Rapid detection of Eurasian and American H7 subtype influenza A viruses using a single TaqManMGB real-time RT-PCR

A real-time reverse transcription PCR (RRT-PCR) targeting a highly conserved HA2 H7 region was developed for the detection of all H7 subtype avian influenza viruses (PanH7). The wide phylogenetic scope and analytical sensitivity and specificity were validated with the use of a panel of 56 diverse influenza A viruses. The detection limit was determined with the use of serial dilutions of Eurasian isolates A/Ck/BE/06775/2003 and A/Ck/It/1067/v99 and North American isolates A/CK/PA/ 143586/2001 and A/Quail/PA/20304/1998, to be 1 log10 higher than the detection limit of the generic influenza A matrix RRT-PCR (about 2.5 EID50/reaction compared to 0.25 EID50/reaction for matrix). Diagnostic test properties of PanH7 were determined with the use of 102 swabs from A/Ck/It/1067/v99 experimentally infected chickens, and were not affected by the increased detection limit of PanH7. In comparison to matrix RRT-PCR and virus isolation in embryonated chicken eggs (VI), the PanH7 detected more weakly positive oropharyngeal swabs at the onset of the infection. PanH7 diagnostic sensitivity compared to virus isolation (VI) was 83.3% (compared to 72.2% for matrix RRT-PCR); and diagnostic specificity was 88.1% (94.0% for matrix). The PanH7 test can also be tailored to detect only American (AmH7) or only Eurasian (EurH7) strains by changing the mix of forward and reverse primers used in combination with the unique probe. Overall, this new test is a valuable tool for the detection and identification of H7 subtype influenza A.