Identification and genetic characterization of a minor norovirus genotype, GIX.1[GII.P15], from China
© 2022. The Author(s)..
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.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2022 |
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| Erschienen: |
2022 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:23 |
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| Enthalten in: |
BMC genomic data - 23(2022), 1 vom: 06. Juli, Seite 50 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Chen, Yanli [VerfasserIn] |
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| Links: |
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| Themen: |
Amino Acids |
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| Anmerkungen: |
Date Completed 08.07.2022 Date Revised 31.07.2022 published: Electronic Citation Status MEDLINE |
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| doi: |
10.1186/s12863-022-01066-6 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM343151510 |
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| 100 | 1 | |a Chen, Yanli |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Identification and genetic characterization of a minor norovirus genotype, GIX.1[GII.P15], from China |
| 264 | 1 | |c 2022 | |
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| 500 | |a Date Revised 31.07.2022 | ||
| 500 | |a published: Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a © 2022. The Author(s). | ||
| 520 | |a 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 | ||
| 520 | |a 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 | ||
| 520 | |a 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 | ||
| 650 | 4 | |a Case Reports | |
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 4 | |a Full-length genome | |
| 650 | 4 | |a GIX.1[GII.P15] | |
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| 650 | 4 | |a Phylogenetic analysis | |
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| 700 | 1 | |a Wu, Qiongwen |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Guiman |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Hongzhe |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Wenlong |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Heng |e verfasserin |4 aut | |
| 700 | 1 | |a Qin, Li |e verfasserin |4 aut | |
| 700 | 1 | |a Zheng, Huiwen |e verfasserin |4 aut | |
| 700 | 1 | |a Liu, Changkun |e verfasserin |4 aut | |
| 700 | 1 | |a Hou, Min |e verfasserin |4 aut | |
| 700 | 1 | |a Liu, Longding |e verfasserin |4 aut | |
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