Complete Nucleotide Sequence Analysis of the Norovirus GII.4 Sydney Variant in South Korea

Park, Jaebeom; Lee, Sung-Geun; Jin, Ji-Young; Cho, Han-Gil; Jheong, Weon-Hwa; Paik, Soon-Young

doi:10.1155/2015/374637

Cited by 8 publications

(5 citation statements)

References 35 publications

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“…GIHE confirmed that the sample was infected with the HuNoV GII.4 genotype, and the specimen was sent to the Waterborne Virus Bank (WAVA, Seoul, Korea) in 2013; confirmation that this specimen was the HuNoV GII.4 Sydney variant was reported in a previous study [23]. The complete nucleotide sequence of the GII.4 Sydney variant was analyzed by Park et al [24]. The HuNoV GII.4 variant in 500 µL of phosphate-buffered saline (PBS; pH 7.2) was purchased from WAVA, with a genomic titer of 6.50 log copy number/µL.…”

Section: Virus Stock Preparationmentioning

confidence: 69%

Virucidal Effects of Dielectric Barrier Discharge Plasma on Human Norovirus Infectivity in Fresh Oysters (Crassostrea gigas)

Choi

Jeon

Kim

et al. 2020

Foods

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This study investigates the effects of dielectric barrier discharge (DBD) plasma treatment (1.1 kV, 43 kHz, N2 1.5 L/min, 10~60 min) on human norovirus (HuNoV) GII.4 infectivity in fresh oysters. HuNoV viability in oysters was assessed by using propidium monoazide (PMA) as a nucleic acid intercalating dye before performing a real-time reverse transcription–quantitative polymerase chain reaction (RT-qPCR). Additionally, the impact of the DBD plasma treatment on pH and Hunter colors was assessed. When DBD plasma was treated for 60 min, the HuNoV genomic titer reduction without PMA pretreatment was negligible (<1 log copy number/µL), whereas when PMA treatment was used, HuNoV titer was reduced to >1 log copy number/µL in just 30 min. D1 and D2-value of HuNoV infectivity were calculated as 36.5 and 73.0 min of the DBD plasma treatment, respectively, using the first-order kinetics model (R2 = 0.98). The pH and Hunter colors were not significantly different (p > 0.05) between the untreated and DBD-plasma-treated oysters. The results suggest that PMA/RT-qPCR could help distinguish HuNoV infectivity without negatively affecting oyster quality following >30 min treatment with DBD plasma. Moreover, the inactivation kinetics of nonthermal DBD plasma against HuNoV in fresh oysters might provide basic information for oyster processing and distribution.

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Section: Virus Stock Preparationmentioning

confidence: 69%

Virucidal Effects of Dielectric Barrier Discharge Plasma on Human Norovirus Infectivity in Fresh Oysters (Crassostrea gigas)

Choi

Jeon

Kim

et al. 2020

Foods

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“…If amplification with primers NV107c(s) [30] and NV156(as) [31] failed, alternative reverse primers NV300II [31], G2SKR [32] and G2R1 [32] were used in GGII strains. For analysis of genetic diversity in GII.2 samples, the partial viral RdRp gene and almost the complete VP1 gene was assessed using GII.2 specific primers [33][34][35][36] (Table S1) in RT-PCR and subsequent nucleic acid sequencing.…”

Section: Rna Extraction Detection Sequencing and Typingmentioning

confidence: 99%

Norovirus Epidemiology and Genetic Diversity in Leipzig, Germany during 2013–2017

Ennuschat

Härtel

Pietsch

et al. 2021

Viruses

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Globally and in all age groups, noroviruses are a main cause of gastroenteritis. To assess their local epidemiology and genetic diversity, stool samples of 7509 inpatients with gastrointestinal complaints from all age groups were analyzed. After detection of norovirus genogroup I and II RNA by real-time RT-PCR, viral capsids were genotyped by partial nucleic acid sequencing. In the case of GII.2 strains, polymerase genotypes were also assessed. Between October 2013 and September 2017, presence of norovirus RNA was shown in 611 samples (8.1%), of which 610 (99.8%) were typed successfully. Norovirus positivity rate was higher in patients aged below five years (14.8%) than in older patients (5.7%). Among the 611 norovirus positive samples, GII.4 (56.6%) strains prevailed, followed by GII.6 (11.3%), GII.3 (11.0%) and GII.2 (9.5%). The most common genogroup I (GGI) genotype was GI.3 (3.6%). In addition, rare genotypes such as GII.13, GII.14 and GII.26 were detected. Interestingly, GII.3 infections were most common in children under the age of five years. Assessment of polymerase genotypes in GII.2 viruses showed a shift from P2 to P16, with higher diversity in P2 sequences. The varying distribution of norovirus genotypes depending on season, age and setting of infection highlights the importance of frequent genotyping as a basis for vaccine development and needful adjustments.

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“…Norovirus is one of the most common causes of acute gastroenteritis in people of all ages worldwide. Most previous studies of norovirus have focused on epidemic strains such as GII.4 and GII.17 [28][29][30][31]. However, other genotypes can also cause outbreaks [32][33][34].…”

Section: Discussionmentioning

confidence: 99%

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

Chen

et al. 2022

BMC Genom Data

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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.

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Complete Nucleotide Sequence Analysis of the Norovirus GII.4 Sydney Variant in South Korea

Cited by 8 publications

References 35 publications

Virucidal Effects of Dielectric Barrier Discharge Plasma on Human Norovirus Infectivity in Fresh Oysters (Crassostrea gigas)

Virucidal Effects of Dielectric Barrier Discharge Plasma on Human Norovirus Infectivity in Fresh Oysters (Crassostrea gigas)

Norovirus Epidemiology and Genetic Diversity in Leipzig, Germany during 2013–2017

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

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