The simultaneous differentiation of Potato virus Y strains including the newly described strain PVY(NTN-NW) by multiplex PCR assay.

New recombinant strain and genotype of PVY, designated as PVY(NTN-NW) and SYR-III, respectively, shared properties with PVY(NTN) and PVY(N)W has been reported recently. PVY(NTN-NW) predominated in potato fields in Syria and was able to induce potato tuber necrotic ringspot disease (PTNRD). Due to the rapid spread of the recombinant strains of PVY which might be the case of PVY(NTN-NW), a specific and reliable detection method is an essential step to control this strain and minimize its spread. The shared properties of PVY(NTN-NW) and SYR-III with PVY(NTN) and PVY(N)W, however, complicate their identification involving multiple detection methods. Therefore, a multiplex polymerase chain reaction (PCR), that relies on a combination of previously published and newly designed primers was developed for the detection and identification of PVY(NTN-NW) and SYR-III in single or mixed infections with the main PVY strains, PVY(O), PVY(N), PVY(NTN) and PVY(N)W. In addition, the present PCR assay was able to detect the recombination points in the P1 region enabling the differentiation of the variable genotypes of the recombinant strains PVY(NTN-NW), PVY(NTN) and PVY(N)W. The reliability of this PCR assay was confirmed using a significant number of well characterized PVY isolates collected from Syria and Japan including those of PVY(NTN-NW), SYR-III, PVY(O), NA-PVY(N), PVY(N)W and PVY(NTN).