic analysis indicated that all the sequenced RSV‐A strains belonged to the ON1 genotype and the RSV‐B strains were classified as BA9 genotype. Amino acid substitutions at 15 and 22 positions of the HVR‐2 were identified compared with the ON1 and BA prototype strains, respectively. This study revealed the leading role of RSV as a causative agent of serious respiratory illnesses in early childhood, year‐on‐year fluctuations in RSV incidence, the dominance of RSV‐B, and relatively low genetic diversity in the circulating RSV strains. Highlights We report circulation patterns of RSV in Bulgaria during 2016‐2018. All detected RSV‐A and RSV‐B belonged to the ON1 and B9 genotypes, respectively. Numerous amino acid substitutions, variable N‐ and O‐ glycosylation sites in the HVR‐2 of RSV G proteins were observed.