A generic assay for whole-genome amplification and deep sequencing of enterovirus A71.
J Virol Methods
; 215-216: 30-6, 2015 Apr.
Article
em En
| MEDLINE
| ID: mdl-25704598
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.
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Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Genoma Viral
/
Técnicas de Amplificação de Ácido Nucleico
/
Enterovirus Humano A
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Sequenciamento de Nucleotídeos em Larga Escala
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Doença de Mão, Pé e Boca
Tipo de estudo:
Guideline
/
Observational_studies
Limite:
Child, preschool
/
Humans
País/Região como assunto:
Asia
Idioma:
En
Ano de publicação:
2015
Tipo de documento:
Article