Differentiating PVY super(NTN) from PVY super(N) by annealing to reference RNA transcripts

A method for the differentiation of virus strains based on the shift in electrophoretic mobility of partially annealed RNA transcripts is described. Oppositely oriented RNA transcripts of the NTN- and N-strains of PVY, complementary at their 3'-end variable (strain-specific) region, were annealed to form a partial duplex which moved more slowly in gel than heterologous (NTN+N) unpaired transcripts. Thus, the two virus strains could be identified by annealing to a known reference transcript. The rate of duplex migration was correlated with transcript lengths and could be tightly controlled thereby. Thus, a higher degree of resolution was obtained than with transcript conformation polymorphism, which is empirical and unpredictable in nature.