Aichivirus C isolate is a diarrhoea-causing pathogen in goats.

Aichivirus C is an emerging virus in goats, but its biological significance remains unknown. In this study, 18 diarrheic and 16 non-diarrheic faecal samples of kids were collected from a farm with an on-going diarrheic outbreak in Sichuan Province, China in May 2021. Of these samples, 77.8% (14/18) of diarrheic samples were detected as Aichivirus C positive by RT-PCR, which was significantly higher than that of non-diarrheic faces (0%, p < .001); meanwhile, other common diarrhoea-causing pathogens in goats were not detected in diarrheic samples, except for two samples that were detected as caprine enterovirus positive, suggesting that Aichivirus C was associated with goat diarrhoea. Furthermore, five Aichivirus C strains were successfully isolated from positive samples using Vero cell lines and two isolates were further plaque-purified, named SWUN/F5/2021(10-6.7 TCID50 /0.1 mL) and SWUN/F6/2021(10-7 TCID50 /0.1 mL). Interestingly, Aichivirus C strain could cause systemic infection in experimental kids via oral administration, with the main clinical manifestation being severe watery diarrhoea. Histopathological changes observed in the duodenum and jejunum were characteristic, with shedding of mucosal epithelial cells. In addition, the virus was detected in tissues of diarrhoea kids naturally infected with Aichivirus C, exhibiting pathological changes similar to those of experimental infections. Overall, this study first isolated Aichivirus C and confirmed its pathogenicity in kids, with further study needed to better understand the virus pathogenicity. As Aichivirus C has been detected in South Korea, Italy and the USA and widely prevalent in southwest China, the results obtained here have significant implications for the diagnosis and control of diarrhoea in goats.

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.

An emerging novel bovine coronavirus with a 4-amino-acid insertion in the receptor-binding domain of the hemagglutinin-esterase gene.

The hemagglutinin-esterase (HE) protein of betacoronavirus lineage A is a secondary receptor in the infection process and is involved in the emergence of new betacoronavirus genotypes with altered host specificity and tissue tropism. We previously reported a novel recombinant bovine coronavirus (BCoV) strain that was circulating in dairy cattle in China, but this virus was not successfully isolated, and the genetic characteristics of BCoV are still largely unknown. In this study, 20 diarrheic faecal samples were collected from a farm in Liaoning province that had an outbreak of calf diarrhea (≤ 3 months of age) in November 2018, and all of the samples tested positive for BCoV by RT-PCR. In addition, a BCoV strain with a recombinant HE (designated as SWUN/A1/2018) and another BCoV strain with a recombinant HE containing an insertion (designated as SWUN/A10/2018) were successfully isolated in cell culture (TCID50: 104.25/mL and 104.73/mL, respectively). Unexpectedly, we identified the emergence of a novel BCoV variant characterized by a 12-nt bovine gene insertion in the receptor-binding domain in a natural recombinant HE gene, suggesting a novel evolutionary pattern in BCoV.

First detection and molecular characteristics of caprine kobuvirus in goats in China.

Caprine kobuvirus (CKoV), a member of the genus Kobuvirus, has only been identified in South Korea and Italy until now. In this study, 24 goat diarrheic fecal samples were collected from 3 farms in Sichuan province, China, and 87.5% (21/24) samples were detected as CKoV positive by RT-PCR. Meanwhile, full-length VP0, VP3, and VP1 genes were simultaneously cloned from 17 clinical samples. Phylogenetic analysis showed that all CKoV strains were most closely related to porcine kobuvirus based on amino acid (aa) sequences of VP0 and VP3 proteins, but CKoV strains were closely related to with Aichivirus B strains (ferret, bovine, and sheep kobuvirus) based on aa sequences of the VP1 protein. Interestingly, compared with known CKoV strains in the GenBank database, Chinese CKoV strains have unique amino acid changes in VP0 and VP1 proteins. Moreover, the first Chinese CKoV nearly complete genome was successfully obtained from a diarrheic fecal sample, named SWUN/F11/2019. Compared with the two known CKoV strains, five aa mutations (S60A, L252I, V267T, I, V 306 L, V331I) were found in the VP0 gene and 7 aa mutations (S57N, G, T243A, V244I, T, A248V, L, S251A, R252H, and M255L) were found in VP1 in the SWUN/F11/2019 genome. This was the first report of the detection and molecular characteristics of CKoV from goats in China, which could be helpful for improving the understanding of the prevalence and genetic evolution of CKoV.