Staff View: A generic assay for whole-genome amplification and deep sequencing of enterovirus A71

A generic assay for whole-genome amplification and deep sequencing of enterovirus A71

sometimes fatal hand, foot and mouth disease (HFMD) across the Asia-Pacific region. EV-A71 outbreaks have been associated with (sub)genogroup switches, sometimes accompanied by recombination events. Understanding EV-A71 population dynamics is therefore essential for understanding this emerging infec...

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Main Authors:	Le Van, Tan, Nguyen, Thi Kim Tuyen, Tran, Tan Thanh, Tran, Thuy Ngan, Hoang, Minh Tu Van, Saraswathy, Sabanathan, Tran, Thi My Van, Le, Thi My Thanh, Lam, Anh Nguyet, Jemma L., Geoghegan, Ong, Kien Chai, David, Perera, Vu, Thi Ty Hang, Nguyen, Thi Han Ny, Nguyen, To Anh, Do, Quang Ha, Phan, Tu Qui, Do, Chau Viet, Ha, Manh Tuan, Wong, Kum Thong, Holmes, Edward C., Nguyen, Van Vinh Chau, Thwaites, Guy, H. Rogier, van Doorn
Format:	Article
Language:	English
Published:	Elsevier 2015
Subjects:	Q Science (General) R Medicine (General)
Online Access:	http://ir.unimas.my/id/eprint/6562/1/A%20generic%20assay.pdf http://ir.unimas.my/id/eprint/6562/ http://www.sciencedirect.com/science/article/pii/S0166093415000336#
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id	my.unimas.ir.6562
record_format	eprints
spelling	my.unimas.ir.65622022-01-26T08:47:45Z http://ir.unimas.my/id/eprint/6562/ A generic assay for whole-genome amplification and deep sequencing of enterovirus A71 Le Van, Tan Nguyen, Thi Kim Tuyen Tran, Tan Thanh Tran, Thuy Ngan Hoang, Minh Tu Van Saraswathy, Sabanathan Tran, Thi My Van Le, Thi My Thanh Lam, Anh Nguyet Jemma L., Geoghegan Ong, Kien Chai David, Perera Vu, Thi Ty Hang Nguyen, Thi Han Ny Nguyen, To Anh Do, Quang Ha Phan, Tu Qui Do, Chau Viet Ha, Manh Tuan Wong, Kum Thong Holmes, Edward C. Nguyen, Van Vinh Chau Thwaites, Guy H. Rogier, van Doorn Q Science (General) R Medicine (General) sometimes fatal hand, foot and mouth disease (HFMD) across the Asia-Pacific region. EV-A71 outbreaks have been associated with (sub)genogroup switches, sometimes accompanied by recombination events. Understanding EV-A71 population dynamics is therefore essential for understanding this emerging infection, and may provide pivotal information for vaccine development. Despite the public health burden of EV-A71, relatively few EV-A71 complete-genome sequences are available for analysis and from limited geographical localities. The availability of an efficient procedure for whole-genome sequencing would stimulate effort to generate more viral sequence data. Herein, we report for the first time the development of a next-generation sequencing based protocol for whole-genome sequencing of EV-A71 directly from clinical specimens. We were able to sequence viruses of subgenogroup C4 and B5, while RNA from culture materials of diverse EV-A71 subgenogroups belonging to both genogroup B and C was successfully amplified. The nature of intra-host genetic diversity was explored in 22 clinical samples, revealing 107 positions carrying minor variants (ranging from 0 to 15 variants per sample). Our analysis of EVA71 strains sampled in 2013 showed that they all belonged to subgenogroup B5, representing the first report of this subgenogroup in Vietnam. In conclusion, we have successfully developed a high-throughput next-generation sequencing-based assay for whole-genome sequencing of EV-A71 from clinical samples Elsevier 2015-04 Article PeerReviewed text en http://ir.unimas.my/id/eprint/6562/1/A%20generic%20assay.pdf Le Van, Tan and Nguyen, Thi Kim Tuyen and Tran, Tan Thanh and Tran, Thuy Ngan and Hoang, Minh Tu Van and Saraswathy, Sabanathan and Tran, Thi My Van and Le, Thi My Thanh and Lam, Anh Nguyet and Jemma L., Geoghegan and Ong, Kien Chai and David, Perera and Vu, Thi Ty Hang and Nguyen, Thi Han Ny and Nguyen, To Anh and Do, Quang Ha and Phan, Tu Qui and Do, Chau Viet and Ha, Manh Tuan and Wong, Kum Thong and Holmes, Edward C. and Nguyen, Van Vinh Chau and Thwaites, Guy and H. Rogier, van Doorn (2015) A generic assay for whole-genome amplification and deep sequencing of enterovirus A71. Journal of Virological Methods. pp. 30-36. ISSN 0166-0934 http://www.sciencedirect.com/science/article/pii/S0166093415000336#
institution	Universiti Malaysia Sarawak
building	Centre for Academic Information Services (CAIS)
collection	Institutional Repository
continent	Asia
country	Malaysia
content_provider	Universiti Malaysia Sarawak
content_source	UNIMAS Institutional Repository
url_provider	http://ir.unimas.my/
language	English
topic	Q Science (General) R Medicine (General)
spellingShingle	Q Science (General) R Medicine (General) Le Van, Tan Nguyen, Thi Kim Tuyen Tran, Tan Thanh Tran, Thuy Ngan Hoang, Minh Tu Van Saraswathy, Sabanathan Tran, Thi My Van Le, Thi My Thanh Lam, Anh Nguyet Jemma L., Geoghegan Ong, Kien Chai David, Perera Vu, Thi Ty Hang Nguyen, Thi Han Ny Nguyen, To Anh Do, Quang Ha Phan, Tu Qui Do, Chau Viet Ha, Manh Tuan Wong, Kum Thong Holmes, Edward C. Nguyen, Van Vinh Chau Thwaites, Guy H. Rogier, van Doorn A generic assay for whole-genome amplification and deep sequencing of enterovirus A71
description	sometimes fatal hand, foot and mouth disease (HFMD) across the Asia-Pacific region. EV-A71 outbreaks have been associated with (sub)genogroup switches, sometimes accompanied by recombination events. Understanding EV-A71 population dynamics is therefore essential for understanding this emerging infection, and may provide pivotal information for vaccine development. Despite the public health burden of EV-A71, relatively few EV-A71 complete-genome sequences are available for analysis and from limited geographical localities. The availability of an efficient procedure for whole-genome sequencing would stimulate effort to generate more viral sequence data. Herein, we report for the first time the development of a next-generation sequencing based protocol for whole-genome sequencing of EV-A71 directly from clinical specimens. We were able to sequence viruses of subgenogroup C4 and B5, while RNA from culture materials of diverse EV-A71 subgenogroups belonging to both genogroup B and C was successfully amplified. The nature of intra-host genetic diversity was explored in 22 clinical samples, revealing 107 positions carrying minor variants (ranging from 0 to 15 variants per sample). Our analysis of EVA71 strains sampled in 2013 showed that they all belonged to subgenogroup B5, representing the first report of this subgenogroup in Vietnam. In conclusion, we have successfully developed a high-throughput next-generation sequencing-based assay for whole-genome sequencing of EV-A71 from clinical samples
format	Article
author	Le Van, Tan Nguyen, Thi Kim Tuyen Tran, Tan Thanh Tran, Thuy Ngan Hoang, Minh Tu Van Saraswathy, Sabanathan Tran, Thi My Van Le, Thi My Thanh Lam, Anh Nguyet Jemma L., Geoghegan Ong, Kien Chai David, Perera Vu, Thi Ty Hang Nguyen, Thi Han Ny Nguyen, To Anh Do, Quang Ha Phan, Tu Qui Do, Chau Viet Ha, Manh Tuan Wong, Kum Thong Holmes, Edward C. Nguyen, Van Vinh Chau Thwaites, Guy H. Rogier, van Doorn
author_facet	Le Van, Tan Nguyen, Thi Kim Tuyen Tran, Tan Thanh Tran, Thuy Ngan Hoang, Minh Tu Van Saraswathy, Sabanathan Tran, Thi My Van Le, Thi My Thanh Lam, Anh Nguyet Jemma L., Geoghegan Ong, Kien Chai David, Perera Vu, Thi Ty Hang Nguyen, Thi Han Ny Nguyen, To Anh Do, Quang Ha Phan, Tu Qui Do, Chau Viet Ha, Manh Tuan Wong, Kum Thong Holmes, Edward C. Nguyen, Van Vinh Chau Thwaites, Guy H. Rogier, van Doorn
author_sort	Le Van, Tan
title	A generic assay for whole-genome amplification and deep sequencing of enterovirus A71
title_short	A generic assay for whole-genome amplification and deep sequencing of enterovirus A71
title_full	A generic assay for whole-genome amplification and deep sequencing of enterovirus A71
title_fullStr	A generic assay for whole-genome amplification and deep sequencing of enterovirus A71
title_full_unstemmed	A generic assay for whole-genome amplification and deep sequencing of enterovirus A71
title_sort	generic assay for whole-genome amplification and deep sequencing of enterovirus a71
publisher	Elsevier
publishDate	2015
url	http://ir.unimas.my/id/eprint/6562/1/A%20generic%20assay.pdf http://ir.unimas.my/id/eprint/6562/ http://www.sciencedirect.com/science/article/pii/S0166093415000336#
_version_	1724078445359529984
score	13.211869

A generic assay for whole-genome amplification and deep sequencing of enterovirus A71

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