16Potato is one of the staple crops in Egypt, grown under irrigation almost continuously 17 year-round. Potato virus Y (PVY) has been reported as one of the main viruses affecting potatoes 18 in Egypt, but limited information is available on PVY strains circulating in potato fields in the 19 country. From 2014 to 2016, virus surveys were conducted in several potato-growing 20 governorates of Egypt, and PVY-positive samples were found to represent at least five distinct 21 recombinant PVY strains, including PVY NTN and PVY N-Wi . Whole genome sequences were 22 determined for four isolates representing strains PVY-SYR-III (Egypt7), PVY-261-4 (Egypt11), 23 PVY NTNa (Egypt35), and a novel recombinant named Egypt24 which combined molecular 24 properties of strains PVY-261-4 and PVY-Wilga156var. At least three recombinants found in 25 Egypt in potato were previously found associated with potato tuber necrotic ringspot disease 26 (PTNRD). The identification of multiple recombinant types of PVY in potato in Egypt, including 27 the novel recombinant Egypt24, suggests a wide presence of PTNRD-inducing virus strains in 28 the country.

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Solanum tuberosum (potato) is the second most important vegetable crop in Egypt. It is locally consumed, manufactured or supplied for export to Europe and other Arab countries. Potato is subject to infection by a number of plant viruses, which affect its yield and quality. Potato virus Y (PVY), potato leaf roll virus (PLRV), and Alfalfa mosaic virus (AMV) were detected in major potato-growing areas surveyed. Multiplex-RT-PCR assay was used for the detection of these three viruses in one reaction using three specific primer pairs designed to amplify genomic parts of each virus (1594 bp for PLRV, 795 bp for AMV, 801 bp for PVY). All three viruses were detected in a single reaction mixture in naturally infected field-grown potatoes. Multiplex RT-PCR improved sensitivity necessary for the early detection of infection. Incidence of single, double, or triple infection has been recorded in some locations. Full-length sequencing has been performed for an Egyptian FER isolate of PLRV. Through phylogenetic analysis, it was shown to occupy the same clade with isolate JokerMV10 from Germany. Complete nucleotide sequence of an Egyptian FER isolate of AMV and phylogenetic analysis was also performed; we propose that it is a new distinct strain of AMV belonging to a new subgroup IIC. This is the first complete nucleotide sequence of an Egyptian isolate of AMV. Genetic biodiversity of devastating potato viruses necessitates continuous monitoring of new genetic variants of such viruses.

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