Zika virus outbreak in the Americas: Is Aedes albopictus an overlooked culprit?

Azeem Mehmood Butt; Izza Nasrullah; Raheel Qamar; Yigang Tong

Alternative codons within the same group that codes for the same amino acid are often termed 'synonymous' codons, although their corresponding tRNAs might differ in relative abundance in cells and in the speed by which they are recognized by the ribosome. However, the synonymous codons are not randomly chosen within and between genomes, which is referred to as codon usage bias (Grantham et al., 1980; Marin et al., 1989) . This phenomenon has been observed in a wide range of organisms, from prokaryotes to eukaryotes and viruses. Studies on codon usage have identified several factors that could influence codon usage patterns, including mutation pressure, natural or translational selection, secondary protein structure, replication and selective transcription, hydrophobicity and hydrophilicity of the protein, and the external environment (Gu et al., 2004; Liu et al., 2011; Ma et al., 2013; Moratorio et al., 2013; Sharp et al., 1988; Tao et al., 2009 ). Moreover, considering the virus's genome size and other viral features, such as dependence . CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/044594 doi: bioRxiv preprint on host's machinery for key processes, including replication, protein synthesis, and transmission, compared with prokaryotic and eukaryotic genomes, the interplay of codon usage among viruses and their hosts is expected to affect overall viral survival, fitness, evasion from host's immune system, and evolution (Moratorio et al., 2013; Shackelton et al., 2006) . Therefore, knowledge of codon usage in viruses can reveal information about molecular evolution as well as improve our understanding of the regulation of viral gene expression and aid in vaccine design, where efficient expression of viral proteins may be required to generate immunity.