title: A detailed comparative analysis of codon usage bias in Zika virus.
abstract: Zika virus (ZIKV) is a member of the family Flaviviridae and its genome consists of a single-stranded positive sense RNA molecule with 10,794 nucleotides. Clinical manifestations of disease caused by ZIKV infection range from asymptomatic cases to an influenza-like syndrome. There is an increasing concern about the possible relation among microcephaly and ZIKV infection. To get insight into the relation of codon usage among viruses and their hosts is extremely important to understand virus survival, fitness, evasion from host's immune system and evolution. In this study, we performed a comprehensive analysis of codon usage and composition of ZIKV. The overall codon usage among ZIKV strains is similar and slightly biased. Different codon preferences in ZIKV genes in relation to codon usage of human, Aedes aegypti and Aedes albopictus genes were found. Most of the highly frequent codons are A-ending, which strongly suggests that mutational bias is the main force shaping codon usage in this virus. G+C compositional constraint as well as dinucleotide composition also influence the codon usage of ZIKV. The results of these studies suggest that the emergence of ZIKV outside Africa, in the Pacific and the Americas may also be reflected in ZIKV codon usage. No significant differences were found in codon usage among strains isolated from microcephaly cases and the rest of strains from the Asian cluster enrolled in these studies.
authors.affiliation: Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay. Electronic address: cristina@cin.edu.uy.
authors.forename: Juan
authors.initials: J
authors.lastname: Cristina
authors.affiliation: Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay.
authors.forename: Alvaro
authors.initials: A
authors.lastname: Fajardo
authors.affiliation: Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay.
authors.forename: Martín
authors.initials: M
authors.lastname: Soñora
authors.affiliation: Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay; Viral Populations and Pathogenesis laboratory. Institut Pasteur, CNRS UMR 3569, Paris, France.
authors.forename: Gonzalo
authors.initials: G
authors.lastname: Moratorio
authors.affiliation: Laboratorio de Organización y Evolución del Genoma, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
authors.forename: Héctor
authors.initials: H
authors.lastname: Musto
mesh_terms: D000220:Adaptation, Biological; D001482:Base Composition; D003062:Codon; D019143:Evolution, Molecular; D014644:Genetic Variation; D016679:Genome, Viral; D006801:Humans; D009154:Mutation; D016366:Open Reading Frames; D010802:Phylogeny; D000073336:Whole Genome Sequencing; D000071244:Zika Virus / Q000235:genetics*
chemical_list: D003062:Codon
keywords: Codon bias; Codon usage; Evolution; Zika