• Marthi A Pretorius, Shabir A Madhi, Cheryl Cohen, Dhamari Naidoo, Michelle Groome, Jocelyn Moyes, Amelia Buys, Sibongile Walaza, Halima Dawood, Meera Chhagan, Sumayya Haffjee, Kathleen Kahn, Adrian Puren, and Marietjie Venter.
• National Institute for Communicable Diseases, National Health Laboratory Service, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
• J. Infect. Dis. 2012 Dec 15; 206 Suppl 1: S159-65.

BackgroundData 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.MethodsThe 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.ResultsValidation 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.ConclusionThe 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.

39 keywords...

hide…