A bench-to-data analysis workflow for respiratory syncytial virus whole-genome sequencing with short and long-read approaches

Abstract Genomic surveillance of respiratory syncytial virus (RSV) enables detecting and monitoring of circulating lineages and the emergence of amino acid substitutions affecting transmission, severity, and treatment. We present a comprehensive workflow for RSV whole-genome sequencing, from sample processing to lineage classification. Tiling amplicon protocols adapted for Illumina and Oxford Nanopore Technologies sequencing approaches and an in-house bioinformatic pipeline were developed for the analysis of samples. We validated the workflow on clinical samples, and identified RSV sequences harbouring substitutions associated with monoclonal antibody resistance and the presence of coinfections.