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. 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. 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.

Cryptosporidiosis is a zoonotic disease that occurs acutely or chronically in young or immune-compromised animals and humans, caused by Cryptosporidium species. Cryptosporidium is recognized as one of the major enteropathogens associated with neonatal diarrhea in ruminants. The aim of this study is to determine the prevalence of Cryptosporidium spp. in lambs in Siirt province using microscopic and molecular methods. The fecal materials of the study collected from 194 randomly selected lambs of different sexes, up to 4 weeks of age, in various farms. As a result of microscopic examination, Cryptosporidium spp. oocysts were found in 54 (27.84%) of 194 samples, while specific bands were obtained in 63 (32.47%) samples as a result of Nested PCR analysis. A statistically significant relationship was found between lambs with and without diarrhea (P0.05). In conclusion, the data obtained from this study revealed that Cryptosporidium infection is present in Siirt province, and Cryptosporidium spp. should be considered as one of the agents in the etiology of neonatal diarrhea in lambs.

Giardia duodenalis (G. duodenalis) is an important zoonotic protozoan agent that causes foodborne and waterborne diarrhea in humans and other mammals. Molecular-based tests are critical in diagnosing giardiasis in humans and animals, identifying species, understanding the zoonotic potential and transmission routes, and evaluating taxonomy. Therefore, this study aimed to investigate the molecular characterization of G. duodenalis in buffaloes in the Van region in Türkiye. Buffaloes are a species that has been poorly studied in this regard. For this purpose, 100 fecal samples were collected from buffaloes in the Van region. The DNA extraction was performed using the GeneMATRIX STOOL DNA Purification Kit from stool samples. The nested PCR test was performed with the appropriate primers from the obtained DNA samples. The obtained bands suitable for sequencing were sent for sequence analysis, and the sequence results were aligned bidirectionally and compared with the database of GenBank by BLAST. As a result of the study, an 11% positivity rate for G. duodenalis was found in buffaloes, and assemblage E and assemblage B were isolated. To our knowledge, assemblage B in buffaloes was reported for the first time in this study. As a result, it was concluded that buffaloes are an important reservoir for waterborne and foodborne giardiasis.

Toxocara vitulorum is a pathogenic gastrointestinal nematode found in cattle and buffaloes all over the world, especially in tropical and subtropical regions with humid climates. Buffalo farming is a sector whose value has increased in recent years in Turkey and is intensively performed to obtain various products such as milk, cream, meat, and horns. This study aims to determine the prevalence of T. vitulorum in Anatolian Water Buffaloes in Diyarbakır. Fresh stool samples from animals were placed in individual stool containers. The sex and age of the animal were recorded for each sample collected. The samples were evaluated under the light microscope after the application of the Fulleborn saturated salt solution method and under Scanning Electron Microscope. Positivity was detected in 5 (3.01%) of the 166 samples. Regarding prevalence by age groups, T. vitulorum was detected in 10% of the 0-6 month group, 4.17% of the 6-12 month group, and 0.89% of the older than 12 months group. The prevalence by sex was determined as 3.85% for females and as 1.61% for males. To determine the epidemiology of the disease in the region, it was concluded that larger herds should be studied and serological and molecular methods should be used to confirm and support the findings of microscopic methods.

Ticks harbor the largest diversity of microorganisms, ranging from viruses, prokaryotes, and eukaryotes. Rhipicephalus sanguineus ticks are the most common ticks worldwide. Although dogs are the main host of this tick species, it has been reported that it also infests humans in various parts of the world. This study aimed to examine some bacteria (Coxiella burnetii, Mycoplasma haemocanis, Candidatus Mycoplasma haematoparvum, Wolbachia) in Rhipicephalus sanguineus ticks sampled from dogs. In this study, 350 tick samples collected from 85 dogs in Siirt province were determined to be Rhipicephalus sanguineus ticks. Coxiella DNA was detected in 3 (0.85%) out of 350 ticks using Nested PCR (687 base pairs). None of the samples were found to contain Mycoplasma haemocanis, Candidatus Mycoplasma haematoparvum, and Wolbachia DNA. A partial sequence of the IS1111 gene region was registered in GenBank with OM472143 accession numbers. Considering the zoonotic nature of the Q disease, it is very important for dog owners and related institutions to periodically spray animals against ticks, and to take any other necessary precautions. More samples are needed to determine the Mhc, CMhp, and Wolbachia prevalence.

Cryptosporidiosis, one of the main protozoan infections of the last century, is especially dangerous for calves and causes significant economic losses. This research was carried out to determine the prevalence of Cryptosporidium spp. by microscopic and molecular methods and to determine subtypes in 100 calves up to 6 months old and with diarrhoea in the Siirt Province, Türkiye. As a result of the microscopic examination (Kinyoun’s acid-fast), Cryptosporidium spp. oocysts were found in 8 (8%) of 100 samples. As a result of nested PCR, 826-864 bp specific bands for Cryptosporidium spp. were obtained in 13 (13%) of 100 samples. When the DNA sequences of the SSU rRNA gene were compared with the NCBI Basic Local Alignment Search Tool database, it was determined that eight samples sequence analyses showed 100% similarity with the C. parvum , C. ryanae , and C. bovis samples. The detection of C. parvum , which has zoonotic importance in this study, suggests that calves with diarrhoea may be a source of contamination for other animals and humans. Therefore, animal owners and people in close contact with animals should be informed about the public health of cryptosporidiosis.