Complete Genome Sequencing and Molecular Characterization of Indigenous Enterovirus A71 Genogroups D and G of India

Abstract Enterovirus A71 (EV-A71), a neurotropic member of the Picornaviridae family, comprises seven recognized genogroups (A–G). Despite prior identification of D and G genogroups in India, comprehensive full-genome characterization of these indigenous lineages remains unreported. We performed next-generation sequencing (NGS) and molecular phylogenetic analyses on two Indian isolates: R13223-IND-02 (genogroup D) and V11-2209-01 (genogroup G). Phylogenetic reconstruction revealed robust clustering of these strains within distinct clades, divergent from globally prevalent genogroups B and C, considering bootstrap support ≥99%. Both D and G genogroups appear geographically restricted to India, while genogroup D persists as an endemic lineage. Comparative genomic analyses demonstrated extensive nucleotide divergence, including numerous non-synonymous substitutions across both structural (VP1–VP4) and non-structural (2A–3D) coding regions. These findings highlight the evolutionary independence and sustained circulation of D and G genogroups in India, suggesting a unique regional evolutionary trajectory. The findings hold significant global relevance, offering valuable insights for molecular surveillance, advancing pathogenesis research, and supporting the development of genogroup-specific vaccine strategies tailored to diverse epidemiological landscapes.