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In 2020, 264 samples were collected from potato fields in the Turkish provinces of Bolu, Afyon, Kayseri and Niğde. RT-PCR tests, with primers which amplified its coat protein (CP), detected potato virus S (PVS) in 35 samples. Complete CP sequences were obtained from 14 samples. Phylogenetic analysis using non-recombinant sequences of (i) the 14 CP’s, another 8 from Tokat province and 73 others from GenBank; and (ii) 130 complete ORF, RdRp and TGB sequences from GenBank, found that they fitted within phylogroups, PVSI, PVSII or PVSIII. All Turkish CP sequences were in PVSI, clustering within five subclades. Subclades 1 and 4 were in three to four provinces, whereas 2, 3 and 5 were in one province each. All four genome regions were under strong negative selection constraints (ω = 0.0603–0.1825). Considerable genetic variation existed amongst PVSI and PVSII isolates. Three neutrality test methods showed PVSIII remained balanced whilst PVSI and PVSII underwent population expansion. The high fixation index values assigned to all PVSI, PVSII and PVSIII comparisons supported subdivision into three phylogroups. As it spreads more readily by aphid and contact transmission, and may elicit more severe symptoms in potato, PVSII spread constitutes a biosecurity threat for countries still free from it.

Apple mosaic virus (ApMV) is one of the most important diseases limiting the production of hazelnut and apple in Turkey and the objectives of this research were to determine the convenient and reliable method for RNA isolation and also to determine primer pair for real time polymerase chain reaction (RT-PCR) detection of coat protein gene for Turkish ApMV isolates. Apple mosaic virus isolates were collected in 2007 to 2010 and the presence of the pathogen was detected by double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) and RT-PCR tests. Six different RNA extraction protocols and three primer pairs were applied in RT-PCR amplifications and 44 hazelnut and 15 apple ApMV isolates were obtained. All of the amplicons were subjected to enzymatic digestion with restriction endonuclease enzymes and phylogenetic analysis were performed according to the digestion profiles.

The Alfalfa mosaic virus (AMV) was detected in potato fields in the Tokat province. The coat protein (CP) sequences of AMV isolates from the Tokat province were determined and compared with sequences of reference AMV isolates from GenBank. Total nucleic acid (TNA) was extracted from plants with positive results according to serological test results. Then, reverse-transcription polymerase chain reaction (RT-PCR) was performed using primer pair specific to partial the coat protein region, and positive PCR products were sent for sequence analysis in both directions. Two Turkish AMV isolates (AMV-PN3-5 and AMV-PN3-6) had a 96-99% nt homology amongst themselves, according to nucleotides (nt) sequence analysis. Based on the phylogenetic tree obtained from 24 AMV isolates from GenBank for both sequences, the two Turkish AMV isolates were clustered in subgroup I containing Iranian, Canadian, Turkish, Korean, and Serbian isolates, at the nucleotide level. Sequence comparison showed that these two isolates of AMV shared 96% to 99.7% sequence similarity with the twenty-six reported isolates of AMV obtained from GenBank. This is the first report on the genetic variability of AMV isolates infecting potato crops in the Tokat province.