title: Respiratory viral coinfections identified by a 10-plex real-time reverse-transcription polymerase chain reaction assay in patients hospitalized with severe acute respiratory illness--South Africa, 2009-2010.
abstract: BACKGROUND
  Data about respiratory coinfections with 2009 pandemic influenza A virus subtype H1N1 during the 2009-2010 influenza pandemic in Africa are limited. We used an existing surveillance program for severe acute respiratory illness to evaluate a new multiplex real-time polymerase chain reaction assay and investigate the role of influenza virus and other respiratory viruses in pneumonia hospitalizations during and after the influenza pandemic in South Africa.
  
  
  METHODS
  The multiplex assay was developed to detect 10 respiratory viruses, including influenza A and B viruses, parainfluenza virus types 1-3, respiratory syncytial virus (RSV), enterovirus, human metapneumovirus (hMPV), adenovirus (AdV), and rhinovirus (RV), followed by influenza virus subtyping. Nasopharyngeal and oropharyngeal specimens were collected from patients hospitalized with pneumonia at 6 hospitals during 2009-2010.
  
  
  RESULTS
  Validation against external quality controls confirmed the high sensitivity (91%) and specificity (100%) and user-friendliness, compared with other PCR technologies. Of 8173 patients, 40% had single-virus infections, 17% had coinfections, and 43% remained negative. The most common viruses were RV (25%), RSV (14%), AdV (13%), and influenza A virus (5%). Influenza virus, RSV, PIV type 3, and hMPV showed seasonal patterns.
  
  
  CONCLUSIONS
  The data provide a better understanding of the viral etiology of hospitalized cases of pneumonia and demonstrate the usefulness of this multiplex assay in respiratory disease surveillance in South Africa.
authors.affiliation: National Institute for Communicable Diseases, National Health Laboratory Service, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Marthi A
authors.initials: MA
authors.lastname: Pretorius
authors.forename: Shabir A
authors.initials: SA
authors.lastname: Madhi
authors.forename: Cheryl
authors.initials: C
authors.lastname: Cohen
authors.forename: Dhamari
authors.initials: D
authors.lastname: Naidoo
authors.forename: Michelle
authors.initials: M
authors.lastname: Groome
authors.forename: Jocelyn
authors.initials: J
authors.lastname: Moyes
authors.forename: Amelia
authors.initials: A
authors.lastname: Buys
authors.forename: Sibongile
authors.initials: S
authors.lastname: Walaza
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: Kathleen
authors.initials: K
authors.lastname: Kahn
authors.forename: Adrian
authors.initials: A
authors.lastname: Puren
authors.forename: Marietjie
authors.initials: M
authors.lastname: Venter
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002648:Child; D002675:Child, Preschool; D060085:Coinfection / Q000453:epidemiology* / Q000821:virology; D005260:Female; D006760:Hospitalization; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D007251:Influenza, Human / Q000453:epidemiology* / Q000821:virology; D008297:Male; D008875:Middle Aged; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods*; D009305:Nasopharynx / Q000821:virology; D009960:Oropharynx / Q000821:virology; D012141:Respiratory Tract Infections / Q000453:epidemiology* / Q000821:virology; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D013019:South Africa / Q000453:epidemiology; D014780:Viruses / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D055815:Young Adult