The Distribution of Synonymous Codon Choice in the Translation Initiation Region of Dengue Virus

Abstract

Dengue is the most common arthropod-borne viral (Arboviral) illness in humans. The genetic features concerning the codon usage of dengue virus (DENV) were analyzed by the relative synonymous codon usage, the effective number of codons and the codon adaptation index. The evolutionary distance between DENV and the natural hosts (Homo sapiens, Pan troglodytes, Aedes albopictus and Aedes aegypti) was estimated by a novel formula. Finally, the synonymous codon usage preference for the translation initiation region of this virus was also analyzed. The result indicates that the general trend of the 59 synonymous codon usage of the four genotypes of DENV are similar to each other, and this pattern has no link with the geographic distribution of the virus. The effect of codon usage pattern of Aedes albopictus and Aedes aegypti on the formation of codon usage of DENV is stronger than that of the two primates. Turning to the codon usage preference of the translation initiation region of this virus, some codons pairing to low tRNA copy numbers in the two primates have a stronger tendency to exist in the translation initiation region than those in the open reading frame of DENV. Although DENV, like other RNA viruses, has a high mutation to adapt its hosts, the regulatory features about the synonymous codon usage have been ‘branded’ on the translation initiation region of this virus in order to hijack the translational mechanisms of the hosts.

Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

“…To determine the influence of the overall codon usage of hosts on that of ZIKV, the similarity index D(A , B) [26] was calculated as follows: where R(A , B) is termed as a cosine value of an included angle between A and B spatial vectors and represents the extent of similarity between ZIKV and hosts in the aspect of overall codon usage pattern. a i is defined as the RSCU value for a specific codon among 59 synonymous codons in ZIKV polyprotein-coding region.…”

“…b i is defined as the RSCU value for the same codon of ZIKV’s hosts. D(A , B) represents the potential effect of the overall codon usage of the hosts on that of ZIKV, and its value varies from 0 to 1 [26]. The higher D(A , B) means the stronger influence of environment related synonymous codon usage patterns of hosts on that of ZIKV.…”

Evolutionary characterization of Tembusu virus infection through identification of codon usage patterns

“…To date, analyses of Flavivirus codon usage are fragmentary, and such studies have primarily focused on particular virus species, as previously described (Hu et al, 2011;Moratorio et al, 2013;Zhou et al, 2013). Conversely, the evolutionary characteristics and genetic relationships of codon usage bias in the TMUV genome have not been systematically studied; indeed, only a few genomic sequences of TMUV have been sequenced to date, with many studies only recently performed.…”

“…For viruses, little information exists regarding the extent and origin of synonymous codon variation. Recent efforts to elucidate codon usage biases in Flaviviridae have concentrated mainly on Dengue virus (DGV) (Zhou et al, 2013), West Nile virus (WNV) (Moratorio et al, 2013), and Hepatitis C virus (HCV) (Hu et al, 2011). In contrast, investigations of TMUV have primarily focused on viral isolation and identification Tang et al, 2013a), the establishment and application of diagnostic methods (Li et al, 2012b;Yun et al, 2012), and genetic analyses of complete genome sequences Wan et al, 2012;Zhu et al, 2012), whereas information regarding codon usage patterns is not available.…”

Large-Scale Genomic Analysis of Codon Usage in Dengue Virus and Evaluation of Its Phylogenetic Dependence

“…On the other hand, Zhou et al reported no link of geographic origin to the codon usage of DENV [13]. Behura and Severson found that the silent sites are favoring the geographical diversification [15].…”