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Please cite this paper as: Pabbaraju et al. (2011) Comparison of a singleplex real-time RT-PCR assay and multiplex respiratory viral panel assay for detection of influenza 'A' in respiratory specimens. Influenza and Other Respiratory Viruses 5(2), 99-103. Evaluation of different molecular tests for the detection of pandemic (H1N1) 2009 virus is important before the next wave of the pandemic. To compare a hydrolysis probe-based real-time RT-PCR assay recommended by the CDC to the xTAG respiratory viral panel (RVP) (Luminex Molecular Diagnostics) for the detection of influenza A. Eleven thousand eight hundred and ninety-eight respiratory specimens were tested by the real-time RT-PCR and RVP assays for the detection of influenza A. The distribution of seasonal H1, H3 and pandemic H1N1 subtypes in these specimens was compared. The RVP assay was generally unable to identify influenza A-positive samples with a low viral load, whereas the real-time RT-PCR assay detected most of these samples resulting in a subset of specimens that could not be confirmed as either seasonal or pandemic influenza A subtypes. When the prevalence of influenza A is high, the CDC recommended real-time RT-PCR has significant advantages as a frontline assay, namely higher sensitivity and shorter time to reporting a result. Anticipated scenarios would be during the peaks of the pandemic and episodes of seasonal influenza. Furthermore, the better sensitivity of the RT-PCR makes it the preferred assay to detect influenza in patients with severe respiratory disease tested late in their clinical course. If pandemic (H1N1) 2009 virus is not the dominant virus and there is a high proportion of other respiratory viruses circulating, laboratories will be faced with the decision to use the RVP assay for the detection of pandemic (H1N1) 2009 virus. [ABSTRACT FROM AUTHOR]