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Chandran S, Gibson KE. Improving the Detection and Understanding of Infectious Human Norovirus in Food and Water Matrices: A Review of Methods and Emerging Models. Viruses 2024; 16:776. [PMID: 38793656 PMCID: PMC11125872 DOI: 10.3390/v16050776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Human norovirus (HuNoV) is a leading global cause of viral gastroenteritis, contributing to numerous outbreaks and illnesses annually. However, conventional cell culture systems cannot support the cultivation of infectious HuNoV, making its detection and study in food and water matrices particularly challenging. Recent advancements in HuNoV research, including the emergence of models such as human intestinal enteroids (HIEs) and zebrafish larvae/embryo, have significantly enhanced our understanding of HuNoV pathogenesis. This review provides an overview of current methods employed for HuNoV detection in food and water, along with their associated limitations. Furthermore, it explores the potential applications of the HIE and zebrafish larvae/embryo models in detecting infectious HuNoV within food and water matrices. Finally, this review also highlights the need for further optimization and exploration of these models and detection methods to improve our understanding of HuNoV and its presence in different matrices, ultimately contributing to improved intervention strategies and public health outcomes.
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Affiliation(s)
| | - Kristen E. Gibson
- Department of Food Science, Center for Food Safety, University of Arkansas System Division of Agriculture, Fayetteville, AR 72704, USA;
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Chen Q, Ma J, Gao L, Xian R, Wei K, Shi A, Yuan F, Cao M, Zhao Y, Jin M, Kuai W. Determination and analysis of whole genome sequence of recombinant GII.6[P7] norovirus in Ningxia, China. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 115:105499. [PMID: 37734510 DOI: 10.1016/j.meegid.2023.105499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/23/2023]
Abstract
While the GII.4 norovirus was the predominant genotype, non-GII.4 genotype was increasingly focused since the non-GII.4 genotype caused regional epidemics. In this study, the detection rate was16.51% (183/1108) in Ningxia from January to December 2020. Among identified genotypes, GII.4[P31] and GII.4[P16] were the dominant genotypes (n = 20 and 18, respectively) while GII.6[P7] was the main type (n = 6) in non-GII.4 strains which was mainly detected in from May to July. The whole genome sequences of the norovirus diarrhea samples identified as GII.6 [P7] with Ct ≤ 30 collected in 2020 were determined. In this study, the complete genome sequences of norovirus strains PL20-044 and QTX20-071 were identified and analyzed phylogenetically. Phylogenetic analysis of the ORF1and ORF2 regions showed that these strains evolved from the GII·P7-GII.6 strains detected in recent years from different country. The results showed that PL20-044 had intra-type recombination with GII·P7-GII.6c and GII·P7-GII.6a, while QTX20-071 had intre-type recombination within GII·P7-GII.6a. The evolutionary rates of the RdRp gene region of the GII·P7 genotype and the VP1 gene region of the GII.6 genotype were 2.91 × 10-3 (95%HPDs2.32-3.51 × 10-3) and 2.61 × 10-3 (95%HPDs2.14-3.11 × 10-3) substitutions/site/year, respectively. Comparative analysis of the amino acid mutation sites in VP1 with the GII·P7-GII.6a strains before 1997, the later detected strains have changed in aa131 and aa354. Moreover, PL20-044 strains showed special mutations at aa316 and aa395. These results help to understand the norovirus genotype circulating in the human population in Ningxia, and discover the evolutionary characteristics of the GII·P7-GII.6 strain.
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Affiliation(s)
- Qian Chen
- Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China; School of Public Health, Ningxia Medical University, Yinchuan 750001, China
| | - Jiangtao Ma
- Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China.
| | - Lei Gao
- Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China; School of Public Health, Ningxia Medical University, Yinchuan 750001, China
| | - Ran Xian
- Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China; School of Public Health, Ningxia Medical University, Yinchuan 750001, China
| | - Kaixin Wei
- Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China; School of Public Health, Ningxia Medical University, Yinchuan 750001, China
| | - Anqi Shi
- Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China; School of Public Health, Ningxia Medical University, Yinchuan 750001, China
| | - Fang Yuan
- Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China
| | - Min Cao
- Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China
| | - Yu Zhao
- School of Public Health, Ningxia Medical University, Yinchuan 750001, China
| | - Miao Jin
- National Institute for Viral Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102211, China
| | - Wenhe Kuai
- Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China
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Takahashi T, Kimura R, Shirai T, Sada M, Sugai T, Murakami K, Harada K, Ito K, Matsushima Y, Mizukoshi F, Okayama K, Hayashi Y, Kondo M, Kageyama T, Suzuki Y, Ishii H, Ryo A, Katayama K, Fujita K, Kimura H. Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase ( RdRp) Region and VP1 Gene in Human Norovirus Genotypes GII.P6-GII.6 and GII.P7-GII.6. Viruses 2023; 15:1497. [PMID: 37515184 PMCID: PMC10383674 DOI: 10.3390/v15071497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/24/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
To understand the evolution of GII.P6-GII.6 and GII.P7-GII.6 strains, the prevalent human norovirus genotypes, we analysed both the RdRp region and VP1 gene in globally collected strains using authentic bioinformatics technologies. A common ancestor of the P6- and P7-type RdRp region emerged approximately 50 years ago and a common ancestor of the P6- and P7-type VP1 gene emerged approximately 110 years ago. Subsequently, the RdRp region and VP1 gene evolved. Moreover, the evolutionary rates were significantly faster for the P6-type RdRp region and VP1 gene than for the P7-type RdRp region and VP1 genes. Large genetic divergence was observed in the P7-type RdRp region and VP1 gene compared with the P6-type RdRp region and VP1 gene. The phylodynamics of the RdRp region and VP1 gene fluctuated after the year 2000. Positive selection sites in VP1 proteins were located in the antigenicity-related protruding 2 domain, and these sites overlapped with conformational epitopes. These results suggest that the GII.6 VP1 gene and VP1 proteins evolved uniquely due to recombination between the P6- and P7-type RdRp regions in the HuNoV GII.P6-GII.6 and GII.P7-GII.6 virus strains.
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Affiliation(s)
- Tomoko Takahashi
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi, Gunma 370-0006, Japan
- Iwate Prefectural Research Institute for Environmental Science and Public Health, Morioka-shi, Iwate 020-0857, Japan
| | - Ryusuke Kimura
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, Shibukawa-shi, Gunma 377-0008, Japan
- Department of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi-shi, Gunma 371-8514, Japan
| | - Tatsuya Shirai
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, Shibukawa-shi, Gunma 377-0008, Japan
- Department of Respiratory Medicine, School of Medicine, Kyorin University, Mitaka-shi, Tokyo 181-8611, Japan
| | - Mitsuru Sada
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, Shibukawa-shi, Gunma 377-0008, Japan
- Department of Respiratory Medicine, School of Medicine, Kyorin University, Mitaka-shi, Tokyo 181-8611, Japan
| | - Toshiyuki Sugai
- Department of Nursing Science, Graduate School of Health Science, Hiroshima University, Hiroshima-shi, Hiroshima 734-8551, Japan
| | - Kosuke Murakami
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Kazuhiko Harada
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, Shibukawa-shi, Gunma 377-0008, Japan
| | - Kazuto Ito
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, Shibukawa-shi, Gunma 377-0008, Japan
| | - Yuki Matsushima
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fuminori Mizukoshi
- Department of Microbiology, Tochigi Prefectural Institute of Public Health and Environmental Science, Utsunomiya-shi, Tochigi 329-1196, Japan
| | - Kaori Okayama
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi, Gunma 370-0006, Japan
| | - Yuriko Hayashi
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi, Gunma 370-0006, Japan
| | - Mayumi Kondo
- Department of Clinical Engineering, Faculty of Medical Technology, Gunma Paz University, Takasaki-shi, Gunma 370-0006, Japan
| | - Tsutomu Kageyama
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Yoshiyuki Suzuki
- Division of Biological Science, Department of Information and Basic Science, Graduate School of Natural Sciences, Nagoya City University, Nagoya-shi, Aichi 467-8501, Japan
| | - Haruyuki Ishii
- Department of Respiratory Medicine, School of Medicine, Kyorin University, Mitaka-shi, Tokyo 181-8611, Japan
| | - Akihide Ryo
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection Control, Graduate School of Infection Control Sciences, Ōmura Satoshi Memorial Institute, Kitasato University, Minato-ku, Tokyo 108-8641, Japan
| | - Kiyotaka Fujita
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi, Gunma 370-0006, Japan
| | - Hirokazu Kimura
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi, Gunma 370-0006, Japan
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, Shibukawa-shi, Gunma 377-0008, Japan
- Department of Clinical Engineering, Faculty of Medical Technology, Gunma Paz University, Takasaki-shi, Gunma 370-0006, Japan
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Zhou N, Huang Y, Zhou L, Li M, Jin H. Molecular Evolution of RNA-Dependent RNA Polymerase Region in Norovirus Genogroup I. Viruses 2023; 15:166. [PMID: 36680206 PMCID: PMC9861054 DOI: 10.3390/v15010166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/06/2023] Open
Abstract
Norovirus is the leading viral agent of gastroenteritis in humans. RNA-dependent RNA polymerase (RdRp) is essential in the replication of norovirus RNA. Here, we present a comprehensive evolutionary analysis of the norovirus GI RdRp gene. Our results show that the norovirus GI RdRp gene can be divided into three groups, and that the most recent common ancestor was 1484. The overall evolutionary rate of GI RdRp is 1.821 × 10-3 substitutions/site/year. Most of the amino acids of the GI RdRp gene were under negative selection, and only a few positively selected sites were recognized. Amino acid substitutions in the GI RdRp gene accumulated slowly over time. GI.P1, GI.P3 and GI.P6 owned the higher evolutionary rates. GI.P11 and GI.P13 had the faster accumulation rate of amino acid substitutions. GI.P2, GI.P3, GI.P4, GI.P6 and GI.P13 presented a strong linear evolution. These results reveal that the norovirus GI RdRp gene evolves conservatively, and that the molecular evolutionary characteristics of each P-genotype are diverse. Sequencing in RdRp and VP1 of norovirus should be advocated in the surveillance system to explore the effect of RdRp on norovirus activity.
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Affiliation(s)
- Nan Zhou
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Yue Huang
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Lu Zhou
- Department of Acute Infectious Diseases, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Mingma Li
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Hui Jin
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China
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Oteiza JM, Prez VE, Pereyra D, Jaureguiberry MV, Sánchez G, Sant'Ana AS, Barril PA. Occurrence of Norovirus, Rotavirus, Hepatitis a Virus, and Enterovirus in Berries in Argentina. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:170-177. [PMID: 35305250 DOI: 10.1007/s12560-022-09518-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Berries have been implicated as the probable vehicle of infection in multiple outbreaks of norovirus and hepatitis A virus (HAV). These foods often receive minimal or no processing and may be exposed to virus contamination at each stage of production. In an increasingly globalized world, berries have a wide distribution and can give rise to the spread of diseases in distant parts of the world. With the aim of describing the virological quality of the berries cultivated in Argentina, a total of 184 soft fruits of different varieties (strawberries, blueberries, raspberries, blackberries, currants, pomegranate arils, cassis, and elder) were collected during the periods 2016-2018 and 2020. Viral particles were eluted and concentrated by polyethylene glycol precipitation according to ISO 15216-2:2019 guidelines. Genome detection of norovirus (NoV) genogroups I (GI) and II (GII), HAV, rotavirus, and enterovirus was performed by real-time RT-PCR with TaqMan probes. Positive samples were amplified by conventional RT-PCR and the amplicons were purified and sequenced in both directions. Phylogenetic analysis was performed using the Neighbor-Joining method based on the evolutionary model Kimura-2-parameters. NoV GII.6 was detected in 1/184 (0.5%) of the soft fruits, corresponding to a raspberry sample obtained during the fall of 2017. No presence of other human enteric viruses was found in the other berries analyzed. The collected data are the first in Argentina in relation to the prevalence of enteric viruses in berries and is useful as reference data for a risk assessment of soft fruits as vehicles of foodborne pathogenic viruses.
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Affiliation(s)
- Juan Martín Oteiza
- Laboratorio de Microbiología de los Alimentos, Centro de Investigación y Asistencia Técnica a la Industria (CIATI), Expedicionarios del Desierto 1310, 8309, Centenario, Neuquen, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Verónica Emilse Prez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
- Laboratorio de Gastroenteritis Virales, Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, 5016, Córdoba, Argentina.
- Laboratorio de Gastroenteritis Virales, Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, 5000, Córdoba, Argentina.
| | - Dayana Pereyra
- Laboratorio de Microbiología de los Alimentos, Centro de Investigación y Asistencia Técnica a la Industria (CIATI), Expedicionarios del Desierto 1310, 8309, Centenario, Neuquen, Argentina
| | - María Virginia Jaureguiberry
- Laboratorio de Microbiología de los Alimentos, Centro de Investigación y Asistencia Técnica a la Industria (CIATI), Expedicionarios del Desierto 1310, 8309, Centenario, Neuquen, Argentina
| | - Gloria Sánchez
- Departamento de Tecnologías de Conservación y Seguridad Alimentaria, Instituto de Agroquímica y Tecnología de Alimentos - Consejo Superior de Investigaciones Científicas (IATA-CSIC), C/ Catedrático Agustín Escardino Benlloch 7, 46980, Paterna, Valencia, Spain
| | - Anderson S Sant'Ana
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Patricia Angélica Barril
- Laboratorio de Microbiología de los Alimentos, Centro de Investigación y Asistencia Técnica a la Industria (CIATI), Expedicionarios del Desierto 1310, 8309, Centenario, Neuquen, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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John JL, Mori D, Amit LN, Mosiun AK, Chin AZ, Ahmed K. High proportion of norovirus infection and predominance of GII.3 [P12] genotype among the children younger than 5 in Sabah, Malaysian Borneo. J Clin Virol 2021; 143:104968. [PMID: 34509928 DOI: 10.1016/j.jcv.2021.104968] [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: 03/30/2021] [Revised: 08/18/2021] [Accepted: 08/27/2021] [Indexed: 11/17/2022]
Abstract
Globally, norovirus (NoV) has become one of the important causes of acute gastroenteritis (AGE) in children. It is responsible for death of children younger than 5 years in developing countries. Although there is limited information and the rate of child mortality caused by diarrhea is low in Malaysia, the burden of diarrhea is high, especially in Sabah. NoV GI, GII and GIV genogroups are known to infect humans, and GII.4 is the predominant genotype distributed worldwide. Better understanding of the etiology of NoV will help to inform policies for prevention and control. The aim of this study was to determine the burden and genotype distribution of NoV in children younger than 5 years with AGE who attended health-care facilities in Sabah, Malaysia. Diarrhea stool samples were collected from 299 children with AGE and NoV was detected by amplifying the capsid and RNA-dependent RNA polymerase gene and reverse transcription-polymerase chain reaction (RT-PCR) analysis. Nucleotide sequencing of the amplicons was used for genotypes and phylogenetic analyses . NoV-positive stool samples were found in 17.7% (53/299) among which 13/53 (24.5%), 38/53 (71.7%), and 2/53 (3.8%) identified as NoV GI, GII and combination of GI and GII, respectively. The most common genotypes were GII.3 [P12] (80%) followed by GII.6 [P7] (13.3%), and GII.17 [P17] (6.7%). In the phylogenetic tree, all Sabahan NoV samples were shown to share ancestry with their respective genotype from predominantly East Asian countries and to some extent Australia and Europe. However, the Sabahan strains formed independent clusters with significant bootstrap values, indicating a clonal spread after the strains had entered Sabah.
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Affiliation(s)
- Jecelyn Leaslie John
- Borneo Medical and Health Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Malaysia
| | - Daisuke Mori
- Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Malaysia
| | - Lia Natasha Amit
- Borneo Medical and Health Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Malaysia
| | | | - Abraham Zefong Chin
- Department of Community and Family Medicine, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Malaysia
| | - Kamruddin Ahmed
- Borneo Medical and Health Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Malaysia; Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Malaysia.
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Virological and Epidemiological Features of Norovirus Infections in Brazil, 2017-2018. Viruses 2021; 13:v13091724. [PMID: 34578304 PMCID: PMC8472875 DOI: 10.3390/v13091724] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 12/19/2022] Open
Abstract
Noroviruses are considered an important cause of acute gastroenteritis (AGE) across all age groups. Here, we investigated the incidence of norovirus, genotypes circulation, and norovirus shedding in AGE stool samples from outpatients in Brazil. During a two-year period, 1546 AGE stool samples from ten Brazilian states were analyzed by RT-qPCR to detect and quantify GI and GII noroviruses. Positive samples were genotyped by dual sequencing using the ORF1/2 junction region. Overall, we detected norovirus in 32.1% of samples, with a massive predominance of GII viruses (89.1%). We also observed a significant difference between the median viral load of norovirus GI (3.4×105 GC/g of stool) and GII (1.9×107 GC/g). The most affected age group was children aged between 6 and 24 m old, and norovirus infection was detected throughout the year without marked seasonality. Phylogenetic analysis of partial RdRp and VP1 regions identified six and 11 genotype combinations of GI and GII, respectively. GII.4 Sydney[P16] was by far the predominant genotype (47.6%), followed by GII.2[P16], GII.4 Sydney[P31], and GII.6[P7]. We detected, for the first time in Brazil, the intergenogroup recombinant genotype GIX.1[GII.P15]. Our study contributes to the knowledge of norovirus genotypes circulation at the national level, reinforcing the importance of molecular surveillance programs for future vaccine designs.
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Tohma K, Lepore CJ, Martinez M, Degiuseppe JI, Khamrin P, Saito M, Mayta H, Nwaba AUA, Ford-Siltz LA, Green KY, Galeano ME, Zimic M, Stupka JA, Gilman RH, Maneekarn N, Ushijima H, Parra GI. Genome-wide analyses of human noroviruses provide insights on evolutionary dynamics and evidence of coexisting viral populations evolving under recombination constraints. PLoS Pathog 2021; 17:e1009744. [PMID: 34255807 PMCID: PMC8318288 DOI: 10.1371/journal.ppat.1009744] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 07/28/2021] [Accepted: 06/23/2021] [Indexed: 12/14/2022] Open
Abstract
Norovirus is a major cause of acute gastroenteritis worldwide. Over 30 different genotypes, mostly from genogroup I (GI) and II (GII), have been shown to infect humans. Despite three decades of genome sequencing, our understanding of the role of genomic diversification across continents and time is incomplete. To close the spatiotemporal gap of genomic information of human noroviruses, we conducted a large-scale genome-wide analyses that included the nearly full-length sequencing of 281 archival viruses circulating since the 1970s in over 10 countries from four continents, with a major emphasis on norovirus genotypes that are currently underrepresented in public genome databases. We provided new genome information for 24 distinct genotypes, including the oldest genome information from 12 norovirus genotypes. Analyses of this new genomic information, together with those publicly available, showed that (i) noroviruses evolve at similar rates across genomic regions and genotypes; (ii) emerging viruses evolved from transiently-circulating intermediate viruses; (iii) diversifying selection on the VP1 protein was recorded in genotypes with multiple variants; (iv) non-structural proteins showed a similar branching on their phylogenetic trees; and (v) contrary to the current understanding, there are restrictions on the ability to recombine different genomic regions, which results in co-circulating populations of viruses evolving independently in human communities. This study provides a comprehensive genetic analysis of diverse norovirus genotypes and the role of non-structural proteins on viral diversification, shedding new light on the mechanisms of norovirus evolution and transmission. Norovirus is a highly diverse enteric pathogen. The large genomic database accumulated in the last three decades advanced our understanding of norovirus diversity; however, this information is limited by geographical bias, sporadic times of collection, and missing or incomplete genome sequences. In this multinational collaborative study, we mined archival samples collected since the 1970s and sequenced nearly full-length new genomes from 281 historical noroviruses, including the first full-length genomic sequences for three genotypes. Using this novel dataset, we found evidence for restrictions in the recombination of genetically disparate viruses and that diversifying selection results in new variants with different epidemiological profiles. These new insights on the diversification of noroviruses could provide baseline information for the study of future epidemics and ultimately the prevention of norovirus infections.
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Affiliation(s)
- Kentaro Tohma
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, United States of America
| | - Cara J. Lepore
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, United States of America
| | - Magaly Martinez
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, United States of America
- IICS, National University of Asuncion, Asuncion, Paraguay
| | | | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Holger Mayta
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Amy U. Amanda Nwaba
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, United States of America
| | - Lauren A. Ford-Siltz
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, United States of America
| | - Kim Y. Green
- Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | | | - Mirko Zimic
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Robert H. Gilman
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Gabriel I. Parra
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, United States of America
- * E-mail:
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Bonura F, Urone N, Bonura C, Mangiaracina L, Filizzolo C, Sciortino G, Sanfilippo GL, Martella V, Giammanco GM, De Grazia S. Recombinant GII.P16 genotype challenges RT-PCR-based typing in region A of norovirus genome. J Infect 2021; 83:69-75. [PMID: 33887286 DOI: 10.1016/j.jinf.2021.04.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 03/21/2021] [Accepted: 04/10/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVES In latest years GII.4[P16] and GII.2[P16] noroviruses have become predominant in some temporal/geographical settings. In parallel with the emergence of the GII.P16 polymerase type, norovirus surveillance activity in Italy experienced increasing difficulties in generating sequence data on the RNA polymerase genomic region A, using the widely adopted JV12A/JV13B primer set. Two sets of modified primers (Deg1 and Deg2) were tested in order to improve amplification and typing of the polymerase gene. METHODS Amplification and typing performance of region A primers was assessed in RT-PCR on 452 GII norovirus positive samples obtained from 2194 stool samples collected in 2016-2019 from children hospitalized with acute gastroenteritis. RESULTS The use of Deg1 increased the rate of samples types in region A from 49.5% to 81.4% and from 21.9% to 69.7% in 2016 and 2017, respectively. The rate of Deg1 typed samples remained high in 2018 (90.1%), but sharply decreased to 11.8% in 2019. The second primers set, Deg2, was able to increase to 64.9% the rate of 2019 samples typed in region A, while typing efficiently 73.2%, 69%, and 86.4% of samples collected in 2016, 2017 and 2018, respectively. CONCLUSIONS The plasticity of norovirus genomes requires continuous updates of the primers used for strain characterization.
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Affiliation(s)
- Floriana Bonura
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 133, Palermo I-90127, Italy
| | - Noemi Urone
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 133, Palermo I-90127, Italy
| | - Celestino Bonura
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 133, Palermo I-90127, Italy
| | - Leonardo Mangiaracina
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 133, Palermo I-90127, Italy
| | - Chiara Filizzolo
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 133, Palermo I-90127, Italy
| | - Giuseppa Sciortino
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 133, Palermo I-90127, Italy
| | - Giuseppa L Sanfilippo
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 133, Palermo I-90127, Italy
| | - Vito Martella
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italy
| | - Giovanni M Giammanco
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 133, Palermo I-90127, Italy.
| | - Simona De Grazia
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 133, Palermo I-90127, Italy
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Cheng HY, Lee CC, Chang YC, Tsai CN, Chao HC, Tsai YT, Hsieh CH, Su SS, Chen SY. Viral shedding in gastroenteritis in children caused by variants and novel recombinant norovirus infections. Medicine (Baltimore) 2021; 100:e25123. [PMID: 33761678 PMCID: PMC9282056 DOI: 10.1097/md.0000000000025123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 02/17/2021] [Indexed: 01/05/2023] Open
Abstract
Human norovirus (NoV) is the leading cause of acute gastroenteritis and the rapid transmission of NoV renders infection control problematic. Our study aimed to investigate viral shedding in gastroenteritis in children caused by variants of emerging norovirus strains infections.We used RNA-dependent RNA polymerase (RdRp) sequencing to measure NoV genome copies in stool to understand the relationship between the clinical manifestations and viral shedding in hospitalized patients. The near full-length NoV genome sequence was amplified via reverse transcription-polymerase chain reaction (RT-PCR) and NoV recombination was analyzed using the Recombination Analysis Tool (RAT).From January 2015 to March 2018, 77 fecal specimens were collected from hospitalized pediatric patients with confirmed NoV gastroenteritis. The NoV genotypes were GII.4 (n = 22), non-GII.4 (n = 14), GII.4 Sydney (n = 21), and GII.P16-GII.2 (n = 20). Viral load increased from days 2 to 9 from the illness onset, resulting in an irregular plateau without peaks. After day 9, the viral load declined gradually and most viral shedding in feces ceased by day 15. The average viral load was highest in GII.4 Sydney followed by GII.P16-GII.2 infections and lowest in non-GII.4 infections. GII.4 unclassified infections showed the longest viral shedding time, followed by GII.4 Sydney infections, GII.P16-GII.2 recombinant infection resulted in the shortest duration. NoVs evolved to form a group of GII.P16-GII.2 variants during the 2017 to 2018 period.The viral load and shedding period and was different in variants of NoV infections in children. High mutation rate of emerging and re-emerging variants was observed to an enhanced epidemic risk rendering continuous surveillance.
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Affiliation(s)
- Hung-Yen Cheng
- Division of Pediatric Gastroenterology, Department of Pediatrics, Taipei Medical University-Shuang Ho Hospital, Taipei
| | - Chung-Chan Lee
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan
| | | | - Chi-Neu Tsai
- Graduate Institute of Clinical Medical Sciences, Chang Gung University College of Medicine, Department of Pediatrics, Chang Gung Memorial Hospital
| | - Hsun-Ching Chao
- Division of Pediatric Gastroenterology, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan
| | - Yin-Tai Tsai
- Department of Medicine Laboratory, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Chia-Hsin Hsieh
- Department of Medicine Laboratory, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Sin-Sheng Su
- Department of Medicine Laboratory, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Shih-Yen Chen
- Division of Pediatric Gastroenterology, Department of Pediatrics, Taipei Medical University-Shuang Ho Hospital, Taipei
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