title: The role of influenza, RSV and other common respiratory viruses in severe acute respiratory infections and influenza-like illness in a population with a high HIV sero-prevalence, South Africa 2012-2015.
abstract: BACKGROUND
  Viruses detected in patients with acute respiratory infections may be the cause of illness or asymptomatic shedding.
  
  
  OBJECTIVE
  To estimate the attributable fraction (AF) and the detection rate attributable to illness for each of the different respiratory viruses
  
  
  METHODS
  We compared the prevalence of 10 common respiratory viruses (influenza A and B viruses, parainfluenza virus 1-3; respiratory syncytial virus (RSV); adenovirus, rhinovirus, human metapneumovirus (hMPV) and enterovirus) in both HIV positive and negative patients hospitalized with severe acute respiratory illness (SARI), outpatients with influenza-like illness (ILI), and control subjects who did not report any febrile, respiratory or gastrointestinal illness during 2012-2015 in South Africa.
  
  
  RESULTS
  We enrolled 1959 SARI, 3784 ILI and 1793 controls with a HIV sero-prevalence of 26%, 30% and 43%, respectively. Influenza virus (AF: 86.3%; 95%CI: 77.7-91.6%), hMPV (AF: 85.6%; 95%CI: 72.0-92.6%), and RSV (AF: 83.7%; 95%CI: 77.5-88.2%) infections were associated with severe disease., while rhinovirus (AF: 46.9%; 95%CI: 37.6-56.5%) and adenovirus (AF: 36.4%; 95%CI: 20.6-49.0%) were only moderately associated.
  
  
  CONCLUSIONS
  Influenza, RSV and hMPV can be considered pathogens if detected in ILI and SARI while rhinovirus and adenovirus were commonly identified in controls suggesting that they may cause only a proportion of clinical disease observed in positive patients. Nonetheless, they may be important contributors to disease.
authors.affiliation: National Health Laboratory Service, Tshwane Academic Division, South Africa; Department of Medical Virology, University of Pretoria, South Africa; Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa. Electronic address: marthi.pretorius@up.ac.za.
authors.forename: Marthi A
authors.initials: MA
authors.lastname: Pretorius
authors.affiliation: Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States; Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa.
authors.forename: Stefano
authors.initials: S
authors.lastname: Tempia
authors.affiliation: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
authors.forename: Sibongile
authors.initials: S
authors.lastname: Walaza
authors.affiliation: Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States; Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa.
authors.forename: Adam L
authors.initials: AL
authors.lastname: Cohen
authors.affiliation: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Jocelyn
authors.initials: J
authors.lastname: Moyes
authors.affiliation: Department of Medicine, Klerksdorp Tshepong Hospital, Klerksdorp, South Africa; Department of Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Ebrahim
authors.initials: E
authors.lastname: Variava
authors.affiliation: Department of Medicine, Pietermaritzburg Metropolitan Hospital, Pietermaritzburg, South Africa; Department of Medicine, University of KwaZulu Natal, South Africa.
authors.forename: Halima
authors.initials: H
authors.lastname: Dawood
authors.affiliation: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
authors.forename: Mpho
authors.initials: M
authors.lastname: Seleka
authors.affiliation: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
authors.forename: Orienka
authors.initials: O
authors.lastname: Hellferscee
authors.affiliation: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
authors.forename: Florette
authors.initials: F
authors.lastname: Treurnicht
authors.affiliation: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Cheryl
authors.initials: C
authors.lastname: Cohen
authors.affiliation: Department of Medical Virology, University of Pretoria, South Africa; Global Disease Detection, Centers for Disease Control and Prevention, Pretoria, South Africa.
authors.forename: Marietjie
authors.initials: M
authors.lastname: Venter
mesh_terms: D000256:Adenoviridae; D015658:HIV Infections / Q000097:blood / Q000150:complications*; D006679:HIV Seropositivity; D006801:Humans; D007251:Influenza, Human / Q000097:blood / Q000821:virology; D009975:Orthomyxoviridae; D015995:Prevalence; D018108:Respirovirus; D012229:Rhinovirus; D045169:Severe Acute Respiratory Syndrome / Q000453:epidemiology / Q000209:etiology / Q000821:virology*; D013019:South Africa
keywords: Controls; Disease association; HIV; Influenza like illness; Pneumonia; Respiratory virus infection; Severe acute respiratory illness; South Africa