Evolution of base composition and codon usage bias in the genus Flavivirus

Area of Science:

• Virology
• Genomics
• Evolutionary Biology

Background:

• Base composition and codon usage bias in RNA viruses are not fully understood.
• Flaviviruses are significant human and animal pathogens transmitted by arthropods or directly.
• Understanding viral evolution drivers is crucial for disease control.

Purpose of the Study:

• To investigate if base composition and codon usage bias in Flavivirus correlate with arthropod vector association.
• To determine the extent of these biases and their potential evolutionary significance.

Main Methods:

• Utilized a maximum-likelihood statistical method to analyze genomic data.
• Compared base composition (G+C content) and codon usage across different Flavivirus groups based on vector association (ticks, mosquitoes, non-vector-borne).
• Assessed dinucleotide and codon usage biases independent of base composition.

Main Results:

• Tick-associated Flaviviruses showed significantly lower G+C content genome-wide compared to non-vector-borne viruses.
• Mosquito-borne Flaviviruses had intermediate G+C content, not significantly different from the other groups.
• Dinucleotide and codon usage biases were present in all Flaviviruses but did not correlate with arthropod association, indicating weak selection at synonymous sites.

Conclusions:

• Arthropod vector association, specifically tick-borne transmission, is linked to distinct base composition in Flaviviruses.
• While codon usage biases exist, they appear largely independent of vector specificity within the Flavivirus genus.
• Preliminary findings suggest potential base composition-vector specificity associations in other RNA virus families.