Genomic diversity and comparative phylogenomic analysis of genus Norovirus

Noroviruses consist of ten genogroups, five of which (GI, GII, GIV, GVIII, GIX) infect humans. Noroviruses are traditionally classified based on the VP1 (genotype), RdRP (P-type), or dual-typing nomenclature. However, current classifications solely relying on specific proteins may be insufficient to represent the evolutionary history due to their recombination events. Thus, it is challenging to identify the dual-types in environmental or stool samples co-infected with more than two types using the existing system. We performed a comprehensive genomic analysis using ten assembled genomes with 1417 genomes from NCBI. Our study provides a detailed examination of the genomic characteristics of norovirus and the criteria for current genotypes and P-types. The phylogenomic analysis revealed two key findings: (1) GVIII and GIX are nested within GII and (2) strains of GII.11, GII.18, and GII.19 (swine noroviruses) as well as GIV and GVI form host-based clusters, with GIV.2[GVI.P1] strains in particular suggesting the possibility of another instance of zoonotic transmission. We present a comparison of the phylogenetic findings from gene-based and genome-based analyses. Overall, our study represents an initial step towards the phylogenomic analysis of genus Norovirus. This is valuable for not only interpreting the evolutionary trajectory among norovirus strains but also developing antiviral targeting strategies.