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

## TL;DR

This paper introduces a complete workflow for sequencing the entire genome of respiratory syncytial virus using both short and long-read methods, enabling better tracking of virus lineages and mutations.

## Contribution

The novel contribution is a validated workflow combining tiling amplicon protocols and a custom bioinformatic pipeline for RSV whole-genome sequencing.

## Key findings

- The workflow successfully identified RSV sequences with monoclonal antibody resistance mutations.
- The method detected coinfections in clinical samples.
- The pipeline was validated using clinical samples for accuracy and reliability.

## 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.

The online version contains supplementary material available at 10.1186/s13073-025-01597-4.