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Sequencing RSV Whole Genome Using a Long Amplicon-Based Method with Oxford Nanopore Technologies
Xiaomin Dong1,2, Steven Edwards3, Yi-Mo Deng3,4,5
1WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia. xiaomin.dong@influenzacentre.org.
None:
Respiratory syncytial virus (RSV) infection continues to be a significant burden on public health care systems and is a global health concern. Whole genome sequencing (WGS) provides a useful tool to better understand the viral transmission and emerging mutations that may impact antibody treatments, antiviral drug sensitivity, and vaccine effectiveness. Here, we describe a rapid and sensitive protocol for sequencing clinical samples of both human RSV-A and RSV-B viruses based on the Oxford Nanopore Technology (ONT) sequencing platform. It involves long amplicon generation by setting up two one-step multiplex reverse-transcription polymerase chain reactions (mRT-PCR) for each sample, library preparation with the ONT rapid barcoding kit and NGS data analysis with the ARTIC pipeline.
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