title: Evolution of codon usage in Zika virus genomes is host and vector specific.
abstract: The codon usage patterns of viruses reflect the evolutionary changes that allow them to optimize their survival and adapt their fitness to the external environment and, most importantly, their hosts. Here we report the genotype-specific codon usage patterns of Zika virus (ZIKV) strains from the current and previous outbreaks. Several genotype-specific and common codon usage traits were noted in the ZIKV coding sequences, indicating their independent evolutionary origins from a common ancestor. The overall influence of natural selection was more profound than that of mutation pressure, acting on a specific set of viral genes in the Asian-genotype ZIKV strains from the recent outbreak. An interplay between codon adaptation and deoptimization may have allowed the virus to adapt to multiple host and vectors and is reported for the first time in ZIKV genomes. Combining our codon analysis with geographical data on Aedes populations in the Americas suggested that ZIKV has evolved host- and vector-specific codon usage patterns to maintain successful replication and transmission chains within multiple hosts and vectors.
authors.affiliation: Genomics Laboratory, Department of Biosciences, COMSATS Institute of Information Technology, Islamabad 45550, Pakistan.
authors.forename: Azeem Mehmood
authors.initials: AM
authors.lastname: Butt
authors.affiliation: Genomics Laboratory, Department of Biosciences, COMSATS Institute of Information Technology, Islamabad 45550, Pakistan.
authors.forename: Izza
authors.initials: I
authors.lastname: Nasrullah
authors.affiliation: Genomics Laboratory, Department of Biosciences, COMSATS Institute of Information Technology, Islamabad 45550, Pakistan.
authors.forename: Raheel
authors.initials: R
authors.lastname: Qamar
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
authors.forename: Yigang
authors.initials: Y
authors.lastname: Tong
mesh_terms: D000330:Aedes / Q000821:virology*; D000569:Americas / Q000453:epidemiology; D000818:Animals; D003062:Codon; D004196:Disease Outbreaks; D019143:Evolution, Molecular; D005814:Genes, Viral; D016679:Genome, Viral; D005838:Genotype; D054884:Host-Pathogen Interactions / Q000235:genetics; D006801:Humans; D007303:Insect Vectors; D009154:Mutation; D010802:Phylogeny; D012641:Selection, Genetic; D000071244:Zika Virus / Q000235:genetics*; D000071243:Zika Virus Infection / Q000453:epidemiology / Q000635:transmission / Q000821:virology
chemical_list: D003062:Codon