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Background   Babesia  parasites, mainly  Babesia bovis  and  B. bigemina , are tick-borne hemoparasites inducing bovine babesiosis in cattle globally. The clinical signs of the disease include, among others, anemia, fever and hemoglobinuria. Babesiosis is known to occur in tropical and subtropical regions of the world. In this study, we aim to provide information about the occurrence and phylogenetic relationship of  B. bigemina  and  B. bovis  species in cattle from different locations in nine provinces of South Africa.  A total of 430 blood samples were randomly collected from apparently healthy cattle. These samples were genetically tested for Babesia parasitic infections using nested PCR assays with species-specific primers.    Results  Nested PCR assays with Group I primer sets revealed that the overall prevalence of  B. bigemina  and  B. bovis  in all bovine samples tested was 64.7% (95% CI = 60.0-69.0) and 35.1% (95% CI = 30.6-39.8), respectively. Only 117/430 (27.2%) animals had a mixed infection. The highest prevalence of 87.5% (95% CI = 77.2-93.5) for  B. bigemina  was recorded in the Free State province collection sites (Ficksburg, Philippolis and Botshabelo), while North West collection sites had the highest number of animals infected with  B. bovis  (65.5%; 95% CI = 52.7-76.4). Phylograms were inferred based on  B. bigemina -specific  gp45  and  B. bovis -specific  rap-1  nucleotide sequences obtained with Group II nested PCR primers. Phylogenetic analysis of  gp45  sequences revealed significant differences in the genotypes of  B. bigemina  isolates investigated, including those of strains published in GenBank. On the other hand, a phylogeny based on  B. bovis rap-1  sequences indicated a similar trend of clustering among the sequences of  B. bovis  isolates investigated in this study.    Conclusion  This study demonstrates the occurrence of  Babesia  parasites in cattle from different provinces of South Africa. It was also noted that the situation of  Babesia  parasitic infection in cattle from certain areas within the surveyed provinces had either reached endemic stability or was progressing towards stability.

Molecular diagnosis and phylogenetic analysis of Babesia bigemina and Babesia bovis hemoparasites from cattle in South Africa