Occurrence and genetic diversity of rotavirus A in faeces of diarrheic calves submitted to a veterinary laboratory in Spain

A total of 237 faecal specimens from diarrheic calves younger than two months were collected and submitted for diagnosis of enteropathogens over a two-year period (2017–2018) to a veterinary laboratory. Samples originated from 193 dairy and beef farms in 29 provinces distributed throughout Spain, and were tested for the occurrence of three target enteric pathogens by reverse transcription real-time PCR (RT-qPCR): bovine rotavirus A (RVA), Cryptosporidium parvum and bovine coronavirus (BCoV). RT-PCR and nucleotide sequencing analysis were used to determine the G (VP7 gene) and P (VP4 gene) genotypes of 26 specimens positive for RVA. A total of 188 specimens (79.3 %) were positive for at least one of the three target enteric pathogens, and 101 samples (42.6 %) harbored mixed infections. The individual prevalence was 57.8 %, 50.6 % and 23.6 % for C. parvum, RVA and BCoV, respectively. Molecular analysis of selected RVA strains revealed the presence of the G6, G10, G3, P[5] and P[11] genotypes, with the combinations G6P[5] and G6P[11] being the most prevalent. Alignments of nucleotide sequences of the VP7 and VP4 markers showed a high frequency of single nucleotide polymorphisms (SNPs), with up to 294 SNPs found in 869bp of sequence at the G6 genotype (0.338 SNPs/nt), which reveals the extensive genetic diversity of RVA strains. Phylogenetic analysis of the VP7 gene of the G6 strains revealed four distinct lineages, with most strains clustering in the G6-IV lineage. The discrepancies between the RVA genotypes circulating in the sampled cattle farms and the genotypes contained in commercial vaccines currently available in Spain are discussed. We believe that this is the first study on the molecular characterization of rotavirus infecting cattle in Spain.