Free ranging ungulates, represented in Europe mostly by several deer species, are important hosts for ticks and reservoirs of tick-borne infections. A number of studies have focused on the prevalence of tick borne pathogens in deer chiefly with the aim to determine their potential role as reservoir hosts for important human and livestock pathogens. However, genetic similarity of Babesia spp. forming a group commonly termed as a clade VI that accommodates the deer piroplasms, complicates this task and has led to the description of a bewildering array of poorly characterised strains. This study aims to resolve this issue by using two independent genetic loci, nuclear 18S rRNA and mitochondrial cytochrome c oxidase subunit I genes, used in parallel to identify Babesia isolates in free-ranging red, sika, and roe deer in two areas of their co-occurrence in the Czech Republic. The COX1 loci, in contrast to 18S rRNA gene, shows a clear difference between interspecific and intraspecific variation at the nucleotide level. The findings confirm B. divergens, Babesia sp. EU1 and B. capreoli in studied deer species as well as common presence of another unnamed species that matches a taxon previously referred to as Babesia sp. or Babesia cf. odocoilei or Babesia CH1 group in several other sites throughout Europe. The invasive sika deers enter the life cycle of at least three piroplasmid species detected in native deer fauna. The presence of B. divergens in both sika and red deer in an area where bovine babesiosis is apparently absent raises important questions regarding the epidemiology, host specificity and taxonomic status of the parasite.

Biology Centre Institute of Parasitology Czech Academy of Sciences Branišovská 1160 31 370 05 České Budějovice Czech Republic; Department of Parasitology Faculty of Science Charles University Viničná 7 128 44 Prague Czech Republic

CEITEC VFU University of Veterinary and Pharmaceutical Sciences Palackého tř 1946 1 612 42 Brno Czech Republic; Biology Centre Institute of Parasitology Czech Academy of Sciences Branišovská 1160 31 370 05 České Budějovice Czech Republic; Department of Pathological Morphology and Parasitology University of Veterinary and Pharmaceutical Sciences Palackého tř 1946 1 612 42 Brno Czech Republic

CEITEC VFU University of Veterinary and Pharmaceutical Sciences Palackého tř 1946 1 612 42 Brno Czech Republic; Department of Biology and Wildlife Diseases Faculty of Veterinary Hygiene and Ecology University of Veterinary and Pharmaceutical Sciences Palackého tř 1946 1 612 42 Brno Czech Republic

CEITEC VFU University of Veterinary and Pharmaceutical Sciences Palackého tř 1946 1 612 42 Brno Czech Republic; Department of Virology Veterinary Research Institute Hudcova 296 70 621 00 Brno Czech Republic

Department of Biology and Wildlife Diseases Faculty of Veterinary Hygiene and Ecology University of Veterinary and Pharmaceutical Sciences Palackého tř 1946 1 612 42 Brno Czech Republic

Department of Veterinary Pathology Western College of Veterinary Medicine University of Saskatchewan 52 Campus Dr Saskatoon SK S7N 5B4 Canada

Faculty of Veterinary Hygiene and Ecology University of Veterinary and Pharmaceutical Sciences Palackého tř 1946 1 612 42 Brno Czech Republic

Military Veterinary Institute Opavská 29 748 01 Hlučín Czech Republic

UCD Veterinary Sciences Centre University College Dublin Belfield Dublin 4 Ireland

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