Molecular epidemiology of respiratory syncytial virus in Kilifi district, Kenya

J Med Virol. 2004 Oct;74(2):344-54. doi: 10.1002/jmv.20183.


Respiratory syncytial virus (RSV) causes significant burden of disease during infancy and childhood. This study examined the genetic relatedness of RSV positive samples from child inpatients and outpatients and a birth cohort from a rural coastal district of Kenya and also the distribution of strains between these three groups. Clinical samples were collected over a 4-year period in Kilifi District, Kenya from community and hospital surveillance. Three hundred ninety seven of 1,044 nasal specimens from children (under 5 years old) attending Kilifi District Hospital, and from community-monitored infants, were positive for RSV by multiplex RT-PCR. Of these, 376 samples were analysed further by restriction fragment length polymorphisms (RFLP) of the nucleocapsid (N) and attachment (G) protein genes. The G gene was sequenced for 109 samples and phylogenetic analysis carried out. The group A samples from Kilifi fell into two clusters based on G gene sequences, while only one group B cluster was observed. One RSV-B sample from 2003 demonstrated the presence of a 60-nucleotide duplication within the G gene, clustering with similar isolates from Buenos Aries from 1999. All had similar sequences to isolates from the UK, USA, Spain, or Uruguay. The Kilifi District samples showed greater than 97% homology to isolates from South Africa and Mozambique and 91-94% homology to isolates from The Gambia. Samples from different sources, clearly differing in disease severity, did not differ in genotype characteristics, suggesting that disease causing variants are a general reflection of infections within this community.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Cohort Studies
  • Humans
  • Infant
  • Infant, Newborn
  • Kenya / epidemiology
  • Molecular Epidemiology*
  • Molecular Sequence Data
  • Phylogeny
  • Polymorphism, Restriction Fragment Length
  • Respiratory Syncytial Virus Infections / epidemiology*
  • Respiratory Syncytial Virus Infections / virology
  • Respiratory Syncytial Virus, Human / classification
  • Respiratory Syncytial Virus, Human / genetics*
  • Respiratory Syncytial Virus, Human / isolation & purification
  • Rural Population*
  • Sequence Alignment
  • Sequence Analysis, DNA