Decoding rabies: Phylogenetic insights into the nucleoprotein and glycoprotein genes of rabies virus across domesticated, free-roaming and wild animals in India.

This study investigates the genetic relatedness of rabies virus (RABV) strains circulating among domesticated, free-roaming, and wild animals in India, utilizing Nucleoprotein (N) and Glycoprotein (G) gene sequencing, along with maximum-likelihood molecular analysis. Our findings revealed that despite a broad host range, the RABV strains exhibit high sequence similarity, supporting the potential for using a common vaccine to control rabies in animals across the region. Specifically, RABV strains affecting domesticated animals, free-roaming dogs, and wild species-Jackal (Canis aureus) and Indian Wolf (Canis lupus pallipes)-clustered within the AL 1a lineage, showing strong bootstrap support for a shared evolutionary history. Based on strict genetic distance thresholds, we partitioned the AL 1a lineage into three regional AL 1a.1, AL 1a.2 and AL 1a.3 sublineages. Pairwise distance matrix revealed zero-node epidemiological links (distance = 0.000000) between canine and livestock variants across distant states, validating aggressive, human-mediated long-distance viral translocation. Tight regional transmission clusters demonstrated cross-species spillovers between free-roaming dogs, diverse livestock, and wild carnivores. Conversely, historical baseline circulation remains preserved in Tamil Nadu and Kerala within the Indian subcontinent lineage. These deep phylogeographic stratifications underscore the necessity for coordinated, sublineage-specific mass canine vaccination frameworks to break cross-border transmission chains.