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

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dc.contributor.author Pretorius, Marthi A.
dc.contributor.author Madhi, Shabir A.
dc.contributor.author Cohen, Cheryl
dc.contributor.author Naidoo, Dhamari
dc.contributor.author Groome, Michelle
dc.contributor.author Moyes, Jocelyn
dc.contributor.author Buys, Amelia
dc.contributor.author Walaza, Sibongile
dc.contributor.author Dawood, Halima
dc.contributor.author Chhagan, Meera
dc.contributor.author Haffejee, Summaya
dc.contributor.author Kahn, Kathleen
dc.contributor.author Puren, Adrian
dc.contributor.author Venter, Marietjie
dc.date.accessioned 2013-05-30T06:35:56Z
dc.date.available 2013-12-31T00:20:04Z
dc.date.issued 2012
dc.description.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. en_US
dc.description.librarian hb2013 en_US
dc.description.sponsorship Funding provided by co-operative agreement 5U51/IP000155 with the Centers for Disease Control and Prevention, Atlanta, Georgia, USA. en_US
dc.description.uri http://www.journals.uchicago.edu/toc/jid/current en_US
dc.identifier.citation Pretorius, MA ... et al. 2012, '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', Journal of Infectious Diseases, vol. 206, Suppl., 1, pp. S159-S165. en_US
dc.identifier.issn 0022-1899 (print)
dc.identifier.issn 1537-6613 (online)
dc.identifier.other 10.1093/infdis/jis538
dc.identifier.uri http://hdl.handle.net/2263/21576
dc.language.iso en en_US
dc.publisher Oxford University Press en_US
dc.rights © The Author 2012. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. en_US
dc.subject Co-infection en_US
dc.subject Pandemic influenza H1N1 en_US
dc.subject Multiplex assay en_US
dc.subject Respiratory virus infection en_US
dc.subject Severe acute respiratory illness en_US
dc.subject South Africa en_US
dc.title 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 en_US
dc.type Postprint Article en_US


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