A detailed comparative analysis on the overall codon usage patterns in West Nile virus |
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| Affiliation: | 1. Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay;2. Unidad de Biofísica de Proteínas, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay;3. Laboratorio de Organización y Evolución del Genoma, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay;4. Laboratorio de Evolución, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay;5. Unidad de Proteínas Recombinantes, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay;1. Institut für Virologie, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany;2. Institut für Veterinärpathologie, Freie Universität Berlin, Robert-von-Ostertag-Str. 15, 14163 Berlin, Germany;3. Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany;4. Institut für Immunologie, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany;5. IRI Life Sciences, Institute of Biology, Humboldt-Universität zu Berlin, Philippstraße 13, 10115 Berlin, Germany;1. Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA |
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| Abstract: | West Nile virus (WNV) is a member of the family Flaviviridae and its genome consists of an 11-kb single-stranded, positive-sense RNA. WNV is maintained in an enzootic cycle between mosquitoes and birds, but can also infect and cause disease in horses and humans, which serve as incidental dead-end hosts. Understanding the extent and causes of biases in codon usage is essential to the comprehension of viral evolution. In this study, we performed a comprehensive analysis of 449 WNV strains, for which complete genome sequences are available. Effective number of codons (ENC) indicates that the overall codon usage among WNV strains is only slightly biased. Codon adaptation index (CAI) values found for WNV genes are different from the CAI values found for human genes. The relative synonymous codon usage among WNV strains isolated from birds, equines, humans and mosquitoes are roughly similar and are influenced by the relative dinucleotide frequencies. Taking together, the results of this work suggest that WNV genomic biases are the result of the evolution of genome composition, the need to escape the antiviral cell responses and a dynamic process of mutation and selection to re-adapt its codon usage to different environments. |
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| Keywords: | Codon usage Evolution |
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