Avian Influenza Virus Detection and Quantitation by Real-Time RT-PCR

Real-time RT-PCR (rRT-PCR) has been used for avian influenza virus (AIV) detection since the early 2000s. This method has been applied to surveillance, outbreaks and research. Some of the advantages of rRT-PCR are high sensitivity, high specificity, rapid time to result, scalability, cost, and its inherently quantitative nature. Furthermore, rRT-PCR can be used with numerous sample types and is less expensive than virus isolation in chicken embryos, and since infectious virus is inactivated early during processing, biosafety and biosecurity are also easier to maintain. However, the high genetic variability of AIV may decrease sensitivity and increases the chances of a false negative result with novel strains. This chapter will provide an overview of the USDA-validated rRT-PCR procedure for the detection of type A influenza.