Evolution of codon usage in Zika virus genomes is host and vector specific

Area of Science:

• Virology
• Evolutionary Biology
• Genomics

Background:

• Viral codon usage patterns are key indicators of evolutionary adaptation and host-specific fitness.
• Zika virus (ZIKV) exhibits diverse genetic strains, necessitating an understanding of its evolutionary trajectory.

Purpose of the Study:

• To investigate genotype-specific codon usage patterns in Zika virus (ZIKV) strains.
• To elucidate the evolutionary forces, including natural selection and mutation pressure, shaping ZIKV genomes.
• To explore the interplay of codon adaptation and deoptimization in ZIKV's adaptation to various hosts and vectors.

Main Methods:

• Analysis of ZIKV coding sequences from current and historical outbreaks.
• Comparative analysis of codon usage patterns across different ZIKV genotypes.
• Integration of codon usage data with geographical distribution of Aedes mosquito populations.

Main Results:

• Identified distinct genotype-specific and common codon usage traits in ZIKV, suggesting independent evolutionary origins.
• Determined that natural selection exerts a more significant influence than mutation pressure on Asian-genotype ZIKV strains.
• Observed an interplay between codon adaptation and deoptimization, a novel finding in ZIKV genomes.
• Correlated ZIKV codon usage patterns with geographical data of Aedes populations, indicating host- and vector-specific adaptations.

Conclusions:

• Zika virus (ZIKV) exhibits genotype-specific codon usage reflecting independent evolutionary pathways.
• Natural selection plays a crucial role in ZIKV evolution, particularly in Asian strains, driving adaptation to hosts and vectors.
• The virus employs a combination of codon adaptation and deoptimization to ensure successful replication and transmission across diverse environments.