Assessing the applicability of transcript conformation polymorphism for differentiation among «Prunus nocrotic ringspot virus» isolates

Abstract

The applicability of single and double-stranded transcript conformation polymorphism (TCP) for differentiation among Prunus necrotic ringspot virus (PNRSV) isolates was evaluated and compared with other molecular differentiation procedures. Single-stranded TCP was found to be suitable to differentiate closely related virus isolates. However, due to its high variability, it was not suitable for grouping virus isolates. Double-stranded TCP, on the other hand, enabled the division of virus isolates into major groups. Restriction fragment length polymorphism (RFLP) of the PCR products confirmed the grouping of the virus isolates but this technique was limited in its ability to detect a wide range of nucleotide modifications. Nucleotide sequence analysis was essential for the detection of strain-specific sequences but did not clearly identify most other minor modifications that are necessary for virus classification. The combination of all methods is therefore sometimes required for complete analysis.