Rapid identification of the raccoon rabies virus variant using a real-time reverse-transcriptase polymerase chain reaction

The raccoon-associated variant of rabies virus (RRV) is enzootic throughout the eastern seaboard of the United States with frequent incursions into Canada. Many wildlife management agencies are actively engaged in control programmes targeting elimination of this disease and rapid identification of raccoon rabies cases is crucial to the success of these operations. This report documents the development of a reverse transcriptase real-time PCR (RT-qPCR) that specifically identifies this rabies virus variant (RRV RT-qPCR) and which can be readily multiplexed with a generic rabies virus RT-qPCR for use as a typing tool. Using a large collection of rabies virus samples representative of the variants circulating around the world, but with a focus on those occurring in the Americas, the RRV RT-qPCR was 100% sensitive and 99.31% specific. To further apply these assays for diagnostic purposes, addition of an RT-qPCR targeting the host beta-actin mRNA, which serves as an internal amplification control, in a triplex format was shown to yield highly comparable results using a subset of our viral collection. Use of these assays for early and accurate identification of this viral variant will help to optimize the utilization of resources required for control of this disease.