ArticleInfluenza and other respiratory viruses2025
An Improved Rapid and Sensitive Long Amplicon Method for Nanopore-Based RSV Whole-Genome Sequencing.
Article in Influenza and other respiratory viruses, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Whole-Genome Sequencing of RSV and Phylogeographic Assessment of Viral Importations into Russia.Viruses · 2026Article
- A bench-to-data analysis workflow for respiratory syncytial virus whole-genome sequencing with short and long-read approaches.Genome medicine · 2026Article
- Sequencing RSV Whole Genome Using a Long Amplicon-Based Method with Oxford Nanopore Technologies.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Epidemiological characteristics and whole-genome analysis of respiratory syncytial virus in Jining city from February 2023 to December 2024.Frontiers in microbiology · 2026Article
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11 authors.
Funding
Abstract
backgroundWhole-genome sequencing (WGS) provides critical insights into the respiratory syncytial virus (RSV) transmission and any emerging mutations that could impair the efficacy of monoclonal antibodies or vaccines that have been recently licenced for clinical use worldwide. However, the ability to sequence RSV genomes at large scale is limited by expensive and time-consuming sequencing methods. Oxford Nanopore Technology (ONT) offers significant improvements in next generation sequencing (NGS) both in turnaround time and cost, compared with other platforms for viral WGS.
methodsWe have developed and modified an RSV long amplicon-based WGS protocol for the ONT platform using a one-step multiplex RT-PCR assay and the rapid barcoding kit. One hundred thirty-five RSV positive Australian clinical specimens (91 RSV-A and 44 RSV-B) sampled in 2023 with cycle threshold (Ct) values between 14 to 35 were tested in this study. This ONT workflow was compared with other recent RSV WGS amplification assays based on short amplicons.
resultsA PCR amplicon clean-up step prior to library preparation significantly improved WGS result for samples with poor amplicon generation, but it is not necessary or beneficial for ones that generated high concentrations of amplicons. Overall, a success rate of 85.9% was achieved for WGS. This method performed as well as the more complex short amplicon methods in terms of genome coverage and sequencing depth.
conclusionsThe workflow described here was highly successful in generating RSV WGS on ONT platform and had improved turnaround times and excellent results with RSV clinical samples with Ct values up to 30.
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