Wastewater-Based Genomic Surveillance of Respiratory Syncytial Virus

Wastewater-Based Genomic Surveillance of RSV: Computational Analysis (2022-2024)

---

Repository Structure

This repository contains configuration files and reference materials for RSV wastewater data 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): utilities/shared/
• RSV-A Specific Analysis: utilities/shared/RSV_A_analysis/
• RSV-B Specific Analysis: utilities/shared/RSV_B_analysis/

Conda environments

• Downstream Analysis (envs/downstream_analysis.yml)
• annotate_vcf.py
• extract_coverage_RSV_Vpipe.py
• make_mutation_tsv.py
• make_tallymut.py
• Lineage deconvolution (envs/lollipop.yml)
• Data visualization (envs/data_viz.yml)
• coverage_plots.py
• mutation_heatmap_aa.py
• relative_abundances_rsva.py, relative_abundances_rsvb.py

Figures Published in the preprint

• File Location: preprint/plots/

---

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.

---

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, https://doi.org/10.1101/2025.02.28.25321637