Differences in codon usage between host-species-specific rabies virus clades are driven by non-GC3 nucleotide composition

Viral genes sometimes use certain codons more than others due to their nucleotide content, translational efficiency, and selection pressure from the host immune system. The rabies virus (RABV) is a negative strand RNA virus which can infect a broad range of mammalian hosts, with many of its clades circulating predominantly in specific host species. Previous work on codon usage in RABV has focused only on broader viral clades. We use publicly available RABV nucleoprotein gene sequences to investigate how dinucleotide content and codon usage biases differ between host-associated clades, and what drives these differences. We found that codon usage varies most between bat- and carnivore-associated RABV clades, and more subtly between host-species-specific minor clades within these groups. C1, GA3 and GT3 content were found to have a strong influence over codon usage patterns, and CpG content was higher in carnivore-associated RABV clades than in bat-associated clades. This, along with lower numbers of zinc-finger antiviral protein binding motifs than would be expected based on (di)nucleotide composition in bat-associated RABV sequences, suggests that bat-associated RABV clades may be under higher selection pressure from the host’s zinc-finger antiviral protein than carnivore-associated clades are, warranting further investigation of the mechanism underpinning this change.