Genome Characterization of a Turkish Bovine Rotavirus Field Isolate by Shotgun Metagenomics

Abstract Bovine rotavirus (BRV) which is the leading viral agent of neonatal calf diarrhea. In recent years, the use of shotgun metagenomics has emerged as a powerful tool for the detection and characterization of viruses. In the present study, BRV was isolated on MA-104 cells from feces of a neonatal calf with diarrhea and shotgun metagenomics was performed in order to obtain whole genome of BRV isolate. From nine sequenced segments, five segments encoding VP1, VP6, NSP3, NSP4, and NSP5/6 proteins was sequenced in full-length and four segments encoding the VP2, VP3, VP7, and NSP2 proteins was sequenced partially and are deposited in GenBank. Sequences of 9 out of 11 segments of BRV can be gained from metagenomics and the BRV isolate which is named as “RVA/Cow-tc/TUR/KIRSEHIR/2019/G10P[X]” is genotyped as G10-P[X]-I2-R2-C2-M2-AX-N2-T6-E2-H3. The VP1 and VP7 nucleotide and amino acid sequences of the present virus are conserved among Turkish BRV strains. Moreover, the VP2 gene/protein was genetically close to a number of RVA strains of cat and dog. Interestingly, for the NSP4 gene/protein, many equine rotaviruses from Japan and feline rotaviruses were found to be similar to KIRSEHIR strain. Although the highest nucleotide identity for NSP5/6 gene was with buffalo rotaviruses, amino acid identity and similarity were highest with human rotaviruses. Additionally, the study found that the present virus had some variations in its amino acid sequences and findings from amino acid sequence identity and similarity are almost compatible with nucleotide sequences. Our results suggested that the present bovine RVA field isolate might be genetic ancestor of canine, equine and feline rotaviruses and support the findings of previous studies about interspecies transmission.