Prediction of Bovine coronavirus immune epitopes using selection and phylogenetic analysis

Abstract

Bovine betacoronavirus (BoCoV) is a pneumoenteric pathogen of cattle, which is closely related to the common cold Human coronavirus OC43. Vaccines are administered to protect against diseases caused by BoCoV, but knowledge gaps exist with regards correlates of protection and the effect of immune evasion on driving evolution. Immune epitopes predicted for each structural protein were corroborated with selective pressure analysis and sequencing of genes encoding two surface proteins, spike and haemagglutinin esterase (HE). Eleven of the sixteen predicted spike immune epitopes and three of the six predicted HE immune epitopes overlapped residues under diversifying selection or residues where amino acid changes were found. Four of the nineteen residues predicted to be important for recognition of spike by neutralising antibodies (nAb) were under diversifying selection or amino acid changes were observed. Increased prevalence of amino acid changes in specific immune epitopes suggests an effective immune response recognises these regions as non-synonymous mutations would provide a selective advantage for the virus due to immune escape. Selection analysis and sequencing provided more support for MHC-II, B cell receptor and nAb epitopes and less support for MHC-I epitopes. Downregulation of MHC-I antigen presentation has been demonstrated for several coronaviruses and the reduced support for predicted MHC-I epitopes, compared to other immune epitopes, suggests this could also be true for BoCoV.