| 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. | ||
| Author | Pretorius, Marthi A; Madhi, Shabir A; Cohen, Cheryl; Naidoo, Dhamari; Groome, Michelle; Moyes, Jocelyn; Buys, Amelia; Walaza, Sibongile; Dawood, Halima; Chhagan, Meera; Haffjee, Sumayya; Kahn, Kathleen; Puren, Adrian; Venter, Marietjie | ||
| Journal | J Infect Dis | Publication Year/Month | 2012-Dec |
| PMID | 23169964 | PMCID | -N/A- |
| Affiliation | 1.National Institute for Communicable Diseases, National Health Laboratory Service, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. | ||
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. CONCLUSION: 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.