Recently, several reports in the Journal of Infection have demonstrated the codon usage bias of influenza virus.1–3 Equine influenza (EI) is a severe and highly contagious disease in horses. Equine influenza virus (EIV) is the antigen that causes this important horse disease.4 The prevalent subtype of the virus is H3N8.5 To our knowledge, an evolutionary analysis of codon usage bias of H3N8 EIV has not been investigated. HA and NA are its main surface proteins, responsible for binding the virus to the cell and releasing progeny virus respectively.