Continued circulation, recombination and evolution of the ancient subcontinent lineage despite predominance of the recent arctic-like lineage rabies viruses (RABV) in India

Background Rabies is an emerging and re-emerging lethal encephalitis causing 26,400 to 61,000 human deaths annually. Approximately 20,000 people die of rabies every year in India that accounts to 36% of the world’s rabies deaths. Rabies is endemic among domestic dogs in India and there are conflicting reports on the currently circulating RABV lineages in domestic dogs in India. Further, movement of humans and animals between Sri Lanka and southern coastal states of India was proposed to be a source of the emergence of variant RABV in India. For effective prevention and control of rabies in India it is essential to establish the genetic diversity and evolutionary dynamics of RBAV currently circulating in India. Methods: We carried out molecular evolution and recombination analyses of nucleoprotein (N) and glycoprotein (G) genes of 26 RABV isolates from southern Indian states of Tamil Nadu and Goa. Results: We found continued co-circulation of ancient subcontinent lineage despite predominance of the recent arctic-like lineage RABVs in southern India. The mean rate of nucleotide substitution in G and N genes was 1.32 x 10-3 and 1.91 x 10-4 substitutions/site/yr respectively .The study also found recombination in both N and G genes and a higher mean rate of evolutionary changes in G gene among Indian dog RABV isolates than those of lyssaviruses. The Indian subcontinent lineage RABV isolates investigated in this study clustered closely with other subcontinent lineage viruses from Sri Lanka highlighting the continued incursion and/or circulation of the variant subcontinent lineages of RABVs between India and Sri Lanka. Conclusion We report that there is enzootic viral establishment of two distinct RABV lineages in domestic dogs in India that are evolving at a greater rate.