Chikungunya Virus 3′ Untranslated Region: Adaptation to Mosquitoes and a Population Bottleneck as Major Evolutionary Forces

Abstract

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.

Comprehensive Genome Scale Phylogenetic Study Provides New Insights on the Global Expansion of Chikungunya Virus

“…The 3= UTR insertion, which represents an approximate duplication of the previously defined DR(1 ϩ 2) region, has been shown to improve CHIKV fitness for replication in mosquito cells without a significant effect in Vero cells (39). Previous in vivo studies with A. aegypti mosquitoes and CD-1 infant mice suggested a similar fitness effect of DR(1 ϩ 2) duplication in mosquitoes but a slightly deleterious phenotype in mammals (49). Therefore, to some extent, increased fitness in A. aegypti mosquitoes, the only vector directly implicated in CHIKV transmission in the Americas (50), mediated by this duplication may have facilitated transmission and spread from the Caribbean.…”

“…Therefore, to some extent, increased fitness in A. aegypti mosquitoes, the only vector directly implicated in CHIKV transmission in the Americas (50), mediated by this duplication may have facilitated transmission and spread from the Caribbean. The selection of longer CHIKV 3= UTRs has been shown to occur mainly during replication in the mosquito host (49), suggesting that this duplication probably arose in the vector. However, the putative fitness advantage was apparently not strong enough for establishment in South Pacific islands, as suggested by the predominance of Asian lineage strains with the shorter 3= UTR there.…”

The role of type I interferon in the immunobiology of chikungunya virus

“…RNA-Seq of the tissues also revealed a 44 bp deletion in the 3'UTR of the parental virus. The 3'UTR of CHIKV varies widely between different strains due to direct sequence repeats that are duplicated, inverted or deleted in different CHIKV strains (Chen, Wang et al 2013). These variations are thought to facilitate viral fitness in different hosts/vectors (Chen, Wang et al 2013, Hyde, Chen et al 2015.…”

“…The 3'UTR of CHIKV varies widely between different strains due to direct sequence repeats that are duplicated, inverted or deleted in different CHIKV strains (Chen, Wang et al 2013). These variations are thought to facilitate viral fitness in different hosts/vectors (Chen, Wang et al 2013, Hyde, Chen et al 2015. The 44 bp deletion detected in the parental virus sequence corresponds to part of a direct sequence repeat that occurs twice in the Asian lineage, and once in the ECSA lineage, of which LR2006_OPY1 derives (Chen, Wang et al 2013).…”

“…These variations are thought to facilitate viral fitness in different hosts/vectors (Chen, Wang et al 2013, Hyde, Chen et al 2015. The 44 bp deletion detected in the parental virus sequence corresponds to part of a direct sequence repeat that occurs twice in the Asian lineage, and once in the ECSA lineage, of which LR2006_OPY1 derives (Chen, Wang et al 2013). The parental virus used herein thus likely acquired the site changes and the deletion in the 3'UTR during the two passages in C6/36 mosquito cells.…”