Divergence and codon usage bias of Betanodavirus, a neurotropic pathogen in fish

- Betanodaviral RNA polymerase and coat protein genes shared a similar moderate rate.
- The primary bifurcation events of the two genes both took place ∼700 years ago.
- The divergence scenarios of the two genes were different.
- Each gene had additional codon usage bias independent of compositional constraint.
- Codon choice of betanodavirus was not fully complied with that of fish host.

Betanodavirus is a small bipartite RNA virus of global economical significance that can cause severe neurological disorders to an increasing number of marine fish species. Herein, to further the understanding of the evolution of betanodavirus, Bayesian coalescent analyses were conducted to the time-stamped entire coding sequences of their RNA polymerase and coat protein genes. Similar moderate nucleotide substitution rates were then estimated for the two genes. According to age calculations, the divergence of the two genes into the four genotypes initiated nearly simultaneously at ∼700 years ago, despite the different scenarios, whereas the seven analyzed chimeric isolates might be the outcomes of a single genetic reassortment event taking place in the early 1980s in Southern Europe. Furthermore, codon usage bias analyses indicated that each gene had influences in addition to mutational bias and codon choice of betanodavirus was not completely complied with that of fish host.