Wastewater-Based Genomic Surveillance of Respiratory Syncytial Virus

Computational Analysis of Wastewater-Derived NGS Data (2022/2023 and 2023/2024 Seasons) of RSV (Subtypes A and B)

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Repository Structure

This repository contains configuration files and reference materials for RSV analysis using V-pipe.

Workflow Configuration Files

• Path: workflow/configuration/
• Configuration files for RSV analysis using V-pipe.
• samples.tsv files are available.

Reference Genomes

Reference genomes used for RSV analysis:

• RSV-A: hRSV/A/England/397/2017 (GISAID accession no. EPI_ISL_412866)
• RSV-B: HRSV/B/AUS/VIC-RCH056/2019 (GISAID accession no. EPI_ISL_1653999)
• File Location: workflow/references/concat_EPI_ISL_412866_EPI_ISL_1653999.fasta

Primers & Inserts Genomic Coordinates (BED Files)

• RSV-A: workflow/references/primers/RSV-A/
• RSV-B: workflow/references/primers/RSV-B/

RSV Data Analysis Scripts

• General Analysis (Subtype Independent): workflow/shared/
• RSV-A Specific Analysis: workflow/shared/RSV_A_analysis/
• RSV-B Specific Analysis: workflow/shared/RSV_B_analysis/

Figures Published in the Preprint

• File Location: preprint/plots/

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About This Study

This study explores the potential of wastewater-based genomic surveillance for tracking RSV lineages and identifying key mutations. Given the importance of the RSV F gene in vaccine and therapeutic strategies, our findings highlight the value of wastewater as a complementary approach for monitoring RSV evolution.

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Citation

If you use this repository in your research, please cite:
Wastewater-based sequencing of Respiratory Syncytial Virus enables tracking of lineages and identifying mutations at antigenic sites.
Jolinda de Korne-Elenbaas, Auguste Rimaite, Ivan Topolsky, David Dreifuss, Charlyne Bürki, Lara Fuhrmann, Louis du Plessis, William J. Fitzsimmons, Emily E. Bendall, Tanja Stadler, Niko Beerenwinkel, Timothy R Julian; MedRxiv, 2025