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

Autor: Tan le V; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam. Electronic address: tanlv@oucru.org., Tuyen NT; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam., Thanh TT; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam., Ngan TT; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam., Van HM; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Children's Hospital 2, Ho Chi Minh City, Viet Nam., Sabanathan S; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK., Van TT; Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam., Thanh le TM; Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam., Nguyet LA; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam., Geoghegan JL; Mahir Bashir Institute for Infectious Diseases & Biosecurity, Charles Perkins Centre, School of Biological Science and Sydney Medical School, The University of Sydney, Sydney, Australia., Ong KC; University of Malaya, Kuala Lumpur, Malaysia., Perera D; Institute of Health and Community Medicine, Universiti Malaysia Sarawak, Sarawak, Malaysia., Hang VT; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam., Ny NT; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam., Anh NT; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam., Ha do Q; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam., Qui PT; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam., Viet do C; Children's Hospital 2, Ho Chi Minh City, Viet Nam., Tuan HM; Children's Hospital 2, Ho Chi Minh City, Viet Nam., Wong KT; University of Malaya, Kuala Lumpur, Malaysia., Holmes EC; Mahir Bashir Institute for Infectious Diseases & Biosecurity, Charles Perkins Centre, School of Biological Science and Sydney Medical School, The University of Sydney, Sydney, Australia., Chau NV; Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam., Thwaites G; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK., van Doorn HR; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
Jazyk: angličtina
Zdroj: Journal of virological methods [J Virol Methods] 2015 Apr; Vol. 215-216, pp. 30-6. Date of Electronic Publication: 2015 Feb 19.
DOI: 10.1016/j.jviromet.2015.02.011
Abstrakt: 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.
(Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.)
Databáze: MEDLINE
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