Identification and genetic characterization of a minor norovirus genotype, GIX.1[GII.P15], from China

Abstract

Background Human noroviruses, single-stranded RNA viruses in the family Caliciviridae, are a leading cause of nonbacterial acute gastroenteritis in people of all ages worldwide. Despite three decades of genomic sequencing and epidemiological norovirus studies, full-length genome analyses of the non-epidemic or minor norovirus genotypes are rare and genomic regions other than ORF2 and 3′-end of ORF1 have been largely understudied, which hampers a better understanding of the evolutionary mechanisms of emergence of new strains. In this study, we detected a rare norovirus genotype, GIX.1[GII.P15], in a vomit sample of a 60 year old woman with acute gastroenteritis using Raji cells and sequenced the complete genome. Results Using electron microscopy, a morphology of spherical and lace-like appearance of norovirus virus particles with a diameter of approximately 30 nm were observed. Phylogenetic analysis of VP1 and the RdRp region indicated that the KMN1 strain could be genotyped as GIX.1[GII.P15]. In addition, the VP1 region of KMN1 strain had 94.15% ± 3.54% percent nucleotide identity (PNI) compared to 26 genomic sequences available in GenBank, indicating a higher degree similarity between KMN1 and other GIX.1[GII.P15] strains. Further analysis of the full genome sequence of KMN1 strain showed that a total of 96 nucleotide substitutions (63 in ORF1, 25 in ORF2, and 8 in ORF3) were found across the genome compared with the consensus sequence of GIX.1[GII.P15] genome, and 6 substitutions caused amino acid changes (4 in ORF1, 1 in ORF2, and 1 in ORF3). However, only one nucleotide substitution results in the amino acid change (P302S) in the VP1 protein and the site was located near one of the predicted conformational B epitopes on the dimer structure. Conclusions The genomic information of the new GIX.1[GII.P15] strain KMN1, which was identified in Kunming, China could provide helpful insights for the study of the genetic evolution of the virus.

First report of coinfection and whole‐genome sequencing of norovirus and sapovirus in an acute gastroenteritis patient from Pakistan

“…Historically, only two subclusters had been marked on phylogenetic maps, reflecting a slow evolutionary pattern of GII.15 genotype. This genotype had exhibited a very close resemblance with the GII.6 genotype on its ORF1 gene polymerase 39 . Previously, limited studies are available from Pakistan that explain genetic diversity of NoV primarily based on partial sequencing of capsid gene.…”

“…This genotype had exhibited a very close resemblance with the GII.6 genotype on its ORF1 gene polymerase. 39 Previously, limited studies are available from Pakistan that explain genetic diversity of NoV primarily based on partial sequencing of capsid gene.…”

Improving the Detection and Understanding of Infectious Human Norovirus in Food and Water Matrices: A Review of Methods and Emerging Models

“…Strains belonging to the genogroup GIV have recently been reported to infect humans [146]. Additionally, another rare norovirus genotype, GIX.1, which was reported in 1990 to have caused a large outbreak of acute gastroenteritis [26], is being detected sporadically [147]. However, due to their limited circulation, obtaining a sufficient quantity of these less-common strains for research has proven to be arduous.…”