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Article Dans Une Revue Journal of Virological Methods Année : 2024

RSV-GenoScan: An automated pipeline for whole-genome human respiratory syncytial virus (RSV) sequence analysis

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Background: Advances in high-throughput sequencing (HTS) technologies and reductions in sequencing costs have revolutionised the study of genomics and molecular biology by making whole-genome sequencing (WGS) accessible to many laboratories. However, the analysis of WGS data requires significant computational effort, which is the major drawback in implementing WGS as a routine laboratory technique.
Objective: Automated pipelines have been developed to overcome this issue, but they do not exist for all organisms. This is the case for human respiratory syncytial virus (RSV), which is a leading cause of lower respiratory tract infections in infants, the elderly, and immunocompromised adults.
Results: We present RSV-GenoScan, a fast and easy-to-use pipeline for WGS analysis of RSV generated by HTS on Illumina or Nanopore platforms. RSV-GenoScan automates the WGS analysis steps directly from the raw sequence data. The pipeline filters the sequence data, maps the reads to the RSV reference genomes, generates a consensus sequence, identifies the RSV subgroup, and lists amino acid mutations, insertions and deletions in the F and G viral genes. This enables the rapid identification of mutations in these coding genes that are known to confer resistance to monoclonal antibodies.
Availability: RSV-GenoScan is freely available at https://github.com/AlexandreD-bio/RSV-GenoScan.
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hal-04600904 , version 1 (04-06-2024)

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Alexandre Dosbaa, Romane Guilbaud, Anna-Maria Franco Yusti, Valentine Marie Ferré, Charlotte Charpentier, et al.. RSV-GenoScan: An automated pipeline for whole-genome human respiratory syncytial virus (RSV) sequence analysis. Journal of Virological Methods, 2024, 327, pp.114938. ⟨10.1016/j.jviromet.2024.114938⟩. ⟨hal-04600904⟩
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