Identification of a novel Aichivirus D in sheep

A novel kobuvirus was found in diarrheal fecal samples of Tibetan sheep using a viral metagenomics approach, and a full kobuvirus genome was successfully obtained by RT-PCR from a diarrheal fecal sample. The full genomic sequence was 8485 nucleotides (nt) in length with a standard picornavirus genome organization. The novel genome shares 62.9% and 77.8% nt homology with Aichivirus D1 genotype strain 1-22-KoV, and Aichivirus D2 genotype strain 2-44-KoV, respectively. According to the species classification criteria of the International Committee on Taxonomy of Viruses (ICTV), the new kobuvirus belongs to Aichivirus species D. Interestingly, compared with 2 known Aichivirus D genotype strains, the novel Aichivirus D has unique amino acid substitutions in the 5'untranslated region (-UTR), VP0, VP3, and VP1, with a recombination event in the 2C region.These characteristics make the novel Aichivirus D cluster into an independent branch in the phylogenetic tree, suggesting that strain may represent a novel genotype in Aichivirus D. Moreover, the novel Aichivirus D was detected in 9.2% (18/195) of the sheep diarrheal fecal samples from 4 farms in 3 counties of the Qinghai Tibet Plateau in China. In addition, full-length VP0, VP3, and VP1 genes were successfully obtained from 12 samples from 4 farms, and phylogenetic analysis based on these genes revealed a unique evolutionary pattern for this novel Aichivirus D strain. This study identified a novel Aichivirus D that is circulating in sheep in Qinghai Tibet Plateau in China and these findings provide a better understanding of the epidemiologic and genetic evolution of kobuviruses.