BackgroundTicks 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.ResultsA 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.ConclusionsWidespread 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-017-2279-1) contains supplementary material, which is available to authorized users.

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.

IntroductionEchinococcus granulosus is a zoonotic helminth of the Taeniidae family living in the small intestines of dogs. The hydatid cyst, which is the larval form of this parasite, is observed in sheep, goat, cattle, and many other organisms including humans. It causes a disease called cystic echinococcosis. Identification of strains of E. granulosus in dogs is critical in parasite control and eradication where possible. This study aims to determine the genotype of E. granulosus eggs and prevalence of this parasite in the faeces of dogs in the Van Province using the copro-PCR method.Material and MethodsThis study was conducted between 2015 and 2016 on the faeces obtained from 100 stray dogs from different parts of the Van Province. The coprological examination was conducted using the formalin-ether concentration method.ResultsTaeniidae eggs were found in 10 (10%) out of 100 faecal samples. E. granulosus was detected in 4 out of 10 of these (40%) infected samples. Sequence analysis of positive amplicons obtained from PCR showed that there were sheep strains (G1).ConclusionDogs in Van area are primarily infected with the livestock genotype of E. granulosus, which is thought to be a potential zoonotic threat to humans.

IntroductionToxocara canis and Toxocara cati are roundworms of dogs and cats. The purpose of this study was to investigate the infection caused by these ascarids in cats and dogs, using microscopic and molecular analysis methods.Material and MethodsAdult ascarids were gathered from the faeces of dogs and cats in Van province, in 2015–2016. Existing keys and PCR sequencing of the ITS-2 fragment were used to identify the morphological features of the parasite species.ResultsIt was observed that out of 20 adult ascarids, 17 and 3 were found to be Toxocara canis and Toxocara cati, respectively. The ITS-2 gene region was amplified by PCR to perform molecular analysis. Genotyping indicated that the dogs and cats were infected with T. canis and T. cati, respectively, and none had Toxascaris leonina.ConclusionTo the best of our knowledge, this is the first report on the molecular characteristics of adult ascaridoid nematodes from cats and dogs in Turkey. The molecular approaches established in this study enable molecular identification and genetic structure studies of the ascaridoids.

SummaryThis 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.