Identification of Recombinant Aichivirus D in Cattle, Italy

Kobuviruses (KoVs) are a group of small, non-enveloped RNA viruses classified in the genus Kobuvirus within the Picornaviridae family, comprising Aichivirus species A to F. KoVs have been identified in humans and several mammals, including domestic ungulates. This study investigated the presence of KoVs in a collection of bovine stool samples (n = 38) obtained from animals with enteritis or without clinical signs. By RT-PCR screening, KoV RNA was detected in 10/38 animals (26.3%). Six of the ten positive animals had enteric signs. On sequence analysis of the amplicons, eight strains were related to species Aichivirus B, commonly identified in cattle. In contrast, two strains (ITA/2019/572-1 and ITA/2020/bovine/30-2), displayed the highest nt identity (up to 97.1%) to cattle, yak, and goat Aichivirus D strains. On whole genome analysis, strains ITA/2019/572-1 and ITA/2020/30-2 showed 88.9% nt identity to each other and 87.8-90.3% nt to the bovine kobuvirus strain CHN/2021/ON730709 identified in China. Interestingly these three Aichivirus D strains showed a recombinant makeup, clustering with D1 genotype in the capsid region and with D2 genotype in the non-structural genes. These findings suggest that Aichivirus D KoVs are common components of livestock virome. Understanding the genetic diversity of KoVs in animals will be useful to improve the diagnostics and gather epidemiological data.