Molecular epidemiology of coxsackievirus A16: intratype and prevalent intertype recombination identified

PLoS One. 2013 Dec 10;8(12):e82861. doi: 10.1371/journal.pone.0082861. eCollection 2013.

Abstract

Coxsackievirus A16 (CVA16) is responsible for nearly 50% of all the confirmed hand, foot, and mouth disease (HFMD) cases in mainland China, sometimes it could also cause severe complications, and even death. To clarify the genetic characteristics and the epidemic patterns of CVA16 in mainland China, comprehensive bioinfomatics analyses were performed by using 35 CVA16 whole genome sequences from 1998 to 2011, 593 complete CVA16 VP1 sequences from 1981 to 2011, and prototype strains of human enterovirus species A (EV-A). Analysis on complete VP1 sequences revealed that subgenotypes B1a and B1b were prevalent strains and have been co-circulating in many Asian countries since 2000, especially in mainland China for at least 13 years. While the prevalence of subgenotype B1c (totally 20 strains) was much limited, only found in Malaysia from 2005 to 2007 and in France in 2010. Genotype B2 only caused epidemic in Japan and Malaysia from 1981 to 2000. Both subgenotypes B1a and B1b were potential recombinant viruses containing sequences from other EV-A donors in the 5'-untranslated region and P2, P3 non-structural protein encoding regions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5' Untranslated Regions
  • Base Sequence
  • China
  • Cluster Analysis
  • Computational Biology / methods*
  • DNA Primers / genetics
  • DNA, Viral / analysis*
  • Enterovirus / classification
  • Enterovirus / genetics*
  • Genome, Viral
  • Genomics
  • Genotype
  • Hand, Foot and Mouth Disease / epidemiology
  • Hand, Foot and Mouth Disease / virology*
  • Humans
  • Molecular Epidemiology
  • Molecular Sequence Data
  • Phylogeny
  • Recombination, Genetic
  • Sequence Analysis, DNA

Substances

  • 5' Untranslated Regions
  • DNA Primers
  • DNA, Viral

Associated data

  • GENBANK/KC755228
  • GENBANK/KC755229
  • GENBANK/KC755230
  • GENBANK/KC755231
  • GENBANK/KC755232
  • GENBANK/KC755233
  • GENBANK/KC755234
  • GENBANK/KC755235

Grants and funding

This work was supported by the National Basic Research Program of China (973 Program): (Grant No. 2011CB504902) and Key Technologies Research & Development Program of National Ministry of Science (Grant No. 2013ZX10004-202; 2012ZX10004201-003, 2013ZX09304101). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.