Identification of clade-specific single nucleotide polymorphisms for improved Rabies virus surveillance in Canis familiaris host

Rabies infection continues to be prevalent in many countries, causing a significant number of fatalities annually, predominantly in resource-poor countries. Multiple RABV variants have stabilised throughout evolution, leading to the formation of several clades which have been named after their geographic region of prevalence. Extensive studies have been conducted on the origin, occurrence and spread of RABV clades. However, a systematic understanding of the genetic diversity within and among these clades is still lacking. Previous studies on phylogeny, evolution, and diversity were mainly based on nucleotide sequences of one or two genes. In this study, we utilised whole genome sequences obtained from dog hosts belonging to four major clades to investigate the diversity and phylogeny of the RABV clades. We identify Single Nucleotide Polymorphisms (SNPs) of varying frequencies across the genomes of these clades. We categorise these SNPs into various classes based on their impact on the protein sequence and region of occurrence in the genome. Notably, we report 138 “universal” mutations, which occur with a frequency of more than 90% across all clades. We also report 23 “clade-specific mutations” in three clades: Asian, Arctic, and Africa-2, which could play a crucial role in the fitness of the virus and offer a potential for targeted clade surveillance. Our study also investigates the effects of these mutations on protein function and virus pathogenesis. Overall, our findings contribute to expanding knowledge about RABV diversity and evolution, with important implications for effectively tracking and combatting RABV transmission effectively.