Currently, RT-PCR is the most widely used molecular method for the detection and identification of viruses in biological and environmental sources [27, 28] . Identification of genotypes of virus strains are based on the amplification of specific regions of the viral genome using gene specific primers followed by sequencing of the amplicon by standard procedures [28] . In some instances a preliminary identification is possible using the techniques of single strand conformational polymorphisms (SSCP) or restriction fragment length polymorphisms (RFLP) [5] . Multiplex PCR allows the detection of more than one species of virus in a single analyte [29] . However, these techniques have limitations on sensitivity and versatility, and require extensive prior knowledge of the sequences to be amplified. The requirement of size differences in the amplicons to be analyzed by gel electrophoresis following amplification by multiplex PCR also limits its utility.