Genetic variability of human respiratory syncytial virus A strains circulating in Ontario: a novel genotype with a 72 nucleotide G gene duplication

PLoS One. 2012;7(3):e32807. doi: 10.1371/journal.pone.0032807. Epub 2012 Mar 28.

Abstract

Human respiratory syncytial virus (HRSV) is the main cause of acute lower respiratory infections in children under 2 years of age and causes repeated infections throughout life. We investigated the genetic variability of RSV-A circulating in Ontario during 2010-2011 winter season by sequencing and phylogenetic analysis of the G glycoprotein gene.Among the 201 consecutive RSV isolates studied, RSV-A (55.7%) was more commonly observed than RSV-B (42.3%). 59.8% and 90.1% of RSV-A infections were among children ≤12 months and ≤5 years old, respectively. On phylogenetic analysis of the second hypervariable region of the 112 RSV-A strains, 110 (98.2%) clustered within or adjacent to the NA1 genotype; two isolates were GA5 genotype. Eleven (10%) NA1-related isolates clustered together phylogenetically as a novel RSV-A genotype, named ON1, containing a 72 nucleotide duplication in the C-terminal region of the attachment (G) glycoprotein. The predicted polypeptide is lengthened by 24 amino acids and includes a23 amino acid duplication. Using RNA secondary structural software, a possible mechanism of duplication occurrence was derived. The 23 amino acid ON1 G gene duplication results in a repeat of 7 potential O-glycosylation sites including three O-linked sugar acceptors at residues 270, 275, and 283. Using Phylogenetic Analysis by Maximum Likelihood analysis, a total of 19 positively selected sites were observed among Ontario NA1 isolates; six were found to be codons which reverted to the previous state observed in the prototype RSV-A2 strain. The tendency of codon regression in the G-ectodomain may infer a decreased avidity of antibody to the current circulating strains. Further work is needed to document and further understand the emergence, virulence, pathogenicity and transmissibility of this novel RSV-A genotype with a72 nucleotide G gene duplication.

MeSH terms

  • Amino Acid Sequence
  • Child, Preschool
  • Cluster Analysis
  • Gene Duplication*
  • Genetic Variation*
  • Genotype
  • Glycosylation
  • Humans
  • Infant
  • Molecular Sequence Data
  • Ontario
  • Phylogeny
  • RNA, Viral / chemistry
  • Respiratory Syncytial Virus Infections / virology
  • Respiratory Syncytial Virus, Human / classification
  • Respiratory Syncytial Virus, Human / genetics*
  • Respiratory Syncytial Virus, Human / isolation & purification
  • Sequence Alignment
  • Viral Fusion Proteins / genetics*

Substances

  • G glycoprotein, Respiratory syncytial virus
  • RNA, Viral
  • Viral Fusion Proteins