Virology journal · 2026
Complete genome sequencing and molecular characterization of indigenous enterovirus A71 genogroups D and G of India.
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Kumar Abhinendra, Shete Anita, Varose Swapnil Y, Jadhav Santosh, V S Sunitha Kumari, Yadav Savita, Khurana Juhi, Gupta Nivedita, Yadav Pragya D, Cherian Sarah S, Mohanty Madhu C
Аннотация
BACKGROUND: Enterovirus 71 (EV-A71), a neurotropic member of the Picornaviridae family, is a positive-strand RNA virus comprising of seven recognized genogroups (A-G) and has caused significant outbreaks of hand, foot, and mouth disease worldwide. Despite prior identification of D and G genogroups in India, comprehensive full-genome characterization of these indigenous lineages remains unreported.
METHODS: We performed next-generation sequencing (NGS) and molecular phylogenetic analyses on two Indian isolates from acute flaccid paralysis cases: R13223-IND-02 (genogroup D) and V11-2209-01 (genogroup G). The complete genomes generated through NGS were aligned with publicly available full-length and partial EV-A71 sequences using MAFFT, and phylogenetic trees were constructed employing the maximum-likelihood method. Amino acid variations were then compared across the genogroups, as well as with prototype and neurovirulent reference strains.
RESULTS: Phylogenetic reconstruction revealed robust clustering of these strains within distinct clades (bootstrap support ≥ 99%)", divergent from globally prevalent genogroups B and C. 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. An E-Q substitution at amino acid position 145 in the VP1 structural protein was detected in both D and G genogroups, a site functionally linked to receptor binding and mouse virulence.
CONCLUSION: The findings highlight the evolutionary independence and sustained circulation of D and G genogroups in India, suggesting a unique regional evolutionary trajectory. The implications 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. This study is the first to report the complete genome of EV-A71 D and G genotypes in India, and its unique mutation characteristics provide a direct target for the development of region-specific vaccines.
METHODS: We performed next-generation sequencing (NGS) and molecular phylogenetic analyses on two Indian isolates from acute flaccid paralysis cases: R13223-IND-02 (genogroup D) and V11-2209-01 (genogroup G). The complete genomes generated through NGS were aligned with publicly available full-length and partial EV-A71 sequences using MAFFT, and phylogenetic trees were constructed employing the maximum-likelihood method. Amino acid variations were then compared across the genogroups, as well as with prototype and neurovirulent reference strains.
RESULTS: Phylogenetic reconstruction revealed robust clustering of these strains within distinct clades (bootstrap support ≥ 99%)", divergent from globally prevalent genogroups B and C. 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. An E-Q substitution at amino acid position 145 in the VP1 structural protein was detected in both D and G genogroups, a site functionally linked to receptor binding and mouse virulence.
CONCLUSION: The findings highlight the evolutionary independence and sustained circulation of D and G genogroups in India, suggesting a unique regional evolutionary trajectory. The implications 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. This study is the first to report the complete genome of EV-A71 D and G genotypes in India, and its unique mutation characteristics provide a direct target for the development of region-specific vaccines.