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, PVS^I, PVS^II or PVS^III. All Turkish CP sequences were in PVS^I, 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 PVS^I and PVS^II isolates. Three neutrality test methods showed PVS^III remained balanced whilst PVS^I and PVS^II underwent population expansion. The high fixation index values assigned to all PVS^I, PVS^II and PVS^III comparisons supported subdivision into three phylogroups. As it spreads more readily by aphid and contact transmission, and may elicit more severe symptoms in potato, PVS^II spread constitutes a biosecurity threat for countries still free from it.

Grapevine (Vitis spp.) is one of the major fruit crop with high socioeconomic importance for Turkey. In vineyards, many harmful organism, especially virus infections, weaken the plant and lead to decreases in yield and quality, so it takes the lead in quarantine and certification. This study was carried out to determine some viral agents that cause yield loss in vines produced in Tokat, where viticulture is very important. Samples were collected from young leaves and one-year-old shoots of grapevines showing virus symptoms from some vineyard areas in Tokat Center and its districts. Collected 189 grapevine samples were subjected to the RT-PCR test, which is a molecular method using virus-specific primers, to detect the presence of Grapevine pinot gris virus (GPGV), Grapevine virus A (GVA), Strawberry latent ringspot virus (SLRSV). Out of a total of 189 plant samples, 80 (42.32%) of GVA, 3 (1.58%) of GPGV were detected and SLRSV (0%) was not detected. More than one virus was found in 2 (1.05%) of 189 tested samples. It was determined that the most common virus was GVA, the least detected virus was GPGV in plant samples collected from Tokat Center and its districts. Bidirectional sequence analysis of RT-PCR products of GVA-infected isolates were performed and phylogenetic analyzes were done by comparing them with reference isolates after they were aligned with the MEGAX computer program. Based on phylogenetic analysis studies, GVA showed differential branching with isolates registered in GenBank and isolates obtained in the study. GVA-infected isolates showed similarity with reference isolates at rates of 92-94%. In this study, molecular analysis of Turkish GVA isolates was performed. This molecular information is important as it will shed light on future studies.

The study was conducted in Tokat Center, Niksar, Erbaa and Pazar districts where peppers were grown in the summer of 2016, and leaf samples were collected from plants suspected of the virus. During the surveys, a total of 324 plant samples were collected and the infected pepper samples were subjected to DAS-ELISA test with (Tomato spotted wilt virus) TSWV-specific antiserum, and RT-PCR was performed with virus-specific primers. In DAS-ELISA studies, 324 plants were tested and 13% of the samples were found to be TSWV infected. Samples that were positive in ELISA test were subjected to RT-PCR with nucleocapsid gene specific primers in the S segment and three samples were sent for sequence analysis. According to results, Turkey TSWV isolates Np gene region have shown 98-99% nucleotide identity with the isolates from France and South Korea and grouped with them same group.

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.