Detection and characterization of bovine coronavirus and rotavirus in calves in Ethiopia

Abstract Background Bovine rotavirus A (BRVA) and bovine coronavirus (BCoV) cause significant diarrhea in young calves, leading to health issues and economic losses in the cattle industry. This study aimed to detect and molecularly characterize BRVA and BCoV in calves from Addis Ababa, Ethiopia. Fecal samples were collected from 105 calves under six months old, both with and without diarrhea. BRVA and BCoV were detected using quantitative real-time Polymerase Chain Reaction (qPCR), followed by genome sequencing for phylogenetic analysis and genotype determination. Results BRVA was found in 3.8% of the calves, while BCoV was detected in 2.9%. The identified rotavirus genotypes included G10, found in diarrheic calves, and G8, found in a non-diarrheic calf. All BCoV infections occurred in diarrheic calves. Phylogenetic analysis of the BCoV spike protein 1 (S1) hypervariable region (HVR) and hemagglutinin esterase (HE) gene revealed close relationships with European and Asian strains. The S1 HVR of the current virus sequence PQ249423 was 100% identical at the nucleotide level to previously reported sequences from Ethiopia. Six amino acid substitutions in the HE gene of the current BCoVs were identified compared to the reference Mebus strain of BCoV. Phylogenetic analysis showed that the current G8 BRVA sequences clustered with bovine, caprine, and human rotavirus strains, while the G10 viruses formed a distinct cluster with bovine strains. The G10 viruses showed a 99.37% nucleotide sequence similarity to a previously reported BRVA from Ethiopia, and the G8 virus displayed the highest nucleotide similarity with a caprine isolate from India. Gene segment analysis of the current BRVA viruses indicated varying similarities with human, bovine, caprine, and porcine rotavirus strains, suggesting a potential reassortment event involving artiodactyl, human, and porcine rotavirus. Conclusions This study demonstrates the presence of BRVA and BCoV in Ethiopian dairy calves and provides insights into their genetic diversity. Genetic analysis of BCoV revealed close relationships with strains from Europe and Asia. G10 and G8 were the identified BRVA genotypes, with G8 reported for the first time in Ethiopia. Future research should focus on broader sampling and molecular characterization to understand genetic diversity and devise effective control measures.