Respiratory viral coinfections identified by a 10-plex real-time reverse-transcription polymerase chain reaction assay in patients hospitalized with severe acute respiratory iIllness, South Africa, 2009–2010

Abstract

BACKGROUND: Data about respiratory co-infections of Influenza A H1N1 during the pandemic in Africa are limited. We used an existing surveillance programme for severe acute respiratory illness (SARI) to evaluate a new multiplex real-time polymerase chain reaction assay and investigate the role of influenza and other respiratory viruses in pneumonia hospitalisations during and after the influenza pandemic in South Africa. METHOD: The multiplex assay was developed to detect 10 respiratory viruses including Influenza (INF) A and B, Parainfluenza (PIV1-3), Respiratory Syncytial Virus (RSV), Enterovirus (EV), human metapneumovirus (hMPV), Adenovirus (AdV) and Rhinovirus (RV), followed by influenza subtyping. Nasopharyngeal and oropharyngeal specimens were collected from patients hospitalized with pneumonia at six hospitals during 2009–2010. RESULTS: Validation against external quality controls confirmed the high sensitivity (91%) and specificity (100%) and user-friendliness when compared to other PCR technologies. Of 8173 patients, 40% had single-infections, 17% co-infections and 43% remained negative. The most common viruses were: RV (25%), RSV (14%), AdV (13%), Influenza A (5%). Influenza, RSV, PIV3 and hMPV showed seasonal patterns. CONCLUSION: The data provide a better understanding of the viral aetiology of hospitalized cases of pneumonia and demonstrate the usefulness of this multiplex assay in respiratory disease surveillance in South Africa.