Characterization of a triple-recombinant, reassortant rotavirus strain from the Dominican Republic

J Gen Virol. 2017 Feb;98(2):134-142. doi: 10.1099/jgv.0.000688. Epub 2017 Feb 24.

Abstract

We report the genome of a novel human triple-recombinant G4P[6-8_R] mono-reassortant strain identified in a stool sample from the Dominican Republic during routine facility-based rotavirus strain surveillance. The strain was designated as RVA/Human-wt/DOM/2013840364/2013/G4P[6-8_R], with a genomic constellation of G4-P[6-8_R]-I1-R1-C1-M1-(A1-A8_R)-N1-(T1-T7_R)-E1-H1. Recombinant gene segments NSP1 and NSP3 were generated as a result of recombination between genogroup 1 rotavirus A1 human strain and a genotype A8 porcine strain and between genogroup 1 rotavirus T1 human strain and a genotype T7 bovine strain, respectively. Analyses of the RNA secondary structures of gene segment VP4, NSP1 and NSP3 showed that all the recombinant regions appear to start in a loop (single-stranded) region and terminate in a stem (double-stranded) structure. Also, the VP7 gene occupied lineage VII within the G4 genotypes consisting of mostly porcine or porcine-like G4 strains, suggesting the occurrence of reassortment. The remaining gene segments clustered phylogenetically with genogroup 1 strains. This exchange of whole or partial genetic materials between rotaviruses by recombination and reassortment contributes directly to their diversification, adaptation and evolution.

MeSH terms

  • Adaptation, Physiological / genetics
  • Animals
  • Cattle / virology
  • Dominican Republic
  • Epidemiological Monitoring
  • Evolution, Molecular
  • Feces / virology
  • Gastroenteritis / veterinary
  • Gastroenteritis / virology*
  • Genetic Variation
  • Genome, Viral*
  • Genomics
  • Genotype
  • Humans
  • Multigene Family
  • Nucleic Acid Conformation
  • Phylogeny
  • RNA, Viral / chemistry
  • RNA, Viral / genetics
  • Reassortant Viruses / classification
  • Reassortant Viruses / genetics*
  • Recombination, Genetic*
  • Rotavirus / classification
  • Rotavirus / genetics*
  • Rotavirus / isolation & purification
  • Rotavirus Infections / virology*
  • Sequence Analysis, DNA
  • Swine / virology
  • Viral Nonstructural Proteins / genetics

Substances

  • NSP3 protein, Rotavirus
  • RNA, Viral
  • Viral Nonstructural Proteins
  • nsp1 protein, Rotavirus