title: Serotype and genetic diversity of human rhinovirus strains that circulated in Kenya in 2008.
abstract: BACKGROUND
  Human rhinoviruses (HRVs) are a well-established cause of the common cold and recent studies indicated that they may be associated with severe acute respiratory illnesses (SARIs) like pneumonia, asthma, and bronchiolitis. Despite global studies on the genetic diversity of the virus, the serotype diversity of these viruses across diverse geographic regions in Kenya has not been characterized.
  
  
  OBJECTIVE
  This study sought to characterize the serotype diversity of HRV strains that circulated in Kenya in 2008.
  
  
  METHODS
  A total of 517 archived nasopharyngeal samples collected in a previous respiratory virus surveillance program across Kenya in 2008 were selected. Participants enrolled were outpatients who presented with influenza-like (ILI) symptoms. Real-time RT-PCR was employed for preliminary HRV detection. HRV-positive samples were amplified using RT-PCR and thereafter the nucleotide sequences of the amplicons were determined followed by phylogenetic analysis.
  
  
  RESULTS
  Twenty-five percent of the samples tested positive for HRV. Phylogenetic analysis revealed that the Kenyan HRVs clustered into three main species comprising HRV-A (54%), HRV-B (12%), and HRV-C (35%). Overall, 20 different serotypes were identified. Intrastrain sequence homology among the Kenyan strains ranged from 58% to 100% at the nucleotide level and 55% to 100% at the amino acid level.
  
  
  CONCLUSIONS
  These results show that a wide range of HRV serotypes with different levels of nucleotide variation were present in Kenya. Furthermore, our data show that HRVs contributed substantially to influenza-like illness in Kenya in 2008.
authors.affiliation: College of Health Sciences (COHES), Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya.
authors.forename: Sylvia
authors.initials: S
authors.lastname: Milanoi
authors.affiliation: College of Health Sciences (COHES), Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya.
authors.forename: Juliette R
authors.initials: JR
authors.lastname: Ongus
authors.affiliation: Department of Medical Laboratory Sciences, Kenyatta University, Nairobi, Kenya.
authors.forename: George
authors.initials: G
authors.lastname: Gachara
authors.affiliation: Department of Emerging Infectious Diseases (DEID), United States Medical Research Directorate- Kenya, Nairobi, Kenya.|A Special Field Activity of the Walter Reed Army Institute of Research, Silver Spring, MD, USA.
authors.forename: Rodney
authors.initials: R
authors.lastname: Coldren
authors.affiliation: Department of Emerging Infectious Diseases (DEID), United States Medical Research Directorate- Kenya, Nairobi, Kenya.|A Special Field Activity of the Walter Reed Army Institute of Research, Silver Spring, MD, USA.|Department of Biochemistry, University of Nairobi, Nairobi, Kenya.
authors.forename: Wallace
authors.identifier: http://orcid.org/0000-0001-8475-0586
authors.initials: W
authors.lastname: Bulimo
mesh_terms: D002648:Child; D002675:Child, Preschool; D005260:Female; D005814:Genes, Viral; D014644:Genetic Variation; D006801:Humans; D007223:Infant; D007630:Kenya / Q000453:epidemiology; D008297:Male; D009305:Nasopharynx / Q000821:virology; D010045:Outpatients; D010802:Phylogeny; D010850:Picornaviridae Infections / Q000453:epidemiology* / Q000821:virology*; D060888:Real-Time Polymerase Chain Reaction; D012141:Respiratory Tract Infections / Q000453:epidemiology / Q000821:virology; D012229:Rhinovirus / Q000145:classification / Q000235:genetics* / Q000276:immunology*; D017385:Sequence Homology; D065288:Serogroup
keywords: Diversity; Kenya; genetic; rhinovirus; serotype
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