Sequencing RSV Whole Genome Using a Long Amplicon-Based Method with Oxford Nanopore Technologies

Xiaomin Dong; Steven Edwards; Yi Mo Deng; Clyde Dapat; Arada Hirankitti; Ian G. Barr

doi:10.1007/978-1-0716-5060-8_11

Sequencing RSV Whole Genome Using a Long Amplicon-Based Method with Oxford Nanopore Technologies

Xiaomin Dong
, Steven Edwards
, Yi Mo Deng
, Clyde Dapat
, Arada Hirankitti
, Ian G. Barr

School of Biomedical Sciences

Research output: Chapter in Book/Conference paper › Chapter › peer-review

Abstract

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.

Original language	English
Title of host publication	Methods in Molecular Biology
Editors	Yafeng Ma
Place of Publication	USA
Publisher	Humana Press Inc.
Pages	149-163
Number of pages	15
ISBN (Electronic)	978-1-0716-5060-8, 978-1-0716-5062-2
ISBN (Print)	978-1-0716-5059-2
DOIs	https://doi.org/10.1007/978-1-0716-5060-8_11
Publication status	Published - 2026

Publication series

Name	Methods in Molecular Biology
Volume	3003
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

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10.1007/978-1-0716-5060-8_11

Cite this

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title = "Sequencing RSV Whole Genome Using a Long Amplicon-Based Method with Oxford Nanopore Technologies",

abstract = "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.",

keywords = "ONT, Rapid barcoding, Respiratory syncytial virus, Whole genome sequencing",

author = "Xiaomin Dong and Steven Edwards and Deng, \{Yi Mo\} and Clyde Dapat and Arada Hirankitti and Barr, \{Ian G.\}",

note = "Publisher Copyright: {\textcopyright} The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2026.",

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T1 - Sequencing RSV Whole Genome Using a Long Amplicon-Based Method with Oxford Nanopore Technologies

AU - Dong, Xiaomin

AU - Edwards, Steven

AU - Deng, Yi Mo

AU - Dapat, Clyde

AU - Hirankitti, Arada

AU - Barr, Ian G.

N1 - Publisher Copyright: © The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2026.

PY - 2026

Y1 - 2026

N2 - 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.

AB - 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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KW - Rapid barcoding

KW - Respiratory syncytial virus

KW - Whole genome sequencing

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DO - 10.1007/978-1-0716-5060-8_11

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AN - SCOPUS:105026520417

SN - 978-1-0716-5059-2

T3 - Methods in Molecular Biology

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BT - Methods in Molecular Biology

A2 - Ma, Yafeng

PB - Humana Press Inc.

CY - USA

ER -

Sequencing RSV Whole Genome Using a Long Amplicon-Based Method with Oxford Nanopore Technologies

Abstract

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