Respiratory Syncytial Virus Genotype ON1 Within-host Populations in Hospitalized Children: Deletion of the 72-Nucleotide Duplication in the G Gene

BACKGROUND: Respiratory syncytial virus (RSV) is the major pathogen of lower respiratory tract infection in infants and young children. Molecular epidemiology studies allow the surveillance of circulating RSV genotypes worldwide. However, comprehensive data about the genetic variability of RSV strains within an individual host is lacking. The objective of this study was to investigate the genetic within-host variability of RSV strains in pediatric patients in Heidelberg, Germany. METHODS: Nasopharyngeal swabs (NPS) were prospectively screened for RSV from children admitted with acute respiratory tract infection to the Heidelberg University Hospital during the winter seasons 2012-2016. RSV-positive samples with detection of RSV-A genotype ON1 were selected for deep sequencing by next-generation sequencing. RESULTS: In a total of 121 RSV-A genotype ON1 (GA 2.3.5)-positive samples, the second hypervariable region of the G gene was successfully deep sequenced via next-generation sequencing. The dominant RSV within-host variants all belonged to genotype ON1 (GA 2.3.5) and could be divided into 9 different lineages. Deep sequencing revealed that 67.7 % ( n = 82/121) of all samples comprised at least 2 different viral strains of RSV that represented at least 1% of within-host variants. The majority of these samples (67.1%; n = 55/82) contained RSV-A variants that had lost 72-nt-duplication characteristic for genotype ON, representing 1%-3% of within-host variants. CONCLUSIONS: Deep sequencing revealed a substantial genetic within-host variability of RSV in hospitalized children, and we first described the loss of the characteristic ON1 72-nt-duplication in children.