Whole-genome nanopore sequencing and automatic downstream analysis of respiratory syncytial virus using RSVTyper
New Tool Enables Rapid, Comprehensive Analysis of Respiratory Syncytial Virus
researchers have developed RSVTyper, a streamlined bioinformatics pipeline leveraging whole-genome nanopore sequencing for rapid and automated analysis of respiratory syncytial virus (RSV). The tool facilitates detailed characterization of RSV-A and RSV-B strains, including variant identification and phylogenetic analysis, offering a significant advancement in tracking and understanding the evolution of this common respiratory pathogen.
RSV is a leading cause of lower respiratory tract infections in young children and increasingly recognized as a threat to older adults and immunocompromised individuals. Existing diagnostic methods often lack the resolution to fully characterize viral diversity and track transmission patterns. RSVTyper addresses this gap by providing a comprehensive, high-throughput approach to RSV genome analysis, enabling faster public health responses and informing vaccine growth. The pipeline includes barcode assignment using Freyja-barcodes (https://github.com/andersen-lab/Freyja-barcodes/) and only includes variants with an abundance greater than 0.05 in at least one sample.
Methods Detail
Phylogenetic trees were constructed using MAFFT v7.520 for sequence alignment and MEGA v11.03.1344 with the Tamura-Nei model for tree computation, visualized with iTOL v745. Consensus trees were generated using the Mr. Bayes plugin 26 within the ngphylogeny-pipeline (https://ngphylogeny.fr/) with default parameters, based on complete RSV sequences and reference genomes from Genebank. Recombination analysis was performed using the Pairwise Homoplasy Index-Test (Phi)46 implemented in SimPlot++47, employing a window size of 100 and 1000 permutations.