Comparative Analysis Of Real Time RT-PCR And Virus Isolation For Detection And Subtyping Of A(H1N1)Pdm09 Influenza Virus

A comparative study for the detection and identification of A(H1N1)pdm09 influenza viruses was carried-out on respiratory samples collected during the period 2009-2011 when influenza activity in central Greece was dominated by this virus subtype. We evaluated 1500 nasal and pharyngeal swabs for the presence of A(H1N1)pdm09 influenza by virus culture in Madin-Darby Canine Kidney (MDCK) cells and by real-time RT-PCR assay (rt-RT-PCR). By cell culture, A(H1N1)pdm09 viruses were isolated and identified by hemagglutination-inhibition (HAI) in 387 samples (26%), while by rt-RT-PCR, A(H1N1)pdm09 RNA sequences were detected and identified in 510 samples (34%). There was found a 100% correlation of virus type and subtype, following testing by both methods. Using cell culture as the gold standard, rt-RT-PCR had a 100% sensitivity and detected an additional 123 (8%) A(H1N1)pdm09 viruses in the samples evaluated. The rt-RT-PCR assay, for the detection and subtyping of A(H1N1)pdm09 viruses during pandemic influenza activity in central Greece, provided a rapid, sensitive, and low-cost method for the screening and diagnosis of influenza in respiratory samples.