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Abstract The present study evaluated a fluorescence-based method using SYBR green I stain (SG I) to screen antibabesial agents in in vitro cultures of Babesia bovis. The obtained results suggest that the fluorescence-based method might be useful for antibabesial drug screening and may have potential to be developed into a high-throughput screening (HTS) assay. Next, we optimized the assay to be suitable for large-scale screening of drugs and evaluated its usefulness in monitoring the in vitro growth of B. bovis and B. bigemina treated with diminazene aceturate, pyronaridine tetraphosphate, nimbolide or gedunin. Our fluorescence-based assay uses low HCT and does not require daily replacement of culture medium, making it highly suitable for in vitro large-scale drug screening against Babesia parasites that infect cattle. Subsequently, we used our optimized fluorescence based- assay for in vitro screening of 160 anti-malarial compounds (120 drug- like and 40 probe- like) from the Open Access Malaria Box against the growth of bovine Babesia parasites. Eleven novel anti- Babesia hits with nanomole levels of IC50 were identified. The most interesting hits were MMV665939, MMV666093 and MMV396693 with mean selectivity indices (SI) greater than 300 and IC50s ranged from 59 to 403 nM for both bovine Babesia parasites. On the bovine babesiosis diagnosis aspect, we analyzed the infection rates of B. bovis and B. bigemina, using parasite-specific PCR assays in blood–DNA samples sourced from cattle (n = 439), buffaloes (n = 50), and sheep (n = 105) reared in Menoufia, Behera, Giza, and Sohag provinces of Egypt. In cattle, the positive rates of B. bovis and B. bigemina, were 3.18% and 7.97%, respectively. Sequence analysis showed that the B. bovis Rhoptry Associated Protein-1 (RAP-1) and the B. bigemina Apical Membrane Antigen-1 (AMA-1) genes were highly conserved among the samples, with 99.3–100% and 95.3–100% sequence identity values, respectively. The present study, which analyzed bovine Babesia parasites in different livestock animals, may shed an additional light on the epidemiology of hemoprotozoan parasites in Egypt. |