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

Area of Science:

• Virology
• Genomics
• Evolutionary Biology

Background:

• Rabies virus (RABV) exhibits codon usage bias influenced by nucleotide content, translation efficiency, and host immune selection.
• Previous studies on RABV codon usage have primarily focused on broad viral clades.
• RABV infects diverse mammalian hosts, with clades often associated with specific host species.

Purpose of the Study:

• To investigate differences in dinucleotide content and codon usage bias between host-associated RABV clades.
• To identify the factors driving these codon usage variations within RABV.
• To explore potential host immune selection pressures shaping RABV evolution.

Main Methods:

• Analysis of publicly available RABV nucleoprotein gene sequences.
• Comparative analysis of dinucleotide composition (e.g., CpG content) across different RABV clades.
• Investigation of codon usage patterns and their correlation with host association.

Main Results:

• Codon usage variation was most pronounced between bat- and carnivore-associated RABV clades.
• Specific dinucleotides (C1, GA3, GT3) significantly influenced codon usage patterns.
• Carnivore-associated RABV clades showed higher CpG content than bat-associated clades.
• Bat-associated RABV sequences had fewer predicted zinc-finger antiviral protein binding motifs than expected.

Conclusions:

• Host-associated codon usage differences in RABV are linked to dinucleotide content and host immune pressures.
• Bat-associated RABV clades may experience elevated selection from host zinc-finger antiviral proteins.
• Further research is needed to elucidate the specific mechanisms of host antiviral protein interactions with RABV.