Affiliations 

  • 1 Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam. Electronic address: tanlv@oucru.org
  • 2 Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
  • 3 Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Children's Hospital 2, Ho Chi Minh City, Viet Nam
  • 4 Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
  • 5 Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam
  • 6 Mahir Bashir Institute for Infectious Diseases & Biosecurity, Charles Perkins Centre, School of Biological Science and Sydney Medical School, The University of Sydney, Sydney, Australia
  • 7 University of Malaya, Kuala Lumpur, Malaysia
  • 8 Institute of Health and Community Medicine, Universiti Malaysia Sarawak, Sarawak, Malaysia
  • 9 Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam
  • 10 Children's Hospital 2, Ho Chi Minh City, Viet Nam
J. Virol. Methods, 2015 Apr;215-216:30-6.
PMID: 25704598 DOI: 10.1016/j.jviromet.2015.02.011

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.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.