Prediction of Bovine coronavirus immune epitopes using selection and phylogenetic analysis

Bovine betacoronavirus (BoCoV) is a pneumoenteric pathogen of cattle, which is closely related to Human coronavirus OC43. Vaccines are administered to protect against diseases caused by BoCoV, but knowledge gaps exist with regard to correlates of protection and the effect of immune evasion on driving evolution. In this study, immune epitopes were predicted for the BoCoV structural proteins including spike and haemagglutinin esterase (HE) and these predictions were supported through targeted gene sequencing of Irish clinical isolates and selective pressure analysis. Increased prevalence of diversifying selection and amino acid changes in some predicted immune epitopes suggests immune escape is selecting for non-synonymous mutations arising in these regions. Selection analysis and sequencing provided increased support for nAb epitopes compared to other predicted immune epitopes suggesting nAbs are an important arm of the immune response to BoCoV. Phylogenetic analysis of spike and HE sequences showed Irish isolates from this study were in the European clade except for one HE sequence that sat in the Asian/American clade, while the spike gene of this sample was in the European clade. Recombination between a European and an Asian/American isolate could give rise to such a sequence and recombination breakpoints that were detected at the 3 end of HE and 5 end of spike would produce such a sequence. This study presents evidence showing pressure to evade the nAb response is contributing to BoCoV evolution and for the first time, sequenced an isolate likely derived from a recombination event between European and Asian/American strains.