Molecular evolution of protein sequences and codon usage in monkeypox viruses

ABSTRACT The monkeypox virus (mpox virus, MPXV) epidemic in 2022 poses a significant public health risk. However, the evolutionary principles of MPXV are largely unknown. Here, we examined the evolutionary patterns of protein sequences and codon usage in MPXV. We first showed the signal of positive selection in OPG027 specifically in Clade I. We then discovered accelerated protein sequence evolution over time in 2022 outbreak-causing variants. We also found strong epistasis between amino acid substitutions located in different genes. Codon adaptation index (CAI) analysis revealed that MPXV tended to use more unpreferred codons than human genes and that the CAI decreased with time and diverged between clades, with Clade I > IIa and IIb-A > IIb-B. Although the decrease in fatality rate in the three groups matched the CAI pattern, it is unclear whether this is a coincidence or if the deoptimization of codon usage in MPXV induced a decrease in fatality. This study sheds new light on the processes influencing the evolution of MPXV in human populations.