Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, No. 935 alternating current Road, Wuhua District, Kunming, 650118, Yunna, China.
Key Laboratory of Systemic Innovative Research on Virus Vaccine, Chinese Academy of Medical Sciences, Kunming, China.
BMC Genom Data. 2022 Jul 6;23(1):50. doi: 10.1186/s12863-022-01066-6.
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.
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.
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.
人类诺如病毒是杯状病毒科的单链 RNA 病毒，是全球各年龄段人群非细菌性急性肠胃炎的主要病因。尽管对基因组进行了长达 30 年的测序和诺如病毒的流行病学研究，但对非流行或次要诺如病毒基因型的全长基因组分析很少，而且 ORF2 和 ORF1 3'端以外的基因组区域在很大程度上研究不足，这阻碍了人们对新菌株出现的进化机制的更好理解。在这项研究中，我们使用 Raji 细胞从一名 60 岁患有急性肠胃炎的女性呕吐样本中检测到一种罕见的诺如病毒基因型 GIX.1[GII.P15]，并对其进行了全基因组测序。
使用电子显微镜观察到诺如病毒粒子呈球形和花边状外观，直径约为 30nm。VP1 和 RdRp 区的系统进化分析表明，KMN1 株可被分型为 GIX.1[GII.P15]。此外，KMN1 株的 VP1 区与 GenBank 中可用的 26 个基因组序列相比具有 94.15%±3.54%的核苷酸同一性（PNI），表明 KMN1 与其他 GIX.1[GII.P15]株之间具有更高的相似性。对 KMN1 株全基因组序列的进一步分析表明，与 GIX.1[GII.P15]基因组的共识序列相比，整个基因组共发现 96 个核苷酸替换（ORF1 中有 63 个，ORF2 中有 25 个，ORF3 中有 8 个），其中 6 个替换导致氨基酸变化（ORF1 中有 4 个，ORF2 中有 1 个，ORF3 中有 1 个）。然而，只有一个核苷酸替换导致 VP1 蛋白中的氨基酸变化（P302S），该位点位于二聚体结构上预测的构象 B 表位之一附近。
在中国昆明发现的新型 GIX.1[GII.P15] 株 KMN1 的基因组信息可为病毒遗传进化的研究提供有价值的信息。
