title: Epidemiology of severe acute respiratory illness (SARI) among adults and children aged ≥5 years in a high HIV-prevalence setting, 2009-2012.
abstract: OBJECTIVE
  There are few published studies describing severe acute respiratory illness (SARI) epidemiology amongst older children and adults from high HIV-prevalence settings. We aimed to describe SARI epidemiology amongst individuals aged ≥5 years in South Africa.
  
  
  METHODS
  We conducted prospective surveillance for individuals with SARI from 2009-2012. Using polymerase chain reaction, respiratory samples were tested for ten viruses, and blood for pneumococcal DNA. Cumulative annual SARI incidence was estimated at one site with population denominators.
  
  
  RESULTS
  We enrolled 7193 individuals, 9% (621/7067) tested positive for influenza and 9% (600/6519) for pneumococcus. HIV-prevalence was 74% (4663/6334). Among HIV-infected individuals with available data, 41% of 2629 were receiving antiretroviral therapy (ART). The annual SARI hospitalisation incidence ranged from 325-617/100,000 population. HIV-infected individuals experienced a 13-19 times greater SARI incidence than HIV-uninfected individuals (p<0.001). On multivariable analysis, compared to HIV-uninfected individuals, HIV-infected individuals were more likely to be receiving tuberculosis treatment (odds ratio (OR):1.7; 95%CI:1.1-2.7), have pneumococcal infection (OR 2.4; 95%CI:1.7-3.3) be hospitalised for >7 days rather than <2 days (OR1.7; 95%CI:1.2-2.2) and had a higher case-fatality ratio (8% vs 5%;OR1.7; 95%CI:1.2-2.3), but were less likely to be infected with influenza (OR 0.6; 95%CI:0.5-0.8). On multivariable analysis, independent risk indicators associated with death included HIV infection (OR 1.8;95%CI:1.3-2.4), increasing age-group, receiving mechanical ventilation (OR 6.5; 95%CI:1.3-32.0) and supplemental-oxygen therapy (OR 2.6; 95%CI:2.1-3.2).
  
  
  CONCLUSIONS
  The burden of hospitalized SARI amongst individuals aged ≥5 years is high in South Africa. HIV-infected individuals are the most important risk group for SARI hospitalization and mortality in this setting.
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: 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: Sibongile
authors.initials: S
authors.lastname: Walaza
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: Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Michelle
authors.initials: M
authors.lastname: Groome
authors.affiliation: Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America; Influenza Programme, Centers for Disease Control and Prevention-South Africa, 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: Marthi
authors.initials: M
authors.lastname: Pretorius
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: Department of Medicine, Pietermaritzburg Metropolitan Hospital and University of KwaZulu Natal, Pietermaritzburg, South Africa.
authors.forename: Halima
authors.initials: H
authors.lastname: Dawood
authors.affiliation: School of Pathology, University of KwaZulu Natal, Pietermaritzburg, South Africa.
authors.forename: Summaya
authors.initials: S
authors.lastname: Haffejee
authors.affiliation: Department of Medicine, Klerksdorp Tshepong Hospital, 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: MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Centre for Global Health Research, Umeå University, Umeå, Sweden; INDEPTH Network, Accra, Ghana.
authors.forename: Kathleen
authors.initials: K
authors.lastname: Kahn
authors.affiliation: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
authors.forename: Akhona
authors.initials: A
authors.lastname: Tshangela
authors.affiliation: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Anne
authors.initials: A
authors.lastname: von Gottberg
authors.affiliation: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Nicole
authors.initials: N
authors.lastname: Wolter
authors.affiliation: Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America; Influenza Programme, Centers for Disease Control and Prevention-South Africa, 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.
authors.forename: Babatyi
authors.initials: B
authors.lastname: Kgokong
authors.affiliation: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Zoonoses Research Unit, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.
authors.forename: Marietjie
authors.initials: M
authors.lastname: Venter
authors.affiliation: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Shabir A
authors.initials: SA
authors.lastname: Madhi
mesh_terms: D000208:Acute Disease; D000293:Adolescent; D000328:Adult; D000368:Aged; D044966:Anti-Retroviral Agents / Q000627:therapeutic use; D002648:Child; D002675:Child, Preschool; D015897:Comorbidity; D005260:Female; D015658:HIV Infections / Q000188:drug therapy / Q000453:epidemiology*; D006780:Hospitals, Rural / Q000706:statistics & numerical data*; D006786:Hospitals, Urban / Q000706:statistics & numerical data*; D006801:Humans; D007251:Influenza, Human / Q000453:epidemiology / Q000821:virology; D008297:Male; D008875:Middle Aged; D011159:Population Surveillance / Q000379:methods; D015995:Prevalence; D011446:Prospective Studies; D012141:Respiratory Tract Infections / Q000453:epidemiology* / Q000821:virology; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012720:Severity of Illness Index; D013019:South Africa / Q000453:epidemiology; D014780:Viruses / Q000235:genetics; D055815:Young Adult
chemical_list: D044966:Anti-Retroviral Agents