Marthi A Pretorius1, Stefano Tempia2, Sibongile Walaza3, Adam L Cohen2, Jocelyn Moyes4, Ebrahim Variava5, Halima Dawood6, Mpho Seleka3, Orienka Hellferscee3, Florette Treurnicht3, Cheryl Cohen4, Marietjie Venter7. 1. 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. 2. Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States; Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa. 3. Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa. 4. 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. 5. Department of Medicine, Klerksdorp Tshepong Hospital, Klerksdorp, South Africa; Department of Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. 6. Department of Medicine, Pietermaritzburg Metropolitan Hospital, Pietermaritzburg, South Africa; Department of Medicine, University of KwaZulu Natal, South Africa. 7. Department of Medical Virology, University of Pretoria, South Africa; Global Disease Detection, Centers for Disease Control and Prevention, Pretoria, South Africa.
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 STUDY DESIGN: 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.
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 STUDY DESIGN: 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.
Keywords:
Controls; Disease association; HIV; Influenza like illness; Pneumonia; Respiratory virus infection; Severe acute respiratory illness; South Africa
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