Nucleotide substitutions in dengue virus serotypes from Asian and American countries: insights into intracodon recombination and purifying selection

Abstract

BackgroundDengue virus (DENV) infection represents a significant public health problem in many subtropical and tropical countries. Although genetically closely related, the four serotypes of DENV differ in antigenicity for which cross protection among serotypes is limited. It is also believed that both multi-serotype infection as well as the evolution of viral antigenicity may have confounding effects in increased dengue epidemics. Numerous studies have been performed that investigated genetic diversity of DENV, but the precise mechanism(s) of dengue virus evolution are not well understood.ResultsWe investigated genome-wide genetic diversity and nucleotide substitution patterns in the four serotypes among samples collected from different countries in Asia and Central and South America and sequenced as part of the Genome Sequencing Center for Infectious Diseases at the Broad Institute. We applied bioinformatics, statistical and coalescent simulation methods to investigate diversity of codon sequences of DENV samples representing the four serotypes. We show that fixation of nucleotide substitutions is more prominent among the inter-continental isolates (Asian and American) of serotypes 1, 2 and 3 compared to serotype 4 isolates (South and Central America) and are distributed in a non-random manner among the genes encoded by the virus. Nearly one third of the negatively selected sites are associated with fixed mutation sites within serotypes. Our results further show that of all the sites showing evidence of recombination, the majority (~84%) correspond to sites under purifying selection in the four serotypes. The analysis further shows that genetic recombination occurs within specific codons, albeit with low frequency (< 5% of all recombination sites) throughout the DENV genome of the four serotypes and reveals significant enrichment (p < 0.05) among sites under purifying selection in the virus.ConclusionThe study provides the first evidence for intracodon recombination in DENV and suggests that within codons, genetic recombination has a significant role in maintaining extensive purifying selection of DENV in natural populations. Our study also suggests that fixation of beneficial mutations may lead to virus evolution via translational selection of specific sites in the DENV genome.

Recombination in viruses: Mechanisms, methods of study, and evolutionary consequences

“…As a result, several mutations previously incorporated in a genomic region can be transferred simultaneously to another region by a single recombination event. Interestingly, at the codon level, recombination can also alter the codon state by intra-codon recombination events (Arenas and Posada, 2010a), a process observed in viruses (Behura and Severson, 2013). Nevertheless, the fate of these genetic changes will be ultimately determined by natural selection and genetic drift.…”

Bicluster pattern of codon context usages between flavivirus and vector mosquito Aedes aegypti: relevance to infection and transcriptional response of mosquito genes

“…Our recent studies have revealed genome-wide differential usage of codon sequences in different insect species including A. aegypti (Behura and Severson 2012b). In addition to that, we have also shown that codon bias is a significant factor in genetic diversity of DENV populations (Behura and Severson 2013b). Specifically, codon usage bias is known to have an association with translational efficiency and/or accuracy (Rocha 2006; Behura and Severson 2011; Rodriguez et al 2012; Novoa et al 2012) as well as expression levels of protein coding genes (Akashi 2001; Najafabadi and Salavati 2008; Najafabadi et al 2009; Camiolo et al 2012).…”

Genome Investigations of Vector Competence in Aedes aegypti to Inform Novel Arbovirus Disease Control Approaches

“…Further, as DENV is dependent on the host translational apparatus, we and others have reported that DENV isolates show significant biases in synonymous codon usage that are consistent with their geographic origin and likely result from adaptive interaction with the mosquito and human hosts [109,119,120]. We also observed that codon context (the propensity of adjacent codons to consistently pair with themselves or another codon) among Asian and American DENV isolates showed a bias toward (A)(A/T)(A)-(A)(A/T)(A) coding sequences and general avoidance of (C/G)(C/A)(C/G)-(C/G)(C/A)(C/G) coding sequences across all four serotypes [119].…”

“…We also observed that codon context (the propensity of adjacent codons to consistently pair with themselves or another codon) among Asian and American DENV isolates showed a bias toward (A)(A/T)(A)-(A)(A/T)(A) coding sequences and general avoidance of (C/G)(C/A)(C/G)-(C/G)(C/A)(C/G) coding sequences across all four serotypes [119]. In addition to DENV, we also compared [121] the codon context bias of other flaviviruses, including West Nile virus (WNV) and yellow fever virus (YFV), and determined that codon context bias varies in a bicluster manner with A. aegypti genes that have been shown to be differentially expressed following infection by these viruses [92].…”