Whole-genome nanopore sequencing and automatic downstream analysis of respiratory syncytial virus using RSVTyper

Duyen Bao Le ¹, Inga Tometten ¹, Nadine Lübke ¹

⁰Institute of Virology , University Hospital Düsseldorf Heinrich Heine University Düsseldorf , Düsseldorf, Germany.

Scientific Reports +

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November 1, 2025

View abstract on PubMed

Summary

A new RSVTyper method enables whole-genome sequencing of respiratory syncytial virus (RSV) from patient and wastewater samples. This cost-effective tool aids in tracking RSV variants and detecting escape mutations for enhanced public health surveillance.

Area Of Science

Virology
Genomics
Bioinformatics

Background

Respiratory syncytial virus (RSV) causes severe respiratory illness in vulnerable populations.
Recent vaccine approvals necessitate robust surveillance of circulating RSV strains.
Existing methods may not be sufficiently scalable or cost-effective for comprehensive RSV monitoring.

Purpose Of The Study

To develop an integrated method for whole-genome sequencing of RSV from clinical and environmental samples.
To establish a bioinformatics pipeline (RSVTyper) for efficient analysis of RSV genomic data.
To assess the utility of RSVTyper for surveillance and detection of viral evolution.

Main Methods

Developed RSVTyper, an integrated pipeline for RSV amplification, Oxford Nanopore sequencing, and bioinformatics analysis.
Utilized multiplex tiling PCR to generate overlapping amplicons for whole-genome sequencing.
Analyzed patient isolates (2008-2025) and wastewater samples (2023-2024) using the RSVTyper pipeline.

Main Results

Achieved successful whole-genome sequencing for 213/243 RSV samples, with high coverage for samples above 10,000 copies/mL.
RSVTyper demonstrated suitability for both patient and wastewater samples, reflecting seasonal clade shifts.
No detected RSV variants exhibited known escape mutations from current prophylactic monoclonal antibodies.

Conclusions

RSVTyper provides a cost-effective, scalable solution for integrated RSV genome sequencing and analysis.
The method is adaptable for resource-limited settings and high-throughput surveillance applications.
Enhanced RSV surveillance using RSVTyper can facilitate genomic characterization and rapid detection of immune escape variants.