Date Published: August 29, 2013
Publisher: Public Library of Science
Author(s): Rubing Chen, Eryu Wang, Konstantin A. Tsetsarkin, Scott C. Weaver, Marco Vignuzzi.
The 3′ untranslated genome region (UTR) of arthropod-borne viruses is characterized by enriched direct repeats (DRs) and stem-loop structures. Despite many years of theoretical and experimental study, on-going positive selection on the 3′UTR had never been observed in ‘real-time,’ and the role of the arbovirus 3′UTR remains poorly understood. We observed a lineage-specific 3′UTR sequence pattern in all available Asian lineage of the mosquito-borne alphavirus, chikungunya virus (CHIKV) (1958–2009), including complicated mutation and duplication patterns of the long DRs. Given that a longer genome is usually associated with less efficient replication, we hypothesized that the fixation of these genetic changes in the Asian lineage 3′UTR was due to their beneficial effects on adaptation to vectors or hosts. Using reverse genetic methods, we examined the functional importance of each direct repeat. Our results suggest that adaptation to mosquitoes, rather than to mammalian hosts, is a major evolutionary force on the CHIKV 3′UTR. Surprisingly, the Asian 3′UTR appeared to be inferior to its predicted ancestral sequence for replication in both mammals and mosquitoes, suggesting that its fixation in Asia was not a result of directional selection. Rather, it may have resulted from a population bottleneck during its introduction from Africa to Asia. We propose that this introduction of a 3′UTR with deletions led to genetic drift and compensatory mutations associated with the loss of structural/functional constraints, followed by two independent beneficial duplications and fixation due to positive selection. Our results provide further evidence that the limited epidemic potential of the Asian CHIKV strains resulted from founder effects that reduced its fitness for efficient transmission by mosquitoes there.
Genetic change, which can lead to adaptation to new hosts or vectors, is a major cause of the emergence or re-emergence of arthropod-borne viral (arboviral) and other RNA viral diseases , . However, compared to the numerous investigations of point mutations within viral genomic open reading frames, the evolution and determinants of fitness of untranslated genome regions (UTRs) have received far less attention. The 3′ UTRs of arboviral genomes exhibit large size variations, ranging from ∼100 nt to more than 700 nt, and involving extensive substitutions, insertions and deletions even within viral species. This length variation suggests that the heterogeneous regions may not be essential for replication, a view supported by experimental studies with genetically engineered viruses lacking a large part of the 3′UTR that remain viable, albeit with different levels of attenuation –. However, these seemingly redundant sequences must play some role favored by natural selection, because otherwise longer genomes should theoretically be less efficiently replicated. Improved understanding of the forces driving the evolution of the arboviral 3′UTR is needed to provide important insights on its role on pathogenesis and host/vector adaptation.