Emergence of simian immunodeficiency virus in rhesus macaques is characterized by changes in structural and accessory genes that enhance fitness in the new host species

Abstract

The distribution of lentiviruses among primates reflects a history of interspecies transmission and emergence of new virus-host relationships. The degree to which viruses must adapt to the genetic environment of new host species, and how adaptations to the new host initially affect viral fitness are two understudied elements of emergence. The simian immunodeficiency virus (SIV) of rhesus macaques (SIVmac) emerged as the result of a cross-species transmission of SIV from the sooty mangabey monkey (SIVsm) into rhesus macaques, and comparing cohorts of SIVmac- and SIVsm-infected macaques provides an opportunity to examine a lentivirus evolving during the early stages of emergence. Using archived samples from four cohorts of macaques, we compared evolution of “established” macaque-adapted viruses (SIVmac239, SIVmac251) to incompletely-adapted, “emerging” viruses (SIVsmE543, SIVsmE660). Longitudinal samples included the inoculum for each cohort, as well as acute and chronic plasma samples for each animal. Samples were processed for deep sequencing, and consensus sequences of complete viral coding regions were assembled de novo. Computational and manual analysis of the sequences revealed a set of loci that diverged considerably only in the SIVsm-infected animals, suggesting that adaptations at these loci are important for emergence of SIVsm in rhesus macaques. These candidate adaptations included known adaptations to overcome restriction by macaque TRIM5α. In order to quantify the impact of these candidate adaptations on viral replication, each mutation was introduced into SIVsmE543 (forward mutations, reflecting adaptation to the macaque host) and SIVmac239 (reversions to the ancestral residue). These were then tested in a deep sequencing-based fitness assay, in which changes in the frequencies of mutant and parental sequences replicating in cell culture were used to calculate differences in relative fitness. Substitutions in the coding sequences for the Matrix, Capsid, and Vif proteins were found to enhance fitness of SIVsm in rhesus cells, confirming the hypothesis that they represent species-specific adaptations. Together, these studies represent a novel approach to the identification and functional characterization of viral determinants of cross-species transmission.