Browsing by Author "Dincer, Ender"

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Canine Infections and Partial S Segment Sequence Analysis of Toscana Virus in Turkey
(Mary Ann Liebert, inc, 2016) Dincer, Ender; Karapinar, Zeynep; Oktem, Mert; Ozbaba, Merve; Ozkul, Aykut; Ergunay, Koray
Introduction: Toscana virus (TOSV) is a sandfly-borne bunyavirus with a significant public health impact. Preliminary studies have revealed TOSV exposure in dogs and they were suggested as potential reservoirs. This study was performed to characterize canine TOSV infections in an endemic region. Sequencing of TOSV small (S) segment in several previously identified specimens was also undertaken to reveal viral genealogy. Materials and Methods: Canine and feline plasma were collected in several districts of Mersin province, Mediterranean Anatolia, Turkey, during May-September, 2015. Phlebovirus RNA was screened through two nested polymerase chain reaction (PCR) assays, targeting S and large (L) segments of the viral genome. A kinetoplast minicircle nested PCR was employed for Leishmania DNA detection and typing. Previously collected TOSV-positive specimens from humans, dogs, cats, and sandflies from various regions in Turkey and Cyprus were further evaluated through the S segment PCR. All amplicons were characterized through sequencing. Results: A total of 210 specimens that comprise canine (76.2%) and feline (23.8%) plasma were screened. In three (1.9%) and two (1.3%) canine specimens, TOSV and Leishmania nucleic acids were detected, respectively. The TOSV strains were characterized as genotype B, and Leishmania infantum was identified in positive specimens. Twenty-four partial S segment sequences were amplified, which demonstrated a maximum intramural diversity of 3.88% in the nucleotide level. Sequence comparisons revealed significant similarities to particular genotype B strains characterized in Spain and France, whereas a notable divergence was observed among several TOSV strains. Single or recurrent amino acid substitutions were noted in eight residues of the viral nucleocapsid. Discussion: Canine infections of TOSV genotype B, with temporal and spatial association with L. infantum, were detected. Divergent TOSV S segment sequences with amino acid substitutions, presumably associated with host adaptation, were observed.
Generic Amplification and Next Generation Sequencing Reveal Crimean-Congo Hemorrhagic Fever Virus Ap92-Like Strain and Distinct Tick Phleboviruses in Anatolia, Turkey
(Bmc, 2017) Dincer, Ender; Brinkmann, Annika; Hekimoglu, Olcay; Hacioglu, Sabri; Foldes, Katalin; Karapinar, Zeynep; Ergunay, Koray
Background: Ticks are involved with the transmission of several viruses with significant health impact. As incidences of tick-borne viral infections are rising, several novel and divergent tick-associated viruses have recently been documented to exist and circulate worldwide. This study was performed as a cross-sectional screening for all major tick-borne viruses in several regions in Turkey. Next generation sequencing (NGS) was employed for virus genome characterization. Ticks were collected at 43 locations in 14 provinces across the Aegean, Thrace, Mediterranean, Black Sea, central, southern and eastern regions of Anatolia during 2014-2016. Following morphological identification, ticks were pooled and analysed via generic nucleic acid amplification of the viruses belonging to the genera Flavivirus, Nairovirus and Phlebovirus of the families Flaviviridae and Bunyaviridae, followed by sequencing and NGS in selected specimens. Results: A total of 814 specimens, comprising 13 tick species, were collected and evaluated in 187 pools. Nairovirus and phlebovirus assays were positive in 6 (3.2%) and 48 (25.6%) pools. All nairovirus sequences were closely-related to the Crimean-Congo hemorrhagic fever virus (CCHFV) strain AP92 and formed a phylogenetically distinct cluster among related strains. Major portions of the CCHFV genomic segments were obtained via NGS. Phlebovirus sequencing revealed several tick-associated virus clades, including previously-characterized Antigone, Lesvos, KarMa and Bole tick viruses, as well as a novel clade. A wider host range for tick-associated virus strains has been observed. NGS provided near-complete sequences of the L genomic segments of Antigone and KarMa clades, as well as Antigone partial S segment. Co-infections of CCHFV and KarMa or novel phlebovirus clades were detected in 2.1% of the specimens. Conclusions: Widespread circulation of various tick-associated phlebovirus clades were documented for the first time in Anatolia. Genomes of CCHFV AP92 strains were identified in previously unexplored locations. NGS provided the most detailed genomic characterization of the Antigone and KarMa viruses to date. The epidemiological and health-related consequences must be elucidated.
Impact of Nanopore-Based Metagenome Sequencing on Tick-Borne Virus Detection
(Frontiers Media Sa, 2023) Ergunay, Koray; Dincer, Ender; Justi, Silvia A. A.; Bourke, Brian P. P.; Nelson, Suppaluck P. P.; Liao, Hsiao-Mei; Linton, Yvonne-Marie
IntroductionWe evaluated metagenomic nanopore sequencing (NS) in field-collected ticks and compared findings from amplification-based assays. MethodsForty tick pools collected in Anatolia, Turkey and screened by broad-range or nested polymerase chain reaction (PCR) for Crimean-Congo Hemorrhagic Fever Virus (CCHFV) and Jingmen tick virus (JMTV) were subjected to NS using a standard, cDNA-based metagenome approach. ResultsEleven viruses from seven genera/species were identified. Miviruses Bole tick virus 3 and Xinjiang mivirus 1 were detected in 82.5 and 2.5% of the pools, respectively. Tick phleboviruses were present in 60% of the pools, with four distinct viral variants. JMTV was identified in 60% of the pools, where only 22.5% were PCR-positive. CCHFV sequences characterized as Aigai virus were detected in 50%, where only 15% were detected by PCR. NS produced a statistically significant increase in detection of these viruses. No correlation of total virus, specific virus, or targeted segment read counts was observed between PCR-positive and PCR-negative samples. NS further enabled the initial description of Quaranjavirus sequences in ticks, where human and avian pathogenicity of particular isolates had been previously documented. DiscussionNS was observed to surpass broad-range and nested amplification in detection and to generate sufficient genome-wide data for investigating virus diversity. It can be employed for monitoring pathogens in tick vectors or human/animal clinical samples in hot-spot regions for examining zoonotic spillover.
Molecular Detection of Nosema Spp. and Black Queen-Cell Virus in Honeybees in Van Province, Turkey
(Tubitak Scientific & Technological Research Council Turkey, 2017) Oguz, Bekir; Karapinar, Zeynep; Dincer, Ender; Deger, Mustafa Serdar
This study was planned to determine the prevalences of the Nosema spp. and the black queen-cell virus (BQCV) among honeybees (Apis mellifera) raised in the province of Van by PCR and to determine the molecular characteristics of the determined isolates. A total of 260 adult worker bees from 26 colonies at 5 apiary locations belonging to the province of Van in April and May 2015 were collected for this reason. Samples were examined microscopically. In the case of positivity, spore identification was done by multiplex PCR. Reverse transcription/PCR analysis (RT/PCR) was carried out for the BQCV analysis. At the end of the microscopic examination, Nosema spp. spores were detected in 8 out of 26 colonies (32.5%). The result of multiplex-PCR revealed Nosema ceranae positivity in all of the samples, but no Nosema apis was determined. As a result of the RT/PCR tests of the samples BQCV was detected in 23 (88.5%) of the total 26 colonies. This study is the first to investigate Nosema spp. and BQCV with the PCR technique in bees raised in the province of Van.
Phylogenetic Analysis of Black Queen Cell Virus and Deformed Wing Virus in Honeybee Colonies Infected by Mites in Van, Eastern Turkey
(Polish Soc veterinary Sciences Editorial office, 2018) Karapinar, Zeynep; Oguz, Bekir; Dincer, Ender; Ozturk, Cihat
This study aimed to determine the presence and prevalence of viral and parasitic infections causing high rates of colony loss in honey bee colonies in Van province, eastern Turkey. Twenty-six different apiaries were collected from five counties in Van province. These samples were tested by Reverse-Transcriptase PCR (RT-PCR) for acute bee paralysis virus (ABPV), chronic bee paralysis virus (CBPV), black queen cell virus (BQCV) and deformed wing virus (DWV). Selected positives were sequenced, phylogenetically analyzed and investigated in terms of Varroa. DWV and BQCV were identified in 69.23% (18/26) and 88.46% (23/26) of the bees respectively whereas ABPV and CBPV were not detected in the sampled apiaries. Results of the phylogenetic analysis of DWV and BQCV sequences showed 94-100% similarity to DWV and BQCV isolates obtained from Genbank. Prevalence of varroasis was 89% (23/26) in Van. The obtained samples were identified as Varroa destructor by morphological investigation. The study showed that viral and parasitic agents commonly infect honeybees in Van province, with high prevalence rates for BQCV and DWV. There was also a high degree of conservation of DWV and BQCV sequences distinct from DWV and BQCV isolates from other geographical regions. These findings, including current prevalence and phylogenetic analysis data for DWV, BQCV and varroazis in honeybees, are useful for future studies.
Several Tick-Borne Pathogenic Viruses in Circulation in Anatolia, Turkey
(Mary Ann Liebert, inc, 2022) Dincer, Ender; Timurkan, Mehmet Ozkan; Oguz, Bekir; Sahindokuyucu, Ismail; Sahan, Adem; Ekinci, Mustafa; Ergunay, Koray
Introduction: We screened host-collected ticks for tick-borne viruses, including those recently documented as human pathogens.Methods: During 2020-2021, ticks removed form cattle, sheep, dogs, and cats in 11 provinces in 5 geographically distinct regions of Anatolia were identified, pooled, and screened using pan-nairovirus, pan-flavivirus and individual assays for Jingmen tick virus (JMTV), and Tacheng tick virus 1 and 2 (TcTV-1 and TcTV-2).Results: A total of 901 tick specimens, comprising 6 species were included. Rhipicephalus sanguineus complex was the most abundant species (44.1%), followed by Rhipicephalus bursa (38.3%), Haemaphysalis parva (7.2%), and others. The specimens were screened in 158 pools with 12 pools (7.6%) being positive. Crimean-Congo hemorrhagic fever virus (CCHFV) lineage Europe 2 (genotype VI) sequences were detected in R. bursa in five (3.2%) of the pools, with similar prevalences in central and Mediterranean Anatolian provinces. JMTV was identified in four R. bursa and one Rhipicephalus turanicus pools, collected from Mediterranean and southeastern Anatolia, with a CCHFV and JMTV coinfected R. bursa pool. The JMTV segment 1 sequences formed a separate cluster with those from Turkey and the Balkan peninsula in the maximum likelihood analysis. TcTV-2 was detected in two Dermacentor marginatus specimens (1.3%) collected in central Anatolia, with nucleocapsid sequences forming a phylogenetically segregated group among viruses from humans and ticks from China and Kazakhstan.Discussion: CCHFV Europe 2 was initially documented in ticks from central Anatolian locations, where related orthonairoviruses had been previously recorded. Ongoing activity and a wider distribution of JMTV and TcTV-2 were observed. These viruses should be screened as potential etiological agents in human infections associated with tick bites.
A Snapshot Avian Surveillance Reveals West Nile Virus and Evidence of Wild Birds Participating in Toscana Virus Circulation
(Mary Ann Liebert, inc, 2017) Hacioglu, Sabri; Dincer, Ender; Isler, Cafer Tayer; Karapinar, Zeynep; Ataseven, Veysel Soydal; Ozkul, Aykut; Ergunay, Koray
Introduction: Birds are involved in the epidemiology of several vector-borne viruses, as amplification hosts for viruses, dissemination vehicles for the vectors, and sources of emerging strains in cross-species transmission. Turkey provides diverse habitats for a variety of wild birds and is located along major bird migration routes. This study was undertaken to provide a cross-sectional screening of avian specimens for a spectrum of vector-borne viruses. Materials and Methods: The specimens were collected in Hatay province, in the Mediterranean coast of the Anatolian peninsula, located in the convergence zone of the known migration routes. Generic PCR assays were used for the detection of members of Nairovirus, Flavivirus, and Phlebovirus genera of Flaviviridae and Bunyaviridae families. The circulating viruses were characterized via sequencing and selected specimens were inoculated onto Vero cell lines for virus isolation. Results and Discussion: Specimens from 72 wild birds belonging in 8 orders and 14 species were collected. A total of 158 specimens that comprise 32 sera (20.3%) from 7 species and 126 tissues (79.7%) from 14 species were screened. Eight specimens (8/158, 5%), obtained from 4 individuals (4/72, 5.5%), were positive. West Nile virus (WNV) lineage 1 sequences were characterized in the spleen, heart, and kidney tissues from a lesser spotted eagle (Clanga pomarina), which distinctly clustered from sequences previously identified in Turkey. Toscana virus (TOSV) genotype A and B sequences were identified in brain and kidney tissues from a greater flamingo (Phoenicopterus roseus), a great white pelican (Pelecanus onocrotalus), and a black stork (Ciconia nigra), without successful virus isolation. Partial amino acid sequences of the viral nucleocapsid protein revealed previously unreported substitutions. This study documents the involvement of avians in WNV dispersion in Anatolia as well in TOSV life cycle.