China Animal Husbandry and Veterinary Medicine ›› 2024, Vol. 51 ›› Issue (11): 4984-4995.doi: 10.16431/j.cnki.1671-7236.2024.11.033

• Preventive Veterinary Medicine • Previous Articles    

Whole Genome Sequencing and Genetic Evolution Analysis of Bovine Coronavirus in Inner Mongolia

QI Lemuge1,2, WANG Xufen1,2, HOU Lin1,2, ZHANG Jialei1,2, MA Yutian1,2, ZHANG Zhidan1,2, ZHOU Weiguang1,2   

  1. 1. College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China;
    2. Key Laboratory of Clinical Diagnosis and Treatment Technology for Animal Diseases, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China
  • Received:2024-02-18 Published:2024-10-31

PDF (PC)

56

Abstract: 【Objective】 This study was aimed to understand the whole genome characteristics and genetic evolution of Bovine coronavirus (BCoV) epidemic strains in Inner Mongolia,provide reference for effective prevention and control of BCoV infection. 【Method】 This study performed metavirome sequencing and stepwise RT-PCR amplification on the spleen of calves suspected of being infected with BCoV,obtaining the complete genome sequence of BCoV and conducting bioinformatics and genetic evolution analysis on it.Specific primers were designed to amplify the S gene using Oligo 7.0 software,and genetic evolution,amino acid sequence variation,epitope prediction and tertiary structure prediction were also performed. 【Result】 This study successfully obtained the 30 971 bp BCoV whole genome sequence of the spleen of calves,with NCBI registration number PP352170.1.The nucleotide sequence of the whole genome had the highest similarity with the whole genome sequence of BCoV ABGEB0-62 in Ireland,with a similarity of 99.2%,and was most closely related to the whole genome sequence of the strain.At the same time,it belonged to the same evolutionary branch as BCoV from France (BCoV_2014_13) and Norway (Nes_2012-01-03).The nucleotide length of the amplified S gene was 4 092 bp,which was closest to the S gene sequence of the BCoV ABGEB0-62 in Ireland and belonged to the same evolutionary branch.However,the nucleotide sequence had the highest similarity with S gene of BCoV NMG1 in Inner Mongolia,which was 99.4%.Comparing the amino acid sequences encoded by S gene with those of the Mebus strain,it was found that there were 15 amino acid mutation sites (12 in S1 subunit and 3 in S2 subunit),among which the mutated amino acid residues 154,260,499-520,718,1 192 and 1 344 were located in the antigenic epitope region,leading to changes in the tertiary structure of S protein. 【Conclusion】 This study obtained the complete genome sequence of Inner Mongolia BCoV using metavirus sequencing and genomic 5'end shift RT-PCR method.The variation of the S protein antigen epitope amino acid site and tertiary structural changes indicated a change in S protein antigenicity.The variation of amino acid sites in the polymorphic region of S1 subunit indicated a change in the pathogenicity of S protein.

Key words: Bovine coronavirus (BCoV); whole genome; macrovirome; S gene; genetic evolution

CLC Number: