title: High genotypic diversity among rotavirus strains infecting Gambian children.
abstract: BACKGROUND
  Rotavirus is the leading cause of diarrhea in children <5 years of age. In light of the implementation of rotavirus vaccines of limited valency, it is important to characterize the genotypic diversity of circulating rotavirus in sub-Saharan Africa.
  
  
  METHODS
  We collected stool samples from children 0-59 months of age who presented at the health centres as cases with moderate-to-severe diarrhea in the Upper River Region of The Gambia. Stool samples were also collected from age, sex and area-matched healthy controls. All stool samples were assayed for rotavirus antigens by enzyme-linked immunosorbent assay and genotyping was done using reverse transcriptase polymerase chain reaction.
  
  
  RESULTS
  We enrolled 1029 cases and 1569 controls during the 3-year study period (2008-2010). The detection rate of rotavirus among the cases was 20% (204/1029) and 3% (42/1569) among controls. At least 18 genotypes were found and the predominant genotypes were G2P[6] (28%), G1P[8] (26%) and G1P[10] (10%). The rare identified genotypes (<1%) were G2P[14], G8P[6], G9P[6] and G4P[10]. There was also a strong positive association between rotavirus infection and the dry season (odds ratio: 9.83, 95% confidence interval: 6.18-15.63, P < 0.001). A significant increase in the odds of rotavirus and G1P[8] detection with the use of untreated water and the presence of cats, rodents and cows in the child's residence was also found.
  
  
  CONCLUSIONS
  This study provides important baseline data for the genotypes circulating before vaccine implementation. The wide diversity of genotypes circulating in The Gambia implies the need for vigilant effectiveness surveillance following the implementation of RotaTeq in August 2013.
authors.affiliation: From the *Medical Research Council Unit, Fajara, The Gambia; †Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD; and ‡Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA.
authors.forename: Brenda A
authors.initials: BA
authors.lastname: Kwambana
authors.forename: Usman N
authors.initials: UN
authors.lastname: Ikumapayi
authors.forename: Neneh
authors.initials: N
authors.lastname: Sallah
authors.forename: Michel
authors.initials: M
authors.lastname: Dione
authors.forename: Sheikh
authors.initials: S
authors.lastname: Jarju
authors.forename: Sandra
authors.initials: S
authors.lastname: Panchalingham
authors.forename: James
authors.initials: J
authors.lastname: Jafali
authors.forename: Modou
authors.initials: M
authors.lastname: Lamin
authors.forename: Modupeh
authors.initials: M
authors.lastname: Betts
authors.forename: Mitchell
authors.initials: M
authors.lastname: Adeyemi
authors.forename: Adebayo
authors.initials: A
authors.lastname: Akinsola
authors.forename: Ousman
authors.initials: O
authors.lastname: Bittaye
authors.forename: Momodou
authors.initials: M
authors.lastname: Jasseh
authors.forename: Karen L
authors.initials: KL
authors.lastname: Kotloff
authors.forename: Myron M
authors.initials: MM
authors.lastname: Levine
authors.forename: James P
authors.initials: JP
authors.lastname: Nataro
authors.forename: Tumani
authors.initials: T
authors.lastname: Corrah
authors.forename: M Jahangir
authors.initials: MJ
authors.lastname: Hossain
authors.forename: Debasish
authors.initials: D
authors.lastname: Saha
authors.forename: Martin
authors.initials: M
authors.lastname: Antonio
mesh_terms: D016022:Case-Control Studies; D016009:Chi-Square Distribution; D002675:Child, Preschool; D003967:Diarrhea / Q000453:epidemiology / Q000382:microbiology / Q000821:virology; D005243:Feces / Q000821:virology; D005260:Female; D005714:Gambia / Q000453:epidemiology; D005838:Genotype; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D008297:Male; D011446:Prospective Studies; D012307:Risk Factors; D012401:Rotavirus / Q000235:genetics*; D012400:Rotavirus Infections / Q000453:epidemiology* / Q000821:virology*; D012959:Socioeconomic Factors