Potato virus Y (PVY) is a serious threat to potato production due to effects on tuber yield and quality, in particular, due to induction of potato tuber necrotic ringspot disease (PTNRD), typically associated with recombinant strains of PVY. These recombinant strains have been spreading in the United States for the past several years, although the reasons for this continuing spread remained unclear. To document and assess this spread between 2011 and 2015, strain composition of PVY isolates circulating in the Columbia Basin potato production area was determined from hundreds of seed lots of various cultivars. The proportion of nonrecombinant PVYO isolates circulating in Columbia Basin potato dropped ninefold during this period, from 63% of all PVY-positive plants in 2011 to less than 7% in 2015. This drop in PVYO was concomitant with the rise of the recombinant PVYN-Wi strain incidence, from less than 27% of all PVY-positive plants in 2011 to 53% in 2015. The proportion of the PVYNTN recombinant strain, associated with PTNRD symptoms in susceptible cultivars, increased from 7% in 2011 to approximately 24% in 2015. To further address the shift in strain abundance, screenhouse experiments were conducted and revealed that three of the four most popular potato cultivars grown in the Columbia Basin exhibited strain-specific resistance against PVYO. Reduced levels of systemic movement of PVYO in such cultivars would favor spread of recombinant strains in the field. The negative selection against the nonrecombinant PVYO strain is likely caused by the presence of the Nytbr gene identified in potato cultivars in laboratory experiments. Presence of strain-specific resistance genes in potato cultivars may represent the driving force changing PVY strain composition to predominantly recombinant strains in potato production areas.

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Isolates of Potato virus Y (PVY), collected in Syria, induced vein necrosis in tobacco but reacted to PVYO monoclonal antibody, and were therefore classified as PVYNW (or PVYN:O). The possible recombinant points within the genome were checked using a previously reported multiplex RT‐PCR. These isolates were categorized in two groups according to recombinant points. Isolates with one recombinant point at the HC‐Pro/P3, identical to previously reported PVYNW (or PVYN:O), were designated as group 1. However, the majority of Syrian PVY isolates showed two recombinant points at both HC‐Pro/P3 and 6K2/NIa, revealing a new genomic recombination pattern that had never been reported for PVYNW (or PVYN:O), hereafter referred to as group 2. Further characterizations showed that isolates of group 2 had an additional recombinant point at the N‐terminal of the coat protein gene (CP) of their genome. Based on the bioassay on tobacco, serological and molecular studies, these isolates showed shared characteristics of both PVYNW and the recombinant PVYNTN, making it difficult to include them in any of these variants. We propose them as new isolates of PVYN strain, and label them PVYSYR (SYR is from Syria, the country of origin).

A multiplex reverse-transcription polymerase chain reaction (RT-PCR) assay was previously developed to identify a group of Potato virus Y (PVY) isolates with unusual recombinant structures (e.g., PVYNTN-NW and SYR-III) and to differentiate them from other PVY strains. In the present study, the efficiency of this multiplex RT-PCR assay was validated and extended considerably to include five additional strains and strain groups not tested before. To make the multiplex RT-PCR assay more applicable and suitable for routine virus testing and typing, it was modified by replacing the conventional RNA extraction step with the immunocapture (IC) procedure. The results obtained using well-characterized reference isolates revealed, for the first time, that this multiplex RT-PCR assay is an accurate and robust method to identify and differentiate the nine PVY strains reported to date, including PVYO (both PVYO and PVYO-O5), PVYN, PVYNA-N, PVYNTN, PVYZ, PVYE, PVY-NE11, PVYN-Wi, and PVYN:O, which is not possible by any of the previously reported RT-PCR procedures. This would make the IC-RT-PCR procedure presented here a method of choice to identify PVY strains and assess the strain composition of PVY in a given area. The IC-RT-PCR protocol was successfully applied to typing PVY isolates in potato leaf tissue collected in the field.

Detailed characterization of a number of isolates of PVYSYR, a novel recombinant strain of Potato virus Y (PVY) from Syria, was conducted to elucidate their origin, assess their significance and achieve a final classification of PVYSYR. Recombination analysis grouped isolates of PVYSYR into three recombination patterns, SYR‐I, SYR‐II and SYR‐III, which varied in the first 700 nucleotides of their genomes, with the second recombination pattern, SYR‐II, the most frequent. PVYSYR isolates shared highest genomic identity and close phylogenetic relationships with PVYNTN and PVYNW isolates from Syria, suggesting a common origin and local emergence of these isolates in Syria. All PVYSYR isolates (total of 20) induced tobacco veinal necrosis, but reacted to a PVYO monoclonal antibody, typical characteristics of the previously reported PVYNW (or PVYN:O). In potato, however, four isolates tested (one of SYR‐I and three of SYR‐II) induced potato tuber necrotic ringspot disease (PTNRD), which is the characteristic phenotype of PVYNTN. Given the shared properties of SYR‐I and SYR‐II isolates with PVYNTN and PVYNW, it was decided that they represent a new recombinant strain of the PVYN strain group, with the proposed name PVYNTN‐NW. The classification of SYR‐III will be possible only after testing the phenotype in potato. The high prevalence of PVYNTN‐NW in potatoes and weeds, as well as its ability to induce PTNRD, demonstrates its importance and the necessity for its control.