Use of unique RNA sequence-specific oligonucleotide primers for RT-PCR to detect and differentiate soybean mosaic virus strains

A reverse transcription-polymerase chain reaction (RT-PCR) assay was developed to detect and discriminate between RNAs of individual soybean mosaic virus strains G2 and G7. This assay utilized oligonucleotides complementary to unique regions in the cylindrical inclusion protein cistron. When G2- and G7-specific primers were used, amplification from total RNAs from tri-foliolate soybean leaves infected with either strain or a mixture of strains yielded specific fragments. The specificity of primers was validated further by amplification of only the expected 277-bp fragment characteristic of the G7 strain from infected soybean differential cultivars used to discriminate the strains. Thus, this specifically designed assay allowed discrimination of strains in a mixed infection of a single soybean host plant. This represents a method capable of discriminating between two very closely related pathogens that were previously distinguishable by laborious bioassays.