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    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, Murat
    Aim 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.
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    Epidemiology of bluetongue virus infection among small ruminants in Turkey: Seroprevalence and associated risk factors
    (Elsevier, 2023) Sevik, Murat
    Bluetongue (BT) is an endemic disease of small ruminants in Turkey, and it has substantial socio-economic impact at national level. To reduce this impact, vaccination has been used for the control of BT but sporadic outbreaks have been reported. Although sheep and goat farming plays an important role in rural communities, little is known about the BT epidemiological situation in small ruminants in Turkey. Therefore, this study aimed to estimate the seroprevalence of the bluetongue virus (BTV) and to identify the potential risk factors associated with BTV seropositivity in small ruminants. This study was conducted in the Antalya Province in the Mediter-ranean region of Turkey, from June 2018 to June 2019. A total of 1026 blood samples, from clinically healthy goats (n = 517) and sheep (n = 509), obtained from randomly selected unvaccinated flocks (n = 100) were tested for BTV anti-VP7 antibodies by using a competitive enzyme linked immunosorbent assay test. A questionnaire was administered to the flock owners to obtain data related to sampled flocks and animals. At the animal level, the true prevalence of BTV antibodies was 74.2% (n = 651/1026, 95% CI = 70.7-77.7) with 85.3% (n = 370/ 509, 95% CI = 80.6-89.9) seropositive sheep and 63.3% (n = 281/517, 95% CI = 58.2-68.4) seropositive goats. The true flock-level seroprevalence of BTV was higher in goats (100.0%, 95% CI = 92.8-100.0) than in sheep (98.8%, 95% CI = 86.6-100.0). The intra-flock seroprevalence within seropositive flocks varied between 36.4% and 100%, with a mean value of 85.5% and 61.9% in sheep and goat flocks, respectively. The logistic regression model revealed that odds of seropositivity for sheep were significantly higher in female animals (OR: 1.8, 95% CI = 1.1-2.9), animals older than 24 months old (OR: 5.8, 95% CI = 3.1-10.8), Pirlak breed (OR: 3.3, 95% CI = 1.1-10.0) and Merino breed (OR: 4.9, 95% CI = 1.6-14.9), whereas for goats, it was higher in female animals (OR: 1.7, 95% CI = 1.0-2.6), animals older than 24 months old (OR: 4.2, 95% CI = 2.7-6.6) and Hair breed (OR: 5.6, 95% CI = 2.8-10.9). The use of insecticides was identified as a protective factor. The present study revealed that BTV infection is widespread in sheep and goats in the Antalya Province. It is recommended to implement biosecurity measures in flocks and use insecticides to mitigate the spread of infection and contact between hosts and vectors.
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    Investigation of Tomato Ringspot Virus (ToRSV) by Real-Time TaqMan RT-PCR in Hakkari Province, Turkey
    (Galenos Publ House, 2021) Akdura, Nevin; Sevik, Murat
    Tomato ringspot virus (ToRSV) belongs to the Nepovirus genus in the family Secoviridae. It has a wide host range and is listed as a quarantine virus in Turkey. In this study, 80 leaf samples were collected from tomato, pepper, cucumber and grapevine cultivation sites located in three different parts of Hakkari province: Semdinli, Cukurca and Center districts. Real-time TaqMan reverse transcription-polymerase chain reaction (RT-PCR) method was used for the detection of the virus. Amplification was carried out in reaction mix including QuantiNova Probe RT-PCR kit (Qiagen, Germany) using primers and TaqMan probe based on 3'-UTR (untranslated region) of virus, which amplified a 182 bp product of the genome. ToRSV was detected in 13 of the 80 samples and threshold cycle (CT) values ranged from 23.9 to 37.4. It was found that 16.25% of the samples collected from the districts of Hakkari province were found to be infected with ToRSV whereas no ToRSV was detected in the samples collected from the center of the city. The virus was detected on pepper and cucumber samples in Cukurca district, and it was also detected in tomato, pepper, cucumber and grapevine samples in Semdinli district. To our knowledge, this study is the first report of molecular detection of ToRSV by real-time TaqMan RT-PCR in Turkey.
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    Investigation of Tomato Ringspot Virus (ToRSV) by Real-Time TaqMan RT-PCR in Hakkari Province, Turkey
    (Galenos Publ House, 2021) Akdura, Nevin; Sevik, Murat
    Tomato ringspot virus (ToRSV) belongs to the Nepovirus genus in the family Secoviridae. It has a wide host range and is listed as a quarantine virus in Turkey. In this study, 80 leaf samples were collected from tomato, pepper, cucumber and grapevine cultivation sites located in three different parts of Hakkari province: Semdinli, Cukurca and Center districts. Real-time TaqMan reverse transcription-polymerase chain reaction (RT-PCR) method was used for the detection of the virus. Amplification was carried out in reaction mix including QuantiNova Probe RT-PCR kit (Qiagen, Germany) using primers and TaqMan probe based on 3'-UTR (untranslated region) of virus, which amplified a 182 bp product of the genome. ToRSV was detected in 13 of the 80 samples and threshold cycle (CT) values ranged from 23.9 to 37.4. It was found that 16.25% of the samples collected from the districts of Hakkari province were found to be infected with ToRSV whereas no ToRSV was detected in the samples collected from the center of the city. The virus was detected on pepper and cucumber samples in Cukurca district, and it was also detected in tomato, pepper, cucumber and grapevine samples in Semdinli district. To our knowledge, this study is the first report of molecular detection of ToRSV by real-time TaqMan RT-PCR in Turkey.
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    Risk assessment and seroprevalence of bovine herpesvirus type 1 infection in dairy herds in the inner Aegean Region of Turkey
    (Elsevier Sci Ltd, 2022) Ince, Omer Baris; Sevik, Murat
    This cross-sectional study was performed to investigate the seroprevalence and associated risk factors of bovine herpesvirus type 1 (BoHV-1) infection in dairy cattle herds in Afyonkarahisar province in the Aegean Region of Turkey. Blood samples were collected from 602 cattle from 56 unvaccinated dairy herds between May 2018 and June 2019. Animal and herd-level epidemiological information was collected with a questionnaire during blood collection. Specific antibodies against BoHV-1 and bovine viral diarrhea virus (BVDV) were detected by using a virus neutralization test and a commercial indirect ELISA kit, respectively. Univariable and multivariable logistic regression analyses were used to determine any association between categorical variables and BoHV-1 sempositivity. The animal-level and herd-level sero-prevalences of BoHV-1 infection were determined to be 39.53% (95% confidence interval, CI: 35.71-43.50) and 73.21% (95% CI: 60.41-83.04), respectively. Within-herd prevalence was more than 50% in 34.14% of infected herds. Cattle age (odds ratio, OR= 2.34, 95% CI: 1.58-3.44), BVDV infection (OR= 7.74, 95% CI: 5.08-11.76), and the presence of goats in the herd (OR= 2.84, 95% CI: 1.91-4.19) were identified as risk factors for BoHV-1 sempositivity by the multivariable logistic regression model. This is the first study conducted in Turkey using two-layer sampling and logistic regression analyses to determine the herd-level and animal-level seroprevalence and associated risk factors of BoHV-1 infection.
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    Risk factors and genetic characterization of bovine respiratory syncytial virus in the inner Aegean Region, Turkey
    (Springer, 2022) Ince, Omer Baris; Sevik, Murat; Ozgur, Emrah Gokay; Sait, Ahmet
    Bovine respiratory syncytial virus (BRSV) is one of the causative viral agents of the bovine respiratory disease complex. This study was conducted to determine the seropositivity and risk factors associated with BRSV infection and to evaluate the phylogenetic relatedness of the BRSVs in the inner Aegean region of Turkey. In this cross-sectional study, serum samples (n = 557) and nasal swabs (n = 21) were collected from cattle herds (n = 43) between February 2018 and March 2019. A commercial indirect-ELISA kit was used for the detection of antibodies in the sera samples. Reverse-transcriptase PCR was used to detect viral RNA in nasal swabs. Nasal samples were also examined for the detection of bovine parainfluenza-3, bovine viral diarrhoea virus, and bovine herpesvirus 1 by molecular detection methods. Genetic characterization of the local BRSV field isolates was conducted by sequencing attachment glycoprotein (G) gene segment. Epidemiological data on potential risk factors were collected from each sampled herd during blood collection. All herds had at least one seropositive animal. After adjustment for assay sensitivity and specificity, the overall true seropositivity was 58.48% (95% CI: 53.32-63.47). BRSV RNA was detected in 2 of the 21 nasal swabs, whereas other infectious agents were not detected in the investigated samples. Phylogenetic analysis showed that the field isolates of BRSV obtained in this study belonged to subgroup III, but they were located on separate branch from previously characterised Turkish subgroup III isolates. BRSV field strains from this study displayed 3 new amino acid substitutions (P89S, D115G, and S165L) in the G protein chains compared to other main reference BRSV isolates, demonstrating that BRSV is still evolving. Generalised estimating equation model showed that there were positive associations between BRSV infection, age (OR = 2.36, p = 0.001), herd size (OR = 10.32, p < 0.001), herd type (OR = 8.97, p < 0.001), a past history of respiratory disease (OR = 4.06, p < 0.001). The results of this study revealed that BRSV infection is common among cattle herds in the inner Aegean region of Turkey. The obtained epidemiological and genetic data on BRSV infection from this study could be beneficial for designing effective biosecurity practices and vaccination strategies.
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    Spatiotemporal analysis of foot and mouth disease outbreaks in cattle and small ruminants in Türkiye between 2010 and 2019
    (Springer, 2023) Ince, Omer Baris; Sevik, Murat; Sener, Rumeysa; Turk, Tarik
    Determining the dynamics associated with foot-and-mouth disease (FMD) outbreaks is important for being able to develop effective strategic plans against the disease. In this direction, spatiotemporal analysis of FMD virus (FMDV) epidemic data that occurred in Turkiye between 2010 and 2019 was carried out. Spatiotemporal analysis was performed by the space-time scan statistic using data from a total of 7,796 FMD outbreaks. Standard deviational ellipse analysis (SDE) was performed to analyse the directional trend of FMD. Five, six, and three significant and high-risk clusters were identified by the space-time cluster analysis for serotypes A, O, and Asia-1, respectively. The SDE analysis indicated that direction of FMD transmission was northeast to southwest. A significant decrease in the number of outbreaks and cases were observed between 2014 and 2019 compared to 2010-2013 (p = 0.010). Most of the serotype A, serotype O, and serotype Asia-1 associated FMD outbreaks were observed during the dry season (April to September). Among FMD cases, cattle and small ruminants accounted for 80.75% (180,932 cases) and 19.25% (43,116 cases), respectively. Among the serotypes detected in the cases, the most frequently detected serotype was serotype O (50.84%), followed by serotypes A (35.67%) and Asia-1 (13.49%). The results obtained in this study may contribute to when and where control programs could be implemented more efficiently for the prevention and control of FMD. Developing risk-defined regional control plans by taking into account the current livestock production including uncontrolled animal movements in border regions, rural livestock, livestock trade between provinces are recommended.