Next-Generation Sequencing Reveals Four Novel Viruses Associated with Calf Diarrhea.

Qi Wu,Dongbo Sun,Ga Gong,Xuehan Zhang,Jinzhu Zhou,Dandan Wang,Bin Li,Jizong Li,Wei Wang,Sizhu Suolang,Baochao Fan

doi:10.3390/v13101907

Abstract

Calf diarrhea is one of the common diseases involved in the process of calf feeding. In this study, a sample of calf diarrhea that tested positive for bovine coronavirus and bovine astrovirus was subjected to high-throughput sequencing. The reassembly revealed the complete genomes of bovine norovirus, bovine astrovirus, bovine kobuvirus, and the S gene of bovine coronavirus. Phylogenetic analysis showed that the ORF2 region of bovine astrovirus had the lowest similarity with other strains and gathered in the Mamastrovirus unclassified genogroup, suggesting a new serotype/genotype could appear. Compared with the most closely related strain, there are six amino acid mutation sites in the S gene of bovine coronavirus, most of which are located in the S1 subunit region. The bovine norovirus identified in our study was BNoV-GIII 2, based on the VP1 sequences. The bovine kobuvirus is distributed in the Aichi virus B genus; the P1 gene shows as highly variable, while the 3D gene is highly conserved. These findings enriched our knowledge of the viruses in the role of calf diarrhea, and help to develop an effective strategy for disease prevention and control.

Highlights

Introduction iationsCalf diarrhea is a common gastrointestinal disease in calves, and most cases occur at less than 1 month of age
There are six types of mixed infections, bovine viral diarrhea virus (BVDV) + bovine coronavirus (BCoV), BVDV + bovine astrovirus (BoAstV), BCoV + BRoV, BCoV + BoAstV, BVDV + BCoV + BoAstV, BCoV + BRoV + BoAstV, and the infection rate is as high as 46.03% (Table 1)
BCoV and BoAstV were detected in the mixed infection sample numbered 210,041, the high-quality total RNA was subsequently used for the following deep sequencing

Summary

Introduction

Calf diarrhea is a common gastrointestinal disease in calves, and most cases occur at less than 1 month of age. Calf diarrhea often occurs due to environmental contamination with pathogens, and it is transmitted via fecaoral transmission routes. The main clinical features include diarrhea, dehydration, and foul-smelling feces. Prior studies have implicated several viruses in calf diarrhea, and rotavirus is the main viral causative agent of diarrhea in calves worldwide [2]. Several other viruses, including bovine viral diarrhea virus (BVDV), bovine adenovirus (BAdV), bovine torovirus (BToV), bovine parvovirus (BPV), bovine coronavirus (BCoV), bovine astrovirus (BoAstV), bovine kobuvirus (BKoV), and bovine norovirus (BNoV), have been recognized as the causative agents of diarrhea [3,4,5,6,7]. The economic impact caused by this condition is Licensee MDPI, Basel, Switzerland

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