The simultaneous differentiation of Potato virus Y strains including the newly described strain PVYNTN-NW by multiplex PCR assay

New recombinant strain and genotype of PVY, designated as PVYNTN-NW and SYR-III, respectively, shared properties with PVYNTN and PVYNW has been reported recently. PVYNTN-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 PVYNTN-NW, a specific and reliable detection method is an essential step to control this strain and minimize its spread. The shared properties of PVYNTN-NW and SYR-III with PVYNTN and PVYNW, 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 PVYNTN-NW and SYR-III in single or mixed infections with the main PVY strains, PVYO, PVYN, PVYNTN and PVYNW. 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 PVYNTN-NW, PVYNTN and PVYNW. 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 PVYNTN-NW, SYR-III, PVYO, NA-PVYN, PVYNW and PVYNTN.