Detection and discrimination of European isolates of Soil-borne wheat mosaic virus using immunocapture real-time reverse transcription-polymerase chain reaction

Soil-borne wheat mosaic virus (SBWMV) is a viral pathogen of cereal crops. Although first detected in the United States, it has since been reported in Germany and Poland. To date, two SBWMV strains (Nebraska-like and New-York-like types) have been detected. While the nucleotide sequences of the coat protein (CP) genes from the two strains show only 89% similarity, the deduced amino acid sequences of this region are identical. Therefore, the isolates cannot be differentiated serologically using the double antibody sandwich enzyme-linked immunosorbent assay. An immunocapture real-time reverse transcription-polymerase chain reaction (IC-real-time-RT-PCR) assay was developed for detection and discrimination of SBWMV strains based on the amplification of short CP fragments (∼250 bp). The results showed distinct melting curve profiles related to each strain. The primer pairs gave similar melting points, with a Tm of 82.1 °C for Nebraska-like and 83.5 °C for New-York-like SBWMV strains. This work confirms that IC-real-time-RT-PCR is a valuable technique for rapid detection and discrimination of SBWMV strains.