Isolation, Identification and Genetic Characteristics of an Uncommon Norovirus Genotype, GIX.1[GII.P15], From Kunming, China

Human norovirus, an RNA virus of the family Caliciviridae, is a common viral pathogen causing acute gastroenteritis of all age groups worldwide. To date, tens of thousands genome sequences of norovirus have been uploaded to NCBI database, more than half of them were epidemic strains of GII.4 or GII.17 genotype. However, sequence information on the non-epidemic norovirus strains remains poorly studied. In this study, an uncommon norovirus genotype, GIX.1[GII.P15], was isolated using Raji cells and the full-genome sequence of the strain was extensively characterized. The norovirus virus particles with a diameter of approximately 30 nm and a morphology of spherical and lace-like appearance were observed by electron microscopy. Viral genome replication in Raji cells were confirmed by real-time quantitative reverse transcription-PCR from viral replication kinetics and passaging experiments of the primary virus. Phylogenetic analysis showed that the strain (KMN1) belonged to the GIX.1[GII.P15] genotype and indicated that no recombination has occurred in this strain thus far. Further compared analysis of the full genome sequence with the consensus sequence of GIX.1[GII.P15] genomes revealed a total of 81 nucleotide substitutions (53 in ORF1, 20 in ORF2, and 8 in ORF3) across the genome, but only 6 substitutions resulted in amino acid changes (3 in ORF1, 1 in ORF2, and 2 in ORF3). Moreover, one amino acid substitution at the 302 amino acid site (P302S) was observed in the P2 domain of the capsid protein, and the site was around one of the predicted conformational epitopes on the VP1 protein structure. The genomic information obtained from the novel strain may extend the understanding of the non-epidemic GIX.1[GII.P15] strains.