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Wong OWH, Lam AMW, Or BPN, Mo FYM, Shea CKS, Lai KYC, Ma SL, Hung SF, Chan S, Kwong TNY, Wong S, Leung PWL. Disentangling the relationship of gut microbiota, functional gastrointestinal disorders and autism: a case-control study on prepubertal Chinese boys. Sci Rep 2022; 12:10659. [PMID: 35739175 PMCID: PMC9225987 DOI: 10.1038/s41598-022-14785-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/10/2022] [Indexed: 12/19/2022] Open
Abstract
Emerging evidence of an altered gut microbiome in autism spectrum disorder (ASD) suggests a pathomechanism through the gut-brain axis despite the inconsistent microbiome profile reported across studies. One of the knowledge gaps in the existing ASD microbiota studies is the lack of systematic exploration of the role of comorbid functional gastrointestinal disorder (FGID) in the association of ASD and altered gut microbiome. Consequently, 92 ASD and 112 age-matched typically developing (TD) boys were profiled on general psychopathology, FGID status by Rome IV classification, and gut microbiota using 16S ribosomal RNA amplicon sequencing at the V4 hypervariable region. Compared to TD, a significant decrease in the within-sample abundance of taxa was observed in ASD, regardless of FGID status. The microbiota of ASD FGID+ and ASD FGID- clustered apart from the TD groups. The microbiota of ASD FGID+ also showed qualitative differences from that of ASD FGID- and had the highest-level Firmicutes: Bacteroidetes ratio, which was paralleled by elevated levels of anxiety and overall psychopathology. The altered gastrointestinal microbiota composition in ASD appeared to be independent of comorbid FGID. Further studies should address how FGID may mediate neuropsychiatric symptoms in ASD through inflammation along the microbiota-gut-brain axis.
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Affiliation(s)
- Oscar W H Wong
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong, China.
| | - Angela M W Lam
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong, China
| | - Brian P N Or
- Department of Psychiatry, Tai Po Hospital, Hong Kong, China
| | - Flora Y M Mo
- Department of Psychiatry, Alice Ho Miu Ling Nethersole Hospital, Hong Kong, China
| | - Caroline K S Shea
- Department of Psychiatry, Alice Ho Miu Ling Nethersole Hospital, Hong Kong, China
| | - Kelly Y C Lai
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong, China
| | - Suk Ling Ma
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong, China
| | - Se Fong Hung
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong, China
| | - Sandra Chan
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong, China
| | - Thomas N Y Kwong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Sunny Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Patrick W L Leung
- Department of Psychology, The Chinese University of Hong Kong, Hong Kong, China
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Burska Z, Burghard M, Brożek-Mądry E, Sierdziński J, Krzeski A. Oral cavity morphology among children at risk of sleep disordered breathing. Eur Arch Paediatr Dent 2022; 23:429-435. [PMID: 35366217 DOI: 10.1007/s40368-022-00701-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/02/2022] [Indexed: 11/30/2022]
Abstract
PURPOSE The aim of this study was to evaluate oral cavity morphology in children at risk of sleep disordered breathing (SDB). METHODS The study included children 3-17 years of age. The risk of SDB was evaluated using the paediatric sleep questionnaire (PSQ); afterwards, children at risk of SDB were enrolled in the study group. A control group was randomly established from patients with negative PSQ results. The oral cavity morphology evaluation included assessment of the oropharynx using Mallampati classification (MC), palatine tonsil size using the Pirquet scale, occlusion and the presence of a high-arched palate and lingual frenulum. RESULTS A total of 131 children were evaluated, 65 in the study and 66 in the control group. The mean ages were 9.5 ± 3.0 and 9.4 ± 3.1 years, respectively. The presence of higher scores on the MC, higher scores in the Pirquet scale, a crossbite, a high-arched palate and a short frenulum were significantly more frequent in the study group than the control group. CONCLUSION The evaluation of oral morphology is an important part of paediatric examination. Enlarged palatine tonsils; higher scores on the MC; and the presence of a crossbite, short lingual frenulum and high-arched palate may suggest abnormal breathing during sleep in children.
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Affiliation(s)
- Z Burska
- Department of Otorhinolaryngology, Medical University of Warsaw, Stępińska 19/25, 00-739, Warsaw, Poland
| | - M Burghard
- Medical Center in Ostrołęka, Ostroleka, Poland
| | - E Brożek-Mądry
- Department of Otorhinolaryngology, Medical University of Warsaw, Stępińska 19/25, 00-739, Warsaw, Poland.
| | - J Sierdziński
- Department of Medical Informatics and Telemedicine, Medical University of Warsaw, Warsaw, Poland
| | - A Krzeski
- Department of Otorhinolaryngology, Medical University of Warsaw, Stępińska 19/25, 00-739, Warsaw, Poland
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Norovirus Epidemiology and Genetic Diversity in Leipzig, Germany during 2013-2017. Viruses 2021; 13:v13101961. [PMID: 34696390 PMCID: PMC8541062 DOI: 10.3390/v13101961] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 11/17/2022] Open
Abstract
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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Jeon EB, Choi MS, Kim JY, Choi EH, Lim JS, Choi J, Ha KS, Kwon JY, Jeong SH, Park SY. Assessment of potential infectivity of human norovirus in the traditional Korean salted clam product "Jogaejeotgal" by floating electrode-dielectric barrier discharge plasma. Food Res Int 2021; 141:110107. [PMID: 33641974 DOI: 10.1016/j.foodres.2021.110107] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/28/2020] [Accepted: 01/02/2021] [Indexed: 11/25/2022]
Abstract
This study investigated the antiviral effects of floating electrode-dielectric barrier discharge (FE-DBD) plasma treatment (1.1 kV, 43 kHz, N2 1.5 m/s, 5-30 min) against human norovirus (HuNoV) GII.4 in Jogaejeotgal Infectivity was assessed using real-time quantitative-PCR (RT-qPCR) following treatment of samples with propidium monoazide (PMA) and sodium lauroyl sarcosinate (Sarkosyl). This study also investigated the effects of FE-DBD plasma treatment on Jogaejeotgal quality (assessed using pH value and Hunter colors). Following inoculation, the average titers of HuNoV GII.4 in Jogaejeotgal significantly (P < 0.05) decreased with increases in the FE-DBD plasma treatment time in both the non-PMA-treated and PMA + Sarkosyl-treated samples; in the non-PMA and PMA + Sarkosyl treated Jogaejeotgal, HuNoV GII.4 titers (log10 copy number/µL) were to: 3.16 and 2.95 (5 min), 2.90 and 2.48 (10 min), 2.82 and 2.40 (15 min), 2.58 and 2.26 (20 min), 2.48 and 2.06 (25 min), and 2.23 and 1.91 (30 min), respectively. The average titers of HuNoV demonstrated significant (P < 0.05) reductions of 0.35 log10 (55.3%) in PMA + Sarkosyl-treated samples compared with the non-PMA treated samples following exposure to 5-30 min of FE-DBD plasma. Reductions of >1-log for HuNoV in PMA + Sarkosyl- treated Jogaejeotgal required treatments of FE-DBD of 5-30 min. Using the first order kinetic model (R2 = 0.95), GII.4 decimal reduction time (D-value) resulting from FE-DBD plasma was 23.75 min. The pH and Hunter colors ("L", "a", and "b") were not significantly different (P > 0.05) between the untreated and FE-DBD plasma-treated Jogaejeotgal. Based on these results, the PMA + Sarkosyl/RT-qPCR method could be assessing HuNoV viability following 5-30 min treatment of FE-DBD plasma. Furthermore, may be an optimal treatment for Jogaejeotgal without altering the food quality (color and pH).
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Affiliation(s)
- Eun Bi Jeon
- Department of Seafood and Aquaculture Science/Institute of Marine Industry, Gyeongsang National University, Tongyeong 53064, Republic of Korea
| | - Man-Seok Choi
- Department of Seafood and Aquaculture Science/Institute of Marine Industry, Gyeongsang National University, Tongyeong 53064, Republic of Korea
| | - Ji Yoon Kim
- Department of Seafood and Aquaculture Science/Institute of Marine Industry, Gyeongsang National University, Tongyeong 53064, Republic of Korea
| | - Eun Ha Choi
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul 01987, Republic of Korea
| | - Jun Sup Lim
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul 01987, Republic of Korea
| | - Jinsung Choi
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul 01987, Republic of Korea
| | - Kwang Soo Ha
- Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science, Tongyeong 53085, Republic of Korea
| | - Ji Young Kwon
- Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science, Tongyeong 53085, Republic of Korea
| | - Sang Hyeon Jeong
- Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science, Tongyeong 53085, Republic of Korea
| | - Shin Young Park
- Department of Seafood and Aquaculture Science/Institute of Marine Industry, Gyeongsang National University, Tongyeong 53064, Republic of Korea.
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Choi MS, Jeon EB, Kim JY, Choi EH, Lim JS, Choi J, Ha KS, Kwon JY, Jeong SH, Park SY. Virucidal Effects of Dielectric Barrier Discharge Plasma on Human Norovirus Infectivity in Fresh Oysters ( Crassostrea gigas). Foods 2020; 9:E1731. [PMID: 33255577 PMCID: PMC7760321 DOI: 10.3390/foods9121731] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/04/2020] [Accepted: 11/23/2020] [Indexed: 12/22/2022] Open
Abstract
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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Affiliation(s)
- Man-Seok Choi
- Institute of Marine Industry, Gyeongsang National University, Tongyeong 53064, Korea; (M.-S.C.); (E.B.J.); (J.Y.K.)
- Department of Seafood and Aquaculture Science, Gyeongsang National University, Tongyeong 53064, Korea
| | - Eun Bi Jeon
- Institute of Marine Industry, Gyeongsang National University, Tongyeong 53064, Korea; (M.-S.C.); (E.B.J.); (J.Y.K.)
- Department of Seafood and Aquaculture Science, Gyeongsang National University, Tongyeong 53064, Korea
| | - Ji Yoon Kim
- Institute of Marine Industry, Gyeongsang National University, Tongyeong 53064, Korea; (M.-S.C.); (E.B.J.); (J.Y.K.)
- Department of Seafood and Aquaculture Science, Gyeongsang National University, Tongyeong 53064, Korea
| | - Eun Ha Choi
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul 01987, Korea; (E.H.C.); (J.S.L.); (J.C.)
| | - Jun Sup Lim
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul 01987, Korea; (E.H.C.); (J.S.L.); (J.C.)
| | - Jinsung Choi
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul 01987, Korea; (E.H.C.); (J.S.L.); (J.C.)
| | - Kwang Soo Ha
- Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science, Tongyeong 53085, Korea; (K.S.H.); (J.Y.K.); (S.H.J.)
| | - Ji Young Kwon
- Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science, Tongyeong 53085, Korea; (K.S.H.); (J.Y.K.); (S.H.J.)
| | - Sang Hyeon Jeong
- Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science, Tongyeong 53085, Korea; (K.S.H.); (J.Y.K.); (S.H.J.)
| | - Shin Young Park
- Institute of Marine Industry, Gyeongsang National University, Tongyeong 53064, Korea; (M.-S.C.); (E.B.J.); (J.Y.K.)
- Department of Seafood and Aquaculture Science, Gyeongsang National University, Tongyeong 53064, Korea
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Huang Z, Yao D, Xiao S, Yang D, Ou X. Full-genome sequences of GII.13[P21] recombinant norovirus strains from an outbreak in Changsha, China. Arch Virol 2020; 165:1647-1652. [PMID: 32356188 PMCID: PMC7223583 DOI: 10.1007/s00705-020-04643-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 04/01/2020] [Indexed: 12/27/2022]
Abstract
On 31 March 2019, 68 school students suffered from vomiting, diarrhea, and abdominal pain after participating in a group activity at a commercial park. In this outbreak, multiple norovirus genotypes were observed, including GII.2[P16], GII.17[P17], and GII.13[P21]. Further, we determined the full-genome sequences of two strains of GII.13[P21] recombinant noroviruses, which were 7434 nt long. Phylogenetic analysis based on open reading frames (ORFs) 1 and 2 revealed that these recombinants were related to stains of different genotypes from different countries. The full genome nucleotide sequences of the two isolates were 97.0% and 98.0% identical to those of strains from London and Thailand, respectively. Simplot analysis revealed the presence of a break point at nt 5059 in the ORF1 region. The histo-blood group antigen binding sites were conserved in both recombinant viruses. Our findings not only provide valuable genetic information about a recombinant norovirus but also contribute to our general understanding of the evolution, genetic diversity, and distribution of noroviruses.
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Affiliation(s)
- Zheng Huang
- Changsha Center for Disease Control and Prevention, Beside the Liuyang River Bridge, No. 509, Wanjiali Second North Road, Changsha, Hunan People’s Republic of China
| | - Dong Yao
- Changsha Center for Disease Control and Prevention, Beside the Liuyang River Bridge, No. 509, Wanjiali Second North Road, Changsha, Hunan People’s Republic of China
| | - Shan Xiao
- Changsha Center for Disease Control and Prevention, Beside the Liuyang River Bridge, No. 509, Wanjiali Second North Road, Changsha, Hunan People’s Republic of China
| | - Dong Yang
- Changsha Center for Disease Control and Prevention, Beside the Liuyang River Bridge, No. 509, Wanjiali Second North Road, Changsha, Hunan People’s Republic of China
| | - Xinhua Ou
- Changsha Center for Disease Control and Prevention, Beside the Liuyang River Bridge, No. 509, Wanjiali Second North Road, Changsha, Hunan People’s Republic of China
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Jeon EB, Choi MS, Kim JY, Ha KS, Kwon JY, Jeong SH, Lee HJ, Jung YJ, Ha JH, Park SY. Characterizing the effects of thermal treatment on human norovirus GII.4 viability using propidium monoazide combined with RT-qPCR and quality assessments in mussels. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.106954] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Coding-Complete Genome Sequence of a Recombinant Human Norovirus Strain Identified as Subtype GII.p12_GII.3. Microbiol Resour Announc 2020; 9:9/5/e01385-19. [PMID: 32001565 PMCID: PMC6992869 DOI: 10.1128/mra.01385-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A human norovirus (HuNoV) strain was obtained from a patient with acute gastroenteritis, and its complete coding sequence was determined. The coding-complete viral genome, with three open reading frames, was 7,565 bp long, with a GC content of 49.9%. The genotype of the HuNoV strain obtained in this study was identified as GII.p12_GII.3. A human norovirus (HuNoV) strain was obtained from a patient with acute gastroenteritis, and its complete coding sequence was determined. The coding-complete viral genome, with three open reading frames, was 7,565 bp long, with a GC content of 49.9%. The genotype of the HuNoV strain obtained in this study was identified as GII.p12_GII.3.
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Ludwig-Begall LF, Mauroy A, Thiry E. Norovirus recombinants: recurrent in the field, recalcitrant in the lab - a scoping review of recombination and recombinant types of noroviruses. J Gen Virol 2018; 99:970-988. [PMID: 29906257 DOI: 10.1099/jgv.0.001103] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Noroviruses are recognized as the major global cause of sporadic and epidemic non-bacterial gastroenteritis in humans. Molecular mechanisms driving norovirus evolution are the accumulation of point mutations and recombination. Intragenotypic recombination has long been postulated to be a driving force of GII.4 noroviruses, the predominant genotype circulating in humans for over two decades. Increasingly, emergence and re-emergence of different intragenotype recombinants have been reported. The number and types of norovirus recombinants remained undefined until the 2007 Journal of General Virology research article 'Norovirus recombination' reported an assembly of 20 hitherto unclassified intergenotypic norovirus recombinant types. In the intervening decade, a host of novel recombinants has been analysed. New recombination breakpoints have been described, in vitro and in vivo studies supplement in silico analyses, and advances have been made in analysing factors driving norovirus recombination. This work presents a timely overview of these data and focuses on important aspects of norovirus recombination and its role in norovirus molecular evolution. An overview of intergenogroup, intergenotype, intragenotype and 'obligatory' norovirus recombinants as detected via in silico methods in the field is provided, enlarging the scope of intergenotypic recombinant types to 80 in total, and notably including three intergenogroup recombinants. A recap of advances made studying norovirus recombination in the laboratory is given. Putative drivers and constraints of norovirus recombination are discussed and the potential link between recombination and norovirus zoonosis risk is examined.
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Affiliation(s)
- Louisa F Ludwig-Begall
- 1Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, B43b, Quartier Vallée 2, Avenue de Cureghem, 10, B-4000 Liège, Belgium
| | - Axel Mauroy
- 2Staff direction for risk assessment, Control Policy, Federal Agency for the Safety of the Food Chain, Blv du Jardin Botanique 55, 1000 Brussels, Belgium
| | - Etienne Thiry
- 1Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, B43b, Quartier Vallée 2, Avenue de Cureghem, 10, B-4000 Liège, Belgium
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Forbes JD, Knox NC, Ronholm J, Pagotto F, Reimer A. Metagenomics: The Next Culture-Independent Game Changer. Front Microbiol 2017; 8:1069. [PMID: 28725217 PMCID: PMC5495826 DOI: 10.3389/fmicb.2017.01069] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/29/2017] [Indexed: 02/01/2023] Open
Abstract
A trend towards the abandonment of obtaining pure culture isolates in frontline laboratories is at a crossroads with the ability of public health agencies to perform their basic mandate of foodborne disease surveillance and response. The implementation of culture-independent diagnostic tests (CIDTs) including nucleic acid and antigen-based assays for acute gastroenteritis is leaving public health agencies without laboratory evidence to link clinical cases to each other and to food or environmental substances. This limits the efficacy of public health epidemiology and surveillance as well as outbreak detection and investigation. Foodborne outbreaks have the potential to remain undetected or have insufficient evidence to support source attribution and may inadvertently increase the incidence of foodborne diseases. Next-generation sequencing of pure culture isolates in clinical microbiology laboratories has the potential to revolutionize the fields of food safety and public health. Metagenomics and other 'omics' disciplines could provide the solution to a cultureless future in clinical microbiology, food safety and public health. Data mining of information obtained from metagenomics assays can be particularly useful for the identification of clinical causative agents or foodborne contamination, detection of AMR and/or virulence factors, in addition to providing high-resolution subtyping data. Thus, metagenomics assays may provide a universal test for clinical diagnostics, foodborne pathogen detection, subtyping and investigation. This information has the potential to reform the field of enteric disease diagnostics and surveillance and also infectious diseases as a whole. The aim of this review will be to present the current state of CIDTs in diagnostic and public health laboratories as they relate to foodborne illness and food safety. Moreover, we will also discuss the diagnostic and subtyping utility and concomitant bias limitations of metagenomics and comparable detection techniques in clinical microbiology, food and public health laboratories. Early advances in the discipline of metagenomics, however, have indicated noteworthy challenges. Through forthcoming improvements in sequencing technology and analytical pipelines among others, we anticipate that within the next decade, detection and characterization of pathogens via metagenomics-based workflows will be implemented in routine usage in diagnostic and public health laboratories.
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Affiliation(s)
- Jessica D. Forbes
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, WinnipegMB, Canada
| | - Natalie C. Knox
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada
| | - Jennifer Ronholm
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, MontrealQC, Canada
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, MontrealQC, Canada
| | - Franco Pagotto
- Bureau of Microbial Hazards, Food Directorate, Health Canada, OttawaON, Canada
- Listeriosis Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada, OttawaON, Canada
| | - Aleisha Reimer
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada
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Full-genome sequence analysis of an uncommon norovirus genotype, GII.21, from South Korea. Epidemiol Infect 2017; 145:2231-2240. [PMID: 28651680 DOI: 10.1017/s0950268817001273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Noroviruses (NoVs) are major causal agents of acute gastroenteritis in humans. NoV GII.4 is the predominant genotype globally. However, uncommon and minor types of NoVs are consistently detected and some have been shown to dominate over GII.4. Therefore, the prevalence of dominant and uncommon NoVs makes the identification of these viruses important for the prediction and prevention of pandemics. In this study, the full-genome sequence of a NoV (strain JW) detected in Korea was extensively characterized. The full-length genome was 7510 nucleotides long, and phylogenetic analysis based on the whole-genome sequences, including open reading frame (ORF)1, ORF2, and ORF3, indicated that it belonged to the GII.21 genotype. Strain JW showed maximum identity with strain YO284; however, comparison of the amino acid sequence of ORF2, which functions as an antigen, showed substitutions in several amino acids. GII.21 is not a prevalent epidemiological agent of acute gastroenteritis in humans, but it is consistently found in gastroenteritis patients from several countries. The present study provides the first full-genome sequence analysis of NoV GII.21 isolated from a patient in Korea. Our findings provide not only valuable genome information but also data for epidemiology studies, epidemic prevention, and vaccine development strategies.
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Koo ES, Kim MS, Choi YS, Park KS, Jeong YS. Occurrence of novel GII.17 and GII.21 norovirus variants in the coastal environment of South Korea in 2015. PLoS One 2017; 12:e0172237. [PMID: 28199388 PMCID: PMC5310787 DOI: 10.1371/journal.pone.0172237] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 02/01/2017] [Indexed: 11/18/2022] Open
Abstract
Human norovirus (HNoV), a positive-sense RNA virus, is the main causative agent of acute viral gastroenteritis. Multiple pandemic variants of the genogroup II genotype 4 (GII.4) of NoV have attracted great attention from researchers worldwide. However, novel variants of GII.17 have been overtaking those pandemic variants in some areas of East Asia. To investigate the environmental occurrence of GII in South Korea, we collected water samples from coastal streams and a neighboring waste water treatment plant in North Jeolla province (in March, July, and December of 2015). Based on capsid gene region C analysis, four different genotypes (GII.4, GII.13, GII.17, and GII.21) were detected, with much higher prevalence of GII.17 than of GII.4. Additional sequence analyses of the ORF1-ORF2 junction and ORF2 from the water samples revealed that the GII.17 sequences in this study were closely related to the novel strains of GII.P17-GII.17, the main causative variants of the 2014-2015 HNoV outbreak in China and Japan. In addition, the GII.P21-GII.21 variants were identified in this study and they had new amino acid sequence variations in the blockade epitopes of the P2 domain. From these results, we present two important findings: 1) the novel GII.P17-GII.17 variants appeared to be predominant in the study area, and 2) new GII.21 variants have emerged in South Korea.
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Affiliation(s)
- Eung Seo Koo
- Department of Biology, College of Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Man Su Kim
- Department of Biology, College of Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Yong Seon Choi
- Department of Biology, College of Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Kwon-Sam Park
- Department of Food Science and Biotechnology, Kunsan National University, Gunsan, Republic of Korea
| | - Yong Seok Jeong
- Department of Biology, College of Sciences, Kyung Hee University, Seoul, Republic of Korea
- * E-mail:
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Molecular Epidemiology and Genetic Diversity of Norovirus in Young Children in Phnom Penh, Cambodia. J Trop Med 2016; 2016:2707121. [PMID: 28115947 PMCID: PMC5223043 DOI: 10.1155/2016/2707121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/17/2016] [Indexed: 12/27/2022] Open
Abstract
This study investigated the genetic diversity of noroviruses identified from a previous surveillance study conducted at the National Pediatric Hospital in Phnom Penh, Cambodia, from 2004 to 2006. In the previous study, 926 stool samples were collected from children aged 3–60 months with acute diarrhea (cases) and without diarrhea (controls) with reported 6.7% of cases and 3.2% of controls being positive for norovirus. The initial norovirus diagnostic assay was performed with real-time reverse transcription-polymerase chain reaction (real-time RT PCR) which also distinguished between genogroups I and II (GI and GII). Norovirus infection was most commonly detected in children aged 12–23 months in both cases and controls. Norovirus Genotyping Tool and phylogenetic analysis of partial sequences of the 3′ end of the RNA-dependent RNA Polymerase (RdRp) and the capsid domain region were employed to assign genotypes of the norovirus strains. GII.4 was the most predominant capsid genotype detected at 39.5% followed by GII.6 at 14.9%. The GII.4 Hunter 2004 variant was the predominant strain detected. Six RdRP/capsid recombinants including GII.P7/GII.6, GII.P7/GII.14, GII.P7/GII.20, GII.P12/GII.13, GII.P17/GII.16, and GII.P21/GII.3 were also identified. This study of norovirus infection in young children in Cambodia suggests genetic diversity of norovirus as reported worldwide.
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Brown JR, Roy S, Ruis C, Yara Romero E, Shah D, Williams R, Breuer J. Norovirus Whole-Genome Sequencing by SureSelect Target Enrichment: a Robust and Sensitive Method. J Clin Microbiol 2016; 54:2530-7. [PMID: 27487952 PMCID: PMC5035417 DOI: 10.1128/jcm.01052-16] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/21/2016] [Indexed: 01/11/2023] Open
Abstract
Norovirus full-genome sequencing is challenging due to sequence heterogeneity among genomes. Previous methods have relied on PCR amplification, which is problematic due to primer design, and transcriptome sequencing (RNA-Seq), which nonspecifically sequences all RNA, including host and bacterial RNA, in stool specimens. Target enrichment uses a panel of custom-designed 120-mer RNA baits that are complementary to all publicly available norovirus sequences, with multiple baits targeting each position of the genome, which overcomes the challenge of primer design. Norovirus genomes are enriched from stool RNA extracts to minimize the sequencing of nontarget RNA. SureSelect target enrichment and Illumina sequencing were used to sequence full genomes from 507 norovirus-positive stool samples with reverse transcription-real-time PCR cycle threshold (CT) values of 10 to 43. Sequencing on an Illumina MiSeq system in batches of 48 generated, on average, 81% on-target reads per sample and 100% genome coverage with >12,000-fold read depth. Samples included genotypes GI.1, GI.2, GI.3, GI.6, GI.7, GII.1, GII.2, GII.3, GII.4, GII.5, GII.6, GII.7, GII.13, GII.14, and GII.17. When outliers were accounted for, we generated >80% genome coverage for all positive samples, regardless of CT values. A total of 164 samples were tested in parallel with conventional PCR genotyping of the capsid shell domain; 164/164 samples were successfully sequenced, compared to 158/164 samples that were amplified by PCR. Four of the samples that failed capsid PCR analysis had low titers, which suggests that target enrichment is more sensitive than gel-based PCR. Two samples failed PCR due to primer mismatches; target enrichment uses multiple baits targeting each position, thus accommodating sequence heterogeneity among norovirus genomes.
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Affiliation(s)
- Julianne R Brown
- Microbiology, Virology, and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom NIHR Biomedical Research Centre at Great Ormond Street Hospital for Children NHS Foundation Trust and University College London, London, United Kingdom
| | - Sunando Roy
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Christopher Ruis
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Erika Yara Romero
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Divya Shah
- Microbiology, Virology, and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom NIHR Biomedical Research Centre at Great Ormond Street Hospital for Children NHS Foundation Trust and University College London, London, United Kingdom
| | - Rachel Williams
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Judy Breuer
- Microbiology, Virology, and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom Division of Infection and Immunity, University College London, London, United Kingdom
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Kim MS, Koo ES, Choi YS, Kim JY, Yoo CH, Yoon HJ, Kim TO, Choi HB, Kim JH, Choi JD, Park KS, Shin Y, Kim YM, Ko G, Jeong YS. Distribution of Human Norovirus in the Coastal Waters of South Korea. PLoS One 2016; 11:e0163800. [PMID: 27681683 PMCID: PMC5040428 DOI: 10.1371/journal.pone.0163800] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 09/14/2016] [Indexed: 02/02/2023] Open
Abstract
The presence of human norovirus in the aquatic environment can cause outbreaks related to recreational activities and the consumption of norovirus-contaminated clams. In this study, we investigated the prevalence of norovirus genogroups I (GI) and II (GII) in the coastal aquatic environment in South Korea (March 2014 to February 2015). A total of 504 water samples were collected periodically from four coastal areas (total sites = 63), of which 44 sites were in estuaries (clam fisheries) and 19 were in inflow streams. RT-PCR analysis targeting ORF2 region C revealed that 20.6% of the water samples were contaminated by GI (13.3%) or GII (16.6%). The prevalence of human norovirus was higher in winter/spring than in summer/fall, and higher in inflow streams (50.0%) than in estuaries (7.9%). A total of 229 human norovirus sequences were identified from the water samples, and phylogenetic analysis showed that the sequences clustered into eight GI genotypes (GI.1, 2, 3, 4, 5, 6, 7, and 9) and nine GII genotypes (GII.2, 3, 4, 5, 6, 11, 13, 17, and 21). This study highlighted three issues: 1) a strong correlation between norovirus contamination via inflow streams and coastal areas used in clam fisheries; 2) increased prevalence of certain non-GII.4 genotypes, exceeding that of the GII.4 pandemic variants; 3) seasonal shifts in the dominant genotypes of both GI and GII.
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Affiliation(s)
- Man Su Kim
- Department of Biology and Research Institute of Basic Sciences, Kyung Hee University, Seoul, South Korea
| | - Eung Seo Koo
- Department of Biology and Research Institute of Basic Sciences, Kyung Hee University, Seoul, South Korea
| | - Yong Seon Choi
- Department of Biology and Research Institute of Basic Sciences, Kyung Hee University, Seoul, South Korea
| | - Ji Young Kim
- Department of Biology and Research Institute of Basic Sciences, Kyung Hee University, Seoul, South Korea
| | - Chang Hoon Yoo
- Department of Biology and Research Institute of Basic Sciences, Kyung Hee University, Seoul, South Korea
| | - Hyun Jin Yoon
- Department of Seafood Science and Technology, Institute of Marine Industry, Gyeongsang National University, Tongyeong, Gyeongnam, South Korea
| | - Tae-Ok Kim
- Department of Food Science and Biotechnology, College of Ocean Science and Technology, Kunsan National University, Kunsan, South Korea
| | - Hyun Bae Choi
- Department of Environmental Engineering & Biotechnology, Mokpo National Maritime University, Mokpo, South Korea
| | - Ji Hoon Kim
- Department of Food Science and Technology, Pukyong National University, Busan, South Korea
| | - Jong Deok Choi
- Department of Seafood Science and Technology, Institute of Marine Industry, Gyeongsang National University, Tongyeong, Gyeongnam, South Korea
| | - Kwon-Sam Park
- Department of Food Science and Biotechnology, College of Ocean Science and Technology, Kunsan National University, Kunsan, South Korea
| | - Yongsik Shin
- Department of Environmental Engineering & Biotechnology, Mokpo National Maritime University, Mokpo, South Korea
| | - Young-Mog Kim
- Department of Food Science and Technology, Pukyong National University, Busan, South Korea
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, South Korea
| | - Yong Seok Jeong
- Department of Biology and Research Institute of Basic Sciences, Kyung Hee University, Seoul, South Korea
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Xue L, Cai W, Wu Q, Zhang J, Guo W. Direct sequencing and analysis of the genomes of newly emerging GII.17 norovirus strains in South China. J Appl Microbiol 2016; 120:1130-5. [PMID: 26756909 DOI: 10.1111/jam.13052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 01/07/2016] [Accepted: 01/08/2016] [Indexed: 01/03/2023]
Abstract
AIMS This study aims to develop a quick and sensitive method for obtaining GII.17 norovirus genome sequences based on a novel amplification strategy. METHODS AND RESULTS Based on multiple alignments of GII.17 norovirus genome sequences available in GenBank, a set of primer pairs were first rationally designed, which could amplify six overlapping fragments encompassing the whole genome. Two sequencing primers II.17-Seq1R and II.17-Seq6F were also designed to complement sequences at both ends. The sensitivity of new primers was then evaluated by end-point dilution RT-PCR that was comparable to detection primers G2SKF/G2SKR. In practice, genome sequences of nine Guangzhou GII.17 strains were successfully obtained by the new method in one working day. All genomes comprised 7495 nucleotides with three complete ORFs, and their phylogenetic relationships were verified with other GII norovirus reference strains. CONCLUSIONS Based on the new amplification strategy, a quick and sensitive method for direct sequencing of GII.17 norovirus genomes was successfully established. SIGNIFICANCE AND IMPACT OF THE STUDY The newly developed method can be used as an important tool to collect genetic information of GII.17 noroviruses, and new obtained viral genomes in Guangzhou also provide reference data for norovirus research in future.
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Affiliation(s)
- L Xue
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China.,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - W Cai
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China.,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Q Wu
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China.,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - J Zhang
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China.,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - W Guo
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
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Xue L, Dong R, Wu Q, Li Y, Cai W, Kou X, Zhang J, Guo W. Molecular epidemiology of noroviruses associated with sporadic gastroenteritis in Guangzhou, China, 2013-2015. Arch Virol 2016; 161:1377-84. [PMID: 26906693 DOI: 10.1007/s00705-016-2784-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 01/31/2016] [Indexed: 11/24/2022]
Abstract
Norovirus diarrhea is a great threat to public health worldwide. To characterize the prevalence of circulating noroviruses associated with sporadic gastroenteritis cases in Guangzhou, 215 stool specimens were collected during two consecutive cold seasons in 2013-2015. Noroviruses were detected in 25 (11.63 %) samples, and GII.4 (6/9) and GII.17 (10/16) were identified as the most predominant variants of each of those seasons. The remaining strains belonged to the genotypes GII.P12/GII.3, GII.2, and GI.Pb/GI.6. The phylogenetic relationships of the GII.17 strains were analyzed based on their capsid protein sequences. This study suggests a significant shift of predominant variants associated with sporadic gastroenteritis in Guangzhou.
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Affiliation(s)
- Liang Xue
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, No. 100, Xianlie Zhong Road, Guangzhou, 510070, People's Republic of China.,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, 510070, People's Republic of China
| | - Ruimin Dong
- Department of Cardiology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, People's Republic of China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, No. 100, Xianlie Zhong Road, Guangzhou, 510070, People's Republic of China. .,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, 510070, People's Republic of China.
| | - Yonglai Li
- Laboratory Department, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, People's Republic of China
| | - Weicheng Cai
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, No. 100, Xianlie Zhong Road, Guangzhou, 510070, People's Republic of China.,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, 510070, People's Republic of China
| | - Xiaoxia Kou
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, No. 100, Xianlie Zhong Road, Guangzhou, 510070, People's Republic of China.,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, 510070, People's Republic of China
| | - Jumei Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, No. 100, Xianlie Zhong Road, Guangzhou, 510070, People's Republic of China.,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, 510070, People's Republic of China
| | - Weipeng Guo
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, No. 100, Xianlie Zhong Road, Guangzhou, 510070, People's Republic of China.,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, 510070, People's Republic of China
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Abstract
Norovirus is a major cause of viral gastroenteritis and a common cause of foodborne and waterborne outbreaks. Norovirus outbreaks are responsible for economic losses, most notably to the public health and food industry field. Norovirus has characteristics such as low infectious dose, prolonged shedding period, strong stability, great diversity, and frequent genome mutations. Besides these characteristics, they are known for rapid and extensive spread in closed settings such as hospitals, hotels, and schools. Norovirus is well known as a major agent of food-poisoning in diverse settings in South Korea. For these reasons, nationwide surveillance for norovirus is active in both clinical and environmental settings in South Korea. Recent studies have reported the emergence of variants and novel recombinants of norovirus. In this review, we summarized studies on the molecular epidemiology and nationwide surveillance of norovirus in South Korea. This review will provide information for vaccine development and prediction of new emerging variants of norovirus in South Korea.
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Affiliation(s)
- Sung-Geun Lee
- Korea Zoonosis Research Institute, Chonbuk National University, Iksan 570-390, Korea
| | - Han-Gil Cho
- Division of Public Health Research, Gyeonggi Province Institute of Health and Environment, Suwon 440-290, Korea
| | - Soon-Young Paik
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 137-701, Korea
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Complete nucleotide sequence analysis of the norovirus GII.4 Sydney variant in South Korea. BIOMED RESEARCH INTERNATIONAL 2015; 2015:374637. [PMID: 25688356 PMCID: PMC4320898 DOI: 10.1155/2015/374637] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 11/21/2014] [Accepted: 11/24/2014] [Indexed: 01/24/2023]
Abstract
Norovirus is the primary cause of acute gastroenteritis in individuals of all ages. In Australia, a new strain of norovirus (GII.4) was identified in March 2012, and this strain has spread rapidly around the world. In August 2012, this new GII.4 strain was identified in patients in South Korea. Therefore, to examine the characteristics of the epidemic norovirus GII.4 2012 variant in South Korea, we conducted KM272334 full-length genomic analysis. The genome of the gg-12-08-04 strain consisted of 7,558 bp and contained three open reading frame (ORF) composites throughout the whole genome: ORF1 (5,100 bp), ORF2 (1,623 bp), and ORF3 (807 bp). Phylogenetic analyses showed that gg-12-08-04 belonged to the GII.4 Sydney 2012 variant, sharing 98.92% nucleotide similarity with this variant strain. According to SimPlot analysis, the gg-12-08-04 strain was a recombinant strain with breakpoint at the ORF1/2 junction between Osaka 2007 and Apeldoorn 2008 strains. This study is the first report of the complete sequence of the GII.4 Sydney 2012 strain in South Korea. Therefore, this may represent the standard sequence of the norovirus GII.4 2012 variant in South Korea and could therefore be useful for the development of norovirus vaccines.
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Truong TC, Than VT, Kim W. Evolutionary phylodynamics of Korean noroviruses reveals a novel GII.2/GII.10 recombination event. PLoS One 2014; 9:e113966. [PMID: 25500567 PMCID: PMC4264735 DOI: 10.1371/journal.pone.0113966] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 10/27/2014] [Indexed: 11/20/2022] Open
Abstract
Viral gastroenteritis is the most common causal agent of public health problems worldwide. Noroviruses cause nonbacterial acute gastroenteritis in humans of all ages. In this study, we investigated the occurrence of norovirus infection in children with acute gastroenteritis admitted to university hospitals in South Korea. We also analyzed the genetic diversity of the viruses and identified novel recombination events among the identified viral strains. Of 502 children with acute gastroenteritis admitted to our three hospitals between January 2011 and March 2012, genotyping of human noroviruses was performed in 171 (34%) norovirus-positive samples. Of these samples, 170 (99.5%) were in genogroup II (GII), while only one (0.5%) was in genogroup I (GI). The most common GII strain was the GII.4-2006b variant (n = 96, 56.5%), followed by GII.6 (n = 23, 13.5%), GII.12 (n = 22, 12.9%), GII.3 (n = 20, 11.8%), GII.2 (n = 6, 3.5%), GII.b (n = 2, 1.2%), and GII.10 (n = 1, 0.6%). Potential recombination events (polymerase/capsid) were detected in 39 GII strains (22.9%), and the most frequent genotypes were GII.4/GII.12 (n = 12, 30.8%), GII.4/GII.6 (n = 12, 30.8%), GII.4/GII.3 (n = 8, 20.5%), GII.b/GII.3 (n = 3, 7.7%), GII.16/GII.2 (n = 2, 5.1%), GII.4/GII.2 (n = 1, 2.6%), and GII.2/GII.10 (n = 1, 2.6%). For the first time, a novel GII.2/GII.10 recombination was detected; we also identified the GII.16/GII.2 strain for the first time in South Korea. Our data provided important insights into new recombination events, which may prove valuable for predicting the emergence of circulating norovirus strains with global epidemic potential.
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Affiliation(s)
- Thoi Cong Truong
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Van Thai Than
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
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Hasing ME, Hazes B, Lee BE, Preiksaitis JK, Pang XL. Detection and analysis of recombination in GII.4 norovirus strains causing gastroenteritis outbreaks in Alberta. INFECTION GENETICS AND EVOLUTION 2014; 27:181-92. [DOI: 10.1016/j.meegid.2014.07.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/25/2014] [Accepted: 07/15/2014] [Indexed: 12/21/2022]
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Novel recombinant GII.P16_GII.13 and GII.P16_GII.3 norovirus strains in Italy. Virus Res 2014; 188:142-5. [DOI: 10.1016/j.virusres.2014.04.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 04/08/2014] [Accepted: 04/08/2014] [Indexed: 01/11/2023]
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