Application of maximum-likelihood models to selection pressure analysis of group I nucleopolyhedrovirus genes

Knowledge of virus genes under positive selection pressure can help identify molecular determinants of species-specific virulence or host range without prior knowledge of the mechanisms governing host range and virulence. Towards this end, codon-based models of substitution were used in a maximum-likelihood approach to analyse selection pressures acting on 83 genes of group I nucleopolyhedroviruses (NPVs). Evidence for positive selection was found for nine genes: ac38, ac66, arif-1, lef-7, lef-10, lef-12, odv-e18, odv-e56 and vp80. The baculovirus DNA helicase gene (dnahel) was not found to be positively selected using models that allowed the intensity of selection pressure to vary among codon sites. Further analysis with a method that allows selection pressure intensity to vary among lineages suggests that positive selection may have occurred in dnahel during the divergence of Bombyx mori NPV and the NPVs of Autographa californica and Rachiplusia ou. NPV genes that have undergone positive selection may modulate the ability of different NPVs to replicate efficiently in cells (lef-7, lef-10, lef-12) or to establish primary infection of the midgut (odv-e18, odv-e56) of different host species.