Spread and Evolution of Respiratory Syncytial Virus A Genotype ON1, Coastal Kenya, 2010-2015

Emerg Infect Dis. 2017 Feb;23(2):264-271. doi: 10.3201/eid2302.161149.


In February 2012, the novel respiratory syncytial virus (RSV) group A, genotype ON1, was detected in Kilifi County, coastal Kenya. ON1 is characterized by a 72-nt duplication within the highly variable G gene (encoding the immunogenic attachment surface protein). Cases were diagnosed through surveillance of pneumonia in children at the county hospital. Analysis of epidemiologic, clinical, and sequence data of RSV-A viruses detected over 5 RSV seasons (2010/2011 to 2014/2015) indicated the following: 1) replacement of previously circulating genotype GA2 ON1, 2) an abrupt expansion in the number of ON1 variants detected in the 2014/2015 epidemic, 3) recently accumulation of amino acid substitutions within the ON1 duplicated sequence, and 4) no clear evidence of altered pathogenicity relative to GA2. The study demonstrates the public health importance of molecular surveillance in defining the spread, clinical effects, and evolution of novel respiratory virus variants.

Keywords: G protein; RSV; evolutionary dynamics; genetic diversity; phylogenetic analysis; respiratory diseases; respiratory infections; respiratory syncytial virus; viruses.

Publication types

  • Historical Article

MeSH terms

  • Amino Acid Substitution
  • Child, Preschool
  • Evolution, Molecular*
  • Female
  • Genetic Variation
  • Genotype*
  • History, 21st Century
  • Humans
  • Infant
  • Infant, Newborn
  • Kenya / epidemiology
  • Male
  • Odds Ratio
  • Phylogeny
  • Public Health Surveillance
  • Respiratory Syncytial Virus Infections / diagnosis
  • Respiratory Syncytial Virus Infections / epidemiology*
  • Respiratory Syncytial Virus Infections / history
  • Respiratory Syncytial Virus Infections / virology*
  • Respiratory Syncytial Virus, Human / classification
  • Respiratory Syncytial Virus, Human / genetics*
  • Sequence Analysis, DNA
  • Viral Envelope Proteins / genetics


  • Viral Envelope Proteins