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.
Highlights
Dengue is a common mosquito-borne flavivirus disease of the international public health threat
Due to the effect of mutation from RNA virus, synonymous codons are selected with different frequencies, the feature is termed as the synonymous codon usage bias
effective number of codons (ENC) and codon adaptation index (CAI) value, together with the content of GC3 (G+C at the third synonymous position of codon) were used to estimate the role of variation of codon usage of gene in the evolutionary processes, here, we can estimate the correlation between the two major axis (f ’1 and f ’2 values, which represent the synonymous codon usage of Dengue virus (DENV), stemming from reducing data dimensionality of the principal component analysis (PCA) performance) and ENC value, CAI value, GC3% for the 119 ORFs of DENV, respectively
Summary
Dengue is a common mosquito-borne flavivirus disease of the international public health threat. Dengue virus (DENV) can lead to a wide range of symptom from the asymptomatic state to a severe, life threatening syndrome [1,2] This virus is a positivesense and single-stranded RNA virus belonging to the flaviviridae family, and the single reading open frame of this virus can encodes three structural proteins, including core, envelope and membrance proteins, and seven non-structural proteins namely NS1, NS2a-b, NS3, NS4a-b and NS5 [3]. The analysis of the synonymous codon usage has been applied to investigate the relationship between mutation pressure from virus and translation selection from host [11], the role of the synonymous codon usage in the formation of the genetic divergence for the four genotypes has not been analyzed up to date. The study has not been carried out to investigate the interaction between the virus and Aedes vector in the evolutionary processes at the level of the synonymous codon usage. By analysis of the similarity degree of codon usage between DENV and its hosts, this study aims to investigate the effects of its hosts on DENV at the aspect of the overall codon usage pattern
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