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<p>Rabies, a neglected tropical zoonotic disease caused by the rabies virus (RABV), results in fatal encephalitis in both humans and animals. India, a high-burden country, accounts for nearly 30% of global rabies-related deaths. Robust surveillance combined with large-scale genomic sequencing of RABV is essential to monitor viral spread, evolution, and diversity, critical for developing targeted interventions. However, the lack of comprehensive whole genome data on Indian RABV isolates hampers detailed molecular epidemiological analysis. In this study, 630 RABV-positive samples from diverse hosts and regions across India were sequenced using an amplicon-based Illumina workflow. Phylogenetic analysis identified the Arctic-like 1a lineage as predominant, exhibiting high genetic homogeneity. Additionally, Arctic-like 1b and the Indian subcontinent lineages were detected, indicating the presence of co-circulating strains. Geographic clustering observed at the state level suggested localised transmission with limited inter-state viral movement. Mutation and selection pressure analyses revealed conserved amino acid substitutions in the glycoprotein, without alterations in key antigenic sites. These findings underscore the feasibility and significance of large-scale genomic surveillance of RABV in India, pivotal for informing effective rabies control strategies and advancing the global goal of eliminating dog-mediated human rabies deaths by 2030.</p>

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Comprehensive genomic analysis of rabies virus in India reveals distinct lineages and evolutionary stability

  • 期刊论文

  • 发表日期：

    2025年12月19日

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  • Chakrakodi N. Varun,
  • Shubhangi Chandel,
  • Dhanya Keshava Kumar,
  • Nayana Siddalingaiah,
  • Surbhi Telang,
  • Preeti Soundarya Bhalke,
  • Shrikrishna Isloor,
  • Vijaylakshmi Reddy,
  • M. A. Ashwini,
  • Anita Mahadevan,
  • Reeta S. Mani

摘要

Rabies, a neglected tropical zoonotic disease caused by the rabies virus (RABV), results in fatal encephalitis in both humans and animals. India, a high-burden country, accounts for nearly 30% of global rabies-related deaths. Robust surveillance combined with large-scale genomic sequencing of RABV is essential to monitor viral spread, evolution, and diversity, critical for developing targeted interventions. However, the lack of comprehensive whole genome data on Indian RABV isolates hampers detailed molecular epidemiological analysis. In this study, 630 RABV-positive samples from diverse hosts and regions across India were sequenced using an amplicon-based Illumina workflow. Phylogenetic analysis identified the Arctic-like 1a lineage as predominant, exhibiting high genetic homogeneity. Additionally, Arctic-like 1b and the Indian subcontinent lineages were detected, indicating the presence of co-circulating strains. Geographic clustering observed at the state level suggested localised transmission with limited inter-state viral movement. Mutation and selection pressure analyses revealed conserved amino acid substitutions in the glycoprotein, without alterations in key antigenic sites. These findings underscore the feasibility and significance of large-scale genomic surveillance of RABV in India, pivotal for informing effective rabies control strategies and advancing the global goal of eliminating dog-mediated human rabies deaths by 2030.