title: Examining strain diversity and phylogeography in relation to an unusual epidemic pattern of respiratory syncytial virus (RSV) in a long-term refugee camp in Kenya.
abstract: BACKGROUND
  A recent longitudinal study in the Dadaab refugee camp near the Kenya-Somalia border identified unusual biannual respiratory syncytial virus (RSV) epidemics. We characterized the genetic variability of the associated RSV strains to determine if viral diversity contributed to this unusual epidemic pattern.
  
  
  METHODS
  For 336 RSV positive specimens identified from 2007 through 2011 through facility-based surveillance of respiratory illnesses in the camp, 324 (96.4%) were sub-typed by PCR methods, into 201 (62.0%) group A, 118 (36.4%) group B and 5 (1.5%) group A-B co-infections. Partial sequencing of the G gene (coding for the attachment protein) was completed for 290 (89.5%) specimens. These specimens were phylogenetically analyzed together with 1154 contemporaneous strains from 22 countries.
  
  
  RESULTS
  Of the 6 epidemic peaks recorded in the camp over the period, the first and last were predominantly made up of group B strains, while the 4 in between were largely composed of group A strains in a consecutive series of minor followed by major epidemics. The Dadaab group A strains belonged to either genotype GA2 (180, 98.9%) or GA5 (2, < 1%) while all group B strains (108, 100%) belonged to BA genotype. In sequential epidemics, strains within these genotypes appeared to be of two types: those continuing from the preceding epidemics and those newly introduced. Genotype diversity was similar in minor and major epidemics.
  
  
  CONCLUSIONS
  RSV strain diversity in Dadaab was similar to contemporaneous diversity worldwide, suggested both between-epidemic persistence and new introductions, and was unrelated to the unusual epidemic pattern.
authors.affiliation: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya. cnyaigoti@kemri-wellcome.org.
authors.forename: Charles N
authors.initials: CN
authors.lastname: Agoti
authors.forename: Lillian M
authors.initials: LM
authors.lastname: Mayieka
authors.forename: James R
authors.initials: JR
authors.lastname: Otieno
authors.forename: Jamal A
authors.initials: JA
authors.lastname: Ahmed
authors.forename: Barry S
authors.initials: BS
authors.lastname: Fields
authors.forename: Lilian W
authors.initials: LW
authors.lastname: Waiboci
authors.forename: Raymond
authors.initials: R
authors.lastname: Nyoka
authors.forename: Rachel B
authors.initials: RB
authors.lastname: Eidex
authors.forename: Nina
authors.initials: N
authors.lastname: Marano
authors.forename: Wagacha
authors.initials: W
authors.lastname: Burton
authors.forename: Joel M
authors.initials: JM
authors.lastname: Montgomery
authors.forename: Robert F
authors.initials: RF
authors.lastname: Breiman
authors.forename: D James
authors.initials: DJ
authors.lastname: Nokes
mesh_terms: D002675:Child, Preschool; D058872:Epidemics; D005260:Female; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D007223:Infant; D007630:Kenya / Q000453:epidemiology; D008297:Male; D058974:Phylogeography; D012036:Refugees / Q000706:statistics & numerical data*; D018357:Respiratory Syncytial Virus Infections / Q000453:epidemiology* / Q000821:virology*; D012136:Respiratory Syncytial Viruses / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*