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Öğe Comparative Evaluation of In-House and Commercial Real-Time PCR Methods for the Detection of the BK and JC Viruses in Clinical Samples(Thieme Medical Publ Inc, 2020) Ozdemir, Mehmet; Ayan, Ugur; Sevik, MuratAim The two most common human polyomaviruses are the BK (BKV) and JC viruses (JCV). Diseases associated with polyomavirus usually occur in cases of severe cellular immunosuppression. BKV and JCV can cause many diseases, especially if they are reactivated in an immunosuppressed host. The aim of this study is to compare and evaluate the results of real-time polymerase chain reaction (PCR) methods targeting the small and large T gene regions of the viral genome, considering polymorphisms occurring in the viral genome of BKV and JCV. Materials and Methods Urinary specimens of 82 patients were taken from immunosuppressed patient and sent to molecular microbiology laboratory of Meram Medical Faculty. The small t gene was investigated using a commercial kit (LightMix, Roche) by real-time PCR method. Large T gene was investigated by using the optimized in-house real-time PCR method. Sequence analysis was accepted as the standard method. Results BKV positivity was detected in 9 samples and JCV positivity in 61 samples by real-time PCR method specific to small t gene region; BKV positivity in 21 samples and JCV positivity in 67 samples were determined by real-time PCR method specific to the large T gene region. Statistically, there was a significant difference for BKV, but not significant difference for JCV detection between the two methods. Conclusion Different polymorphisms in the target gene regions were responsible for the different outcomes obtained from this study. With this sensitivity and specificity, in-house PCR method which we used is a candidate for routine diagnosis.Öğe Detection of Peste des petits ruminants virus RNA in Culicoides imicola (Diptera: Ceratopogonidae) in Turkey(Ist Zooprofilattico Sperimentale Abruzzo & Molise G Caporale-Izs A&M, 2019) Sevik, Murat; Oz, Mustafa EminAn outbreak of Peste des petits ruminants (PPR) occurred in the Antalya Province in Turkey during October 2015. The Antalya Province has suitable habitats for vectors. There is no information available on the role of Culicoides spp. in the transmission of Peste des petits ruminants virus (PPRV). In this study we investigated the potential role of the Culicoides spp. in the transmission of PPRV. Culicoides were trapped throughout middle of October and middle of December, 2015. A total of 12 pools of non-engorged females were analysed with real-time RT-PCR targeting the nucleocapsid (N) gene of the PPRV. PPRV RNA was detected in 7 of 12 Culicoides pools. These pools were negative for the bovine/ovine beta-actin mRNA. Culicoides spp. were identified to the species level by sequence analysis of the mitochondrial cytochrome oxidase subunit I gene. The species of Culicoides found PPRV positive was Culicoides imicola. Molecular characterization of field isolates from recent outbreaks and pools of midges that tested positive for PPRV suggests that PPRV replication might occur in Culicoides imicola, and it may have played a role in transmitting PPRV.Öğe Genomic characterization of pestiviruses isolated from bovine, ovine and caprine foetuses in Turkey: A potentially new genotype of Pestivirus I species(Wiley-Hindawi, 2021) Sevik, MuratThis study was carried out to investigate the frequency and genetic diversity of pestiviruses in abortion cases in cattle and small ruminants in Turkey. During January 2012 and December 2017, a total of 2029 aborted foetuses (553 bovine foetuses, 1,388 sheep foetuses and 88 goat foetuses) were collected from different regions of Turkey. Real-time RT-PCR (RRT-PCR) assays were used to detect pestiviral RNA in aborted foetuses. To confirm the cause of abortion, pestivirus-positive foetuses were also examined for the presence ofBrucellaspp.,Campylobacterspp.,Chlamydophila abortus(C. abortus), akabane virus, bluetongue virus and Schmallenberg virus by molecular detection methods. Pestiviral RNA was detected in 61 (11%) of the 553 bovine foetuses, 124 (8.9%) of the 1,388 sheep foetuses and 3 (3.4%) of the 88 goat foetuses. Furthermore,C. abortusDNA was detected in 3 pestivirus-positive sheep foetuses, whereas other infectious agents were not detected in pestivirus-positive foetuses. Genetic characterization of the pestivirus RRT-PCR positive samples was conducted by sequencing 5 ' untranslated (5 ' UTR) and non-structural autoprotease (N-pro) genomic regions. A total of 68 sequences were obtained, and phylogenetic analyses revealed that all sequences belonged to BVDV-1, including 1b (8/68), 1f (2/68), 1l (4/68), 1r (10/68), Aydin-like pestivirus (20/68) and one unknown genotype (24/68). The 5 ' UTR and N(pro)sequences of this unknown genotype differed from pestiviruses previously described, providing evidence for the presence of an emerging genotype within the species Pestivirus I, tentatively named as 'Konya-like' pestivirus. 'Konya-like' pestivirus was the dominant genotype in sheep foetuses, whereas Aydin-like pestivirus was found to be the predominant genotype in bovine foetuses. To the best my knowledge, this is the first report of Aydin-like pestivirus infection in cattle. The information provided in this study contributes to the understanding the dissemination and evolution of pestiviruses and could be beneficial for developing more effective vaccines.Öğe Molecular Detection of Two New Haemoproteus Mitochondrial Cytb Lineages in Ciconiform and Charadriiform Migratory Birds in Turkey(Univ Agriculture, Fac Veterinary Science, 2024) Zerek, Aykut; Ceylan, Onur; Erdem, Ipek; Simsek, Fatma Nuray; Ungari, Leticia Pereira; Sevik, Murat; Yaman, MehmetAlthough some molecular epidemiological surveys on avian haemosporidian protozoa have been conducted in Turkey, it is of great importance to increase the number of studies on the subject in this country, which has important bird migration routes between Europe and Africa. Hatay province, which is the intersection point of many bird migration routes in the intercontinental crossing, is a very suitable geographical location for the investigation of avian haemosporidian protozoa in a wide variety of bird species that use it as a route. Therefore, this study was planned to survey Haemoproteus spp., Plasmodium spp., and Leucocytozoon spp. in migratory birds sampled from this province. The animal material of the study consisted of Ciconia ciconia (Ciconiformes, n:45), Ichthyaetus melanocephalus (Charadriiformes, n:2), Pelecanus onocrotalus (Pelecaniformes, n:5) and Pelecanus crispus (Pelecaniformes, n:1). Microscopic examinations revealed Haemoproteus spp. gametocytes (5.66%) in one white stork and two Mediterranean gulls. On the other hand, nested PCR assay targeting the mitochondrial cytochrome b (Cytb) gene revealed the presence of Plasmodium / Haemoproteus spp. in 11.3% (6/53) of migratory birds. Leucocytozoon spp. was not detected by either microscopy or PCR. PCRpositive products were sequenced bi-directionally, and the GenBank and MalAvi databases were used for phylogenetic analysis and lineage identification of the isolates. This study revealed H-MYCAME08 lineage (OR227579, OR227580, OR227581, OR227582) in Ciconia ciconia and H-LARCRA01 [ H. ( Parahaemoproteus ) larae ] lineage (OR227577, OR227578) in Ichthyaetus melanocephalus , respectively. There are no studies investigating the haemosporidian parasites of these birds in Turkey, and studies on haemosporidian parasites of these species in different countries are also limited. Although the Haemoproteus MYCAME08 Cytb lineage has been demonstrated in ciconiform birds (Ciconidae) and the LARCRA01 lineage in charadriiform birds (Laridae), this study is unique in terms of reporting these lineages in different species in the same families. Inspired by this, we envisage that the expanding host range of Cytb lineages of haemosporidian protozoa is an indication that there is still a long way to go with avian haemosporidian protozoa.Öğe Orf virus circulation in cattle in Turkey(Elsevier Sci Ltd, 2019) Sevik, MuratOrf virus (ORFV) causes contagious skin disease that mainly affects sheep and goats with zoonotic potential. However, there is not enough information about the association between ORFV and occurrence of skin disease in cattle. The present study describes outbreaks of ORFV infection in cattle in different provinces that are located in the Aegean, Central Anatolian and Mediterranean regions of Turkey. During the months of June and August 2017, vesicular fluid and scab samples were collected from cattle which had proliferative skin lesions. First, presence of lumpy skin disease virus (LSDV) and bovine herpesvirus 2 (BoHV-2, known as the causative agent of pseudo-lumpy skin disease) were investigated by real time PCR and PCR, respectively. Then, samples tested for the presence of parapoxviruses by PCR using primers specific to major envelope protein gene (B2L). Parapoxvirus DNA was detected in investigated samples whereas LSDV and BoHV-2 DNA were not detected. The analysis of the B2L gene sequences revealed that cattle were infected with ORFV. The isolates in the present study shared 100% sequence identity at the nucleotide and amino acid level when compared with previously characterised Turkish field ORFV isolates from goats in 2016. Results of the study show unusual infection of cattle with ORFV, and suggest that ORFV jumps the host species barrier from goats to cattle.