title: Genetic diversity and molecular epidemiology of human rhinoviruses in South Africa.
abstract: BACKGROUND
  Rhinoviruses (RV) are a well-established cause of respiratory illness. RV-C has been associated with more severe illness. We aimed to characterize and compare the clinical presentations and disease severity of different RV type circulating in South Africa.
  
  
  METHODS
  We performed two analyses of RV-positive specimens identified through surveillance in South Africa across all age groups. First, RV-positive specimens identified through severe acute respiratory illness (SARI) surveillance in four provinces was randomly selected from 2009 to 2010 for molecular characterization. Second, RV-positive specimens identified through SARI, influenza-like illness (ILI) and control surveillance at hospitals and outpatient clinics in during 2012-2013 were used to determine the association of RV type with severe disease. Selected specimens were sequenced, and phylogenetic analysis was performed.
  
  
  RESULTS
  Among the 599 sequenced specimens from 2009 to 2010 and 2012 to 2013, RV-A (285, 48%) and RV-C (247, 41%) were more commonly identified than RV-B (67, 11%), with no seasonality and a high genetic diversity. A higher prevalence of RV infection was identified in cases with SARI [515/962 (26%); aRRR = 1.6; 95% CI 1.21; 2.2] and ILI [356/962 (28%); aRRR = 1.9; 95% CI 1.37; 2.6] compared with asymptomatic controls (91/962, 22%). There was no difference in disease severity between the different type when comparing SARI, ILI and controls.
  
  
  CONCLUSIONS
  All three type of RV were identified in South Africa, although RV-A and RV-C were more common than RV-B. RV was associated with symptomatic respiratory illness; however, there was no association between RV type and disease severity.
authors.affiliation: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Department of Medical Virology, University of Pretoria, Pretoria, South Africa.
authors.forename: Marthi A
authors.initials: MA
authors.lastname: Pretorius
authors.forename: Stefano
authors.initials: S
authors.lastname: Tempia
authors.forename: Florette K
authors.initials: FK
authors.lastname: Treurnicht
authors.forename: Sibongile
authors.initials: S
authors.lastname: Walaza
authors.forename: Adam L
authors.initials: AL
authors.lastname: Cohen
authors.forename: Jocelyn
authors.initials: J
authors.lastname: Moyes
authors.forename: Orienka
authors.initials: O
authors.lastname: Hellferscee
authors.forename: Ebrahim
authors.initials: E
authors.lastname: Variava
authors.forename: Halima
authors.initials: H
authors.lastname: Dawood
authors.forename: Meera
authors.initials: M
authors.lastname: Chhagan
authors.forename: Sumayya
authors.initials: S
authors.lastname: Haffjee
authors.forename: Shabir A
authors.initials: SA
authors.lastname: Madhi
authors.forename: Cheryl
authors.initials: C
authors.lastname: Cohen
authors.forename: Marietjie
authors.initials: M
authors.lastname: Venter
mesh_terms: D000293:Adolescent; D000328:Adult; D002648:Child; D002675:Child, Preschool; D005260:Female; D014644:Genetic Variation; D006801:Humans; D007223:Infant; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D010850:Picornaviridae Infections / Q000453:epidemiology / Q000821:virology*; D012229:Rhinovirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D013019:South Africa / Q000453:epidemiology; D055815:Young Adult
keywords: Disease association; South Africa; genetic diversity; rhinovirus