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

Le, Van Tan and Nguyen, Thi Kim Tuyen and Tran, Tan Thanh and Tran, Thuy Ngan and Hoang, Minh Tu Van (2015) A generic assay for whole-genome amplification and deep sequencingof enterovirus A71. Journal of Virological Methods, 215-21. pp. 30-36. ISSN 0166-0934

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Abstract

Enterovirus A71 (EV-A71) has emerged as the most important cause of large outbreaks of severe and 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 EV-A71 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.

Item Type: Article
Uncontrolled Keywords: Deep sequencing; Enterovirus A71; Hand foot and mouth disease; Phylogeny; Picornavirus, unimas, university, universiti, Borneo, Malaysia, Sarawak, Kuching, Samarahan, ipta, education, undergraduate,Postgraduate, research, Universiti Malaysia Sarawak
Subjects: R Medicine > RA Public aspects of medicine
R Medicine > RA Public aspects of medicine > RA0421 Public health. Hygiene. Preventive Medicine
R Medicine > RB Pathology
Divisions: Academic Faculties, Institutes and Centres > Institute of Health and Community Medicine
Depositing User: Karen Kornalius
Date Deposited: 03 Nov 2015 06:29
Last Modified: 28 Jul 2016 01:31
URI: http://ir.unimas.my/id/eprint/9313

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