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    Biological, serological, and molecular characterization of Citrus tristeza virus isolates from different citrus cultivation regions of Turkey
    (Tubitak Scientific & Technological Research Council Turkey, 2008) Korkmaz, Savaş; Cevik, Bayram; Onder, Serkan; Koc, N. Kemal
    Field surveys were carried out in 5 different citrus cultivation regions of Turkey in 2005 and 2006, and 201 samples were collected from different citrus species. Samples were tested for the presence of Citrus tristeza virus (CTV) by double antibody sandwich-enzyme-linked immunosorbent assay (DAS-ELISA) and reverse transcription-polymerase chain reaction (RT-PCR). While DAS-ELISA showed that 41 trees were infected with CTV, an additional 13 trees were found to be positive based on RT-PCR. When CTV-positive samples were tested with the Western blot method using the monoclonal antibody MCA13. which is specific to severe isolates of CTV. 32 isolates, mostly from satsuma, were found to be positive. These isolates were then verified by bidirectional/PCR (BD/PCR), allowing differentiation of the MCA13 positive and negative isolates, and detection of mixed infections. The BD/PCR results were generally in agreement with the results of the Western blot assay with MCA13. In total, 28 isolates representing different geographic locations and hosts were selected for biological indexing. Although none of these 28 isolates induced any symptoms in sour orange, grapefruit, or sweet orange, all isolates induced the vein clearing symptom in Mexican lime. Additionally, all the tested satsuma isolates and 1 kumquat isolate produced stem pitting in Mexican lime. The results revealed that potentially severe isolates of CTV are present in different citrus cultivation regions of Turkey.
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    Detection of Lettuce mosaic virus infection in South Marmara Region of Turkey and coat protein gene characterization
    (Lithuanian Research Centre Agriculture & Forestry, 2018) Karanfil, Ali; Cevik, Bayram; Korkmaz, Savaş
    Lettuce mosaic virus (LMV) is considered as the most destructive virus disease of lettuce. The presence of LMV was detected and LMV isolates were comprehensively characterized at molecular level in different parts of the world. While LMV infection was reported several times in different regions of Turkey, molecular characterization of LMV isolates lagged behind in Turkey compared to other regions of the world. For this purpose, surveys were carried out in Canakkale, Balikesir and Bursa provinces, and their districts which constitute South Marmara Region of Turkey in 2013-2015 lettuce cultivation seasons. A total of 307 samples were collected from lettuce plants showing symptoms of viral infection similar to LMV. The collected samples were tested with double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) to determine the presence of LMV. As a result of the tests, 35 of the 307 samples were infected with LMV. Out of 35 infected samples, 15 were selected considering the provinces and their districts where they were collected for further characterization. The coat protein (CP) genes of selected isolates were amplified with reverse transcription-polymerase chain reaction (RT-PCR) to determine the sequence variation in the CP gene of Turkish isolates. RT-PCR amplified CP genes of LMV isolates were cloned and sequenced. Similarity rates and phylogenetic relationships of South Marmara Region LMV isolates with each other and world LMV isolates obtained from GenBank databases were determined. The results showed that, identity rates of South Marmara Region LMV isolates were 96-100% and 89-99% at nucleotide level, and 97-100% and 93-100% at amino acid level among each other and with world isolates, respectively. In addition, phylogenetic analyses revealed that South Marmara Region LMV isolates were in the LMV-RoW (Rest of the World) group.
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    First report of celery mosaic virus in Turkey
    (Springer, 2019) Karanfil, Ali; Korkmaz, Savaş; Cevik, Bayram
    [Anstract Not Available]
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    Phylogenetic relationships and genetic structure of populations of turnip mosaic virus in Turkey
    (Springer, 2020) Korkmaz, Savaş; Cevik, Bayram; Karanfil, Ali; Onder, Serkan; Ohshima, Kazusato
    Surveys were carried out throughout Turkey and a total of 437 symptomatic samples were collected from winter vegetables and weeds, most of which belong to the Brassicaceae family. Testing the collected samples for the presence of turnip mosaic virus (TuMV) by double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA) and reverse transcription-polymerase chain reaction (RT-PCR) confirmed that 117 samples were infected with TuMV. In total, 20 out of 117 TuMV-infected samples representing different regions and host plants were then selected and further analyzed for biological and molecular characteristics. As a result of biological indexing studies, two host infecting types of TuMV, i.e., B and BR were identified in Turkish TuMV isolates. The partial genomic sequences of the nuclear inclusion b protein and coat protein genes (NIb+CP region) of these isolates were determined. The corresponding sequence of the remaining 61 Turkish TuMV isolates were retrieved from GenBank for further analysis. The phylogenetic analysis showed that Turkish isolates fell into the basal-B, Asian-BR, and world-B phylogenetic groups. The evolutionary divergence value of Turkish isolates in the basal-B, Asian-BR, and world-B phylogroups were determined as 0.0026, 0.0134, and 0.0065 at nucleotide level; 0.0243, 0.0102, and 0.0129 at the amino acid level, respectively. Genetic structure analysis of Turkish TuMV isolates revealed that some isolates were admixed or had migrated among different subgroups. Our analysis provides the first depth study for the biological characteristics and genetic structures of Turkish TuMV populations.
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    The First Identified Citrus tristeza virus Isolate of Turkey Contains a Mixture of Mild and Severe Strains
    (Korean Soc Plant Pathology, 2013) Cevik, Bayram; Yardimci, Nejla; Korkmaz, Savaş
    The presence of Citrus tristeza virus (CTV) has previously been reported in citrus growing regions of Turkey. All serologically and biologically characterized isolates including Igdir, which was the first identified CTV isolates from Turkey, were considered mild isolates. In this study, molecular characteristics of the Igdir isolate were determined by different methods. Analysis of the Igdir isolate by western blot and BD-RT-PCR assays showed the presence of MCA13 epitope, predominantly found in severe isolates, in the Igdir isolate revealing that it contains a severe component. For further characterization, the coat protein (CP) and the RNA-dependent RNA polymerase (RdRp) genes representing the 3' and 5' half of CTV genome, respectively, were amplified from dsRNA by RT-PCR. Both genes were cloned separately and two clones for each gene were sequenced. Comparisons of nucleotide and deduced amino acid sequences showed that while two CP gene sequences were identical, two RdRp clones showed only 90% and 91% sequence identity in their nucleotide and amino acid sequences, respectively, suggesting a mixed infection with different strains. Phylogenetic analyses of the CP and RdRp genes of Igdir isolate with previously characterized CTV isolates from different citrus growing regions showed that the CP gene was clustered with NZRB-TH30, a resistance breaking isolate from New Zealand, clearly showing the presence of severe component. Furthermore, two different clones of the RdRp gene were clustered separately with different CTV isolates with a diverse biological activity. While the RdRp-1 was clustered with T30 and T385, two well-characterized mild isolates from Florida and Spain, respectively, the RdRp-2 was most closely related to NZRB-G90 and NZRB-TH30, two well-characterized resistance breaking and stem pitting (SP) isolates from New Zealand confirming the mixed infection. These results clearly demonstrated that the Igdir isolate, which was previously described as biologically a mild isolate, actually contains a mixture of mild and severe strains.