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Chen D, Shao Q, Ru X, Chen S, Cheng D, Ye Q. Epidemiological and genetic characteristics of norovirus in Hangzhou, China, in the postepidemic era. J Clin Virol 2024; 172:105679. [PMID: 38677156 DOI: 10.1016/j.jcv.2024.105679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/18/2024] [Accepted: 04/21/2024] [Indexed: 04/29/2024]
Abstract
OBJECTIVE Norovirus (NoV) is an important human pathogen that can cause severe gastroenteritis in vulnerable populations. This study aimed to analyze the epidemiological and genetic characteristics of 2021-2023 NoV in Hangzhou, China. METHODS This study enrolled patients aged 0-18 years who underwent NoV RNA detection in the hospital between January 2021 and October 2023 and analyzed the epidemiological characteristics of NoV. Polymerase chain reaction (PCR) was used to detect NoV RNA. Subtype classification and whole-genome sequencing were performed. RESULTS There was a high prevalence of NoV infection in 2023, with NoV-positive samples accounting for 63.10 % of the total number of positive samples collected during the three-year period. The prevalence was abnormally high in summer, and the number of positive samples accounted for 48.20 % of the total positive samples for the whole year, which was much greater than the level in the same period in previous years (2023, 48.20% vs 2021, 13.66% vs 2022, 15.21 %). The GⅡ.4 subtype played a leading role, followed by increased mixed infection with GⅠ.5 and GⅡ.4. Whole-genome sequencing results suggested that GII.P16-GⅡ.4 had R297H and D372N key locus mutations. The evolutionary rate was 4.29 × 10-3 for the RdRp gene and 4.84 × 10-3 for the VP1 gene. The RdRp gene and VP1 gene of NoV GII.P16-GⅡ.4 have undergone rapid population evolution during the COVID-19 epidemic. CONCLUSION In the summer of 2023, an abnormally high incidence of NoV appeared in Hangzhou, China. The major epidemic strain GII.P16-GⅡ.4 showed a certain range of gene mutations and a fast evolutionary rate.
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Affiliation(s)
- Danlei Chen
- Department of Laboratory Medicine, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, China; Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qingyi Shao
- Department of Laboratory Medicine, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, China; Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xuanwen Ru
- Department of Laboratory Medicine, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, China
| | - Simiao Chen
- Department of Laboratory Medicine, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, China
| | - Dongqing Cheng
- Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, China.
| | - Qing Ye
- Department of Laboratory Medicine, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, China.
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Dakouo D, Ouermi D, Ouattara AK, Simpore A, Compaore TR, Traore MAE, Gamsore Z, Zoure AA, Traore L, Zohoncon TM, Yonli AT, Ilboudo PD, Djigma FW, Simpore J. Rotavirus vaccines in Africa and Norovirus genetic diversity in children aged 0 to 5 years old: a systematic review and meta-analysis : Rotavirus vaccines in Africa and Norovirus genetic diversity. BMC Infect Dis 2024; 24:547. [PMID: 38822241 PMCID: PMC11143598 DOI: 10.1186/s12879-024-09434-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024] Open
Abstract
Noroviruses are the second leading cause of death in children under the age of 5 years old. They are responsible for 200 million cases of diarrhoea and 50,000 deaths in children through the word, mainly in low-income countries. The objective of this review was to assess how the prevalence and genetic diversity of noroviruses have been affected by the introduction of rotavirus vaccines in Africa. PubMed, Web of Science and Science Direct databases were searched for articles. All included studies were conducted in Africa in children aged 0 to 5 years old with gastroenteritis. STATA version 16.0 software was used to perform the meta-analysis. The method of Dersimonian and Laird, based on the random effects model, was used for the statistical analyses in order to estimate the pooled prevalence's at a 95% confidence interval (CI). Heterogeneity was assessed by Cochran's Q test using the I2 index. The funnel plot was used to assess study publication bias. A total of 521 studies were retrieved from the databases, and 19 were included in the meta-analysis. The pooled norovirus prevalence's for pre- and post-vaccination rotavirus studies were 15% (95 CI, 15-18) and 13% (95 CI, 09-17) respectively. GII was the predominant genogroup, with prevalence of 87.64% and 91.20% respectively for the pre- and post-vaccination studies. GII.4 was the most frequently detected genotype, with rates of 66.84% and 51.24% respectively for the pre- and post-vaccination studies. This meta-analysis indicates that rotavirus vaccination has not resulted in a decrease in norovirus infections in Africa.
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Affiliation(s)
- Dako Dakouo
- Laboratoire de Biologie Moléculaire et Génétique (LABIOGENE), Université Joseph KI- ZERBO, Ouagadougou 03, 03 BP 7021, Burkina Faso
| | - Djénéba Ouermi
- Laboratoire de Biologie Moléculaire et Génétique (LABIOGENE), Université Joseph KI- ZERBO, Ouagadougou 03, 03 BP 7021, Burkina Faso
- Centre de Recherche Biomoléculaire Pietro Annigoni (CERBA), Ouagadougou 01, 01 BP 364, Burkina Faso
- Département de Biologie et Physiologie Animales, Université Joseph KI-ZERBO, Ouagadougou, Burkina Faso
| | - Abdoul Karim Ouattara
- Laboratoire de Biologie Moléculaire et Génétique (LABIOGENE), Université Joseph KI- ZERBO, Ouagadougou 03, 03 BP 7021, Burkina Faso.
- Centre de Recherche Biomoléculaire Pietro Annigoni (CERBA), Ouagadougou 01, 01 BP 364, Burkina Faso.
| | - Abibou Simpore
- Laboratoire de Biologie Moléculaire et Génétique (LABIOGENE), Université Joseph KI- ZERBO, Ouagadougou 03, 03 BP 7021, Burkina Faso
- Agence Nationale pour la Sécurité Sanitaire de l'Environnement, de l'Alimentation, du Travail et des Produits de Santé (ANSSEAT), Ouagadougou, Burkina Faso
| | - Tégwendé Rebecca Compaore
- Laboratoire de Biologie Moléculaire et Génétique (LABIOGENE), Université Joseph KI- ZERBO, Ouagadougou 03, 03 BP 7021, Burkina Faso
- Département Biomédical et Santé Publique, Institut de Recherche en Sciences de la Santé (IRSS/CNRST), Ouagadougou 03, 03 BP 7192, Burkina Faso
| | - Mah Alima Esther Traore
- Laboratoire de Biologie Moléculaire et Génétique (LABIOGENE), Université Joseph KI- ZERBO, Ouagadougou 03, 03 BP 7021, Burkina Faso
| | - Zakaria Gamsore
- Laboratoire de Biologie Moléculaire et Génétique (LABIOGENE), Université Joseph KI- ZERBO, Ouagadougou 03, 03 BP 7021, Burkina Faso
| | - Abdou Azaque Zoure
- Laboratoire de Biologie Moléculaire et Génétique (LABIOGENE), Université Joseph KI- ZERBO, Ouagadougou 03, 03 BP 7021, Burkina Faso
- Département Biomédical et Santé Publique, Institut de Recherche en Sciences de la Santé (IRSS/CNRST), Ouagadougou 03, 03 BP 7192, Burkina Faso
| | - Lassina Traore
- Laboratoire de Biologie Moléculaire et Génétique (LABIOGENE), Université Joseph KI- ZERBO, Ouagadougou 03, 03 BP 7021, Burkina Faso
- Centre de Recherche Biomoléculaire Pietro Annigoni (CERBA), Ouagadougou 01, 01 BP 364, Burkina Faso
| | - Théodora Mahoukèdè Zohoncon
- Laboratoire de Biologie Moléculaire et Génétique (LABIOGENE), Université Joseph KI- ZERBO, Ouagadougou 03, 03 BP 7021, Burkina Faso
- Centre de Recherche Biomoléculaire Pietro Annigoni (CERBA), Ouagadougou 01, 01 BP 364, Burkina Faso
- Faculté de Médecine, Université Saint Thomas d'Aquin, Ouagadougou 01, 06 BP 10212, Burkina Faso
| | - Albert Théophane Yonli
- Laboratoire de Biologie Moléculaire et Génétique (LABIOGENE), Université Joseph KI- ZERBO, Ouagadougou 03, 03 BP 7021, Burkina Faso
- Centre de Recherche Biomoléculaire Pietro Annigoni (CERBA), Ouagadougou 01, 01 BP 364, Burkina Faso
| | - P Denise Ilboudo
- Laboratoire de Biologie Moléculaire et Génétique (LABIOGENE), Université Joseph KI- ZERBO, Ouagadougou 03, 03 BP 7021, Burkina Faso
| | - Florencia Wendkuuni Djigma
- Laboratoire de Biologie Moléculaire et Génétique (LABIOGENE), Université Joseph KI- ZERBO, Ouagadougou 03, 03 BP 7021, Burkina Faso
- Centre de Recherche Biomoléculaire Pietro Annigoni (CERBA), Ouagadougou 01, 01 BP 364, Burkina Faso
| | - Jacques Simpore
- Laboratoire de Biologie Moléculaire et Génétique (LABIOGENE), Université Joseph KI- ZERBO, Ouagadougou 03, 03 BP 7021, Burkina Faso
- Centre de Recherche Biomoléculaire Pietro Annigoni (CERBA), Ouagadougou 01, 01 BP 364, Burkina Faso
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Li H, He F, Lv Z, Yi L, Zhang Z, Li H, Fu S. Tailored wastewater surveillance framework uncovered the epidemics of key pathogens in a Northwestern city of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171833. [PMID: 38522539 DOI: 10.1016/j.scitotenv.2024.171833] [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: 01/15/2024] [Revised: 03/03/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024]
Abstract
Wastewater surveillance enables rapid pathogen monitoring and community prevalence estimation. However, how to design an integrated and tailored wastewater surveillance framework to monitor major health threats in metropolises remains a major challenge. In this study, we first analyzed the historical clinical data of Xi'an city and designed a wastewater surveillance framework covering five key endemic viruses, namely, SARS-CoV-2, norovirus, influenza A virus (IAV), influenza B virus (IBV), respiratory syncytial virus (RSV), and hantavirus. Amplicon sequencing of SARS-CoV-2, norovirus and hantavirus was conducted biweekly to determine the prevalent community genotypes circulating in this region. The results showed that from April 2023 to August 2023, Xi'an experienced two waves of SARS-CoV-2 infection, which peaked in the middle of May-2023 and late August-2023. The sewage concentrations of IAV and RSV peaked in early March and early May 2023, respectively, while the sewage concentrations of norovirus fluctuated throughout the study period and peaked in late August. The dynamics of the sewage concentrations of SARS-CoV-2, norovirus, IAV, RSV, and hantavirus were in line with the trends in the sentinel hospital percent positivity data, indicating the role of wastewater surveillance in enhancing the understanding of epidemic trends. Amplicon sequencing of SARS-CoV-2 revealed a transition in the predominant genotype, which changed from DY.1 and FR.1.4 to the XBB and EG.5 subvariants. Amplicon sequencing also revealed that there was only one predominant hantavirus genotype in the local population, while highly diverse genotypes of norovirus GI and GII were found in the wastewater. In conclusion, this study provided valuable insights into the dynamics of infection trends and predominant genotypes of key pathogens in a city without sufficient clinical surveillance, highlighting the role of a tailored wastewater surveillance framework in addressing public health priorities. More importantly, our study provides the first evidence demonstrating the applicability of wastewater surveillance for hantavirus, which is a major health threat locally.
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Affiliation(s)
- Haifeng Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Fenglan He
- The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, China
| | - Ziquan Lv
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Liu Yi
- The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, China
| | - Ziqiang Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China
| | - Hui Li
- The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, China.
| | - Songzhe Fu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China; The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, China.
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Gutierrez MB, Arantes I, Bello G, Berto LH, Dutra LH, Kato RB, Fumian TM. Emergence and dissemination of equine-like G3P[8] rotavirus A in Brazil between 2015 and 2021. Microbiol Spectr 2024; 12:e0370923. [PMID: 38451227 PMCID: PMC10986506 DOI: 10.1128/spectrum.03709-23] [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: 10/19/2023] [Accepted: 02/22/2024] [Indexed: 03/08/2024] Open
Abstract
Rotavirus A (RVA) is a major cause of acute gastroenteritis globally that is classically genotyped by its two immunodominant outer capsid proteins, VP7 (G-) and VP4 (P-). Recent evidence suggests that the reassortant equine-like G3P[8] strain played a substantial role in RVA transmission in Brazil since 2015. To understand its global emergence and dissemination in Brazilian territory, stool samples collected from 11 Brazilian states (n = 919) were genotyped by RT-qPCR and proceeded to sequence the VP7 gene (n = 102, 79 being newly generated) of the G3P[8] samples with pronounced viral loads. Our phylogenetic genotyping showed that G3P[8] became the dominant strain in Brazil between 2017 and 2020, with equine-like variants representing 75%-100% of VP7 samples in this period. A Bayesian discrete phylogeographic analysis strongly suggests that the equine-like G3P[8] strain originated in Asia during the early 2010s and subsequently spread to Europe, the Caribbean, and South America. Multiple introductions were detected in Brazil between 2014 and 2017, resulting in five national clusters. The reconstruction of the effective population size of the largest Brazilian cluster showed an expansion until 2017, followed by a plateau phase until 2019 and subsequent contraction. Our study also supports that most mutations fixed during equine-like G3P[8] evolution were synonymous, suggesting that adaptive evolution was not an important driving force during viral dissemination in humans, potentially increasing its susceptibility to acquired immunity. This research emphasizes the need for comprehensive rotavirus genomic surveillance that allows close monitoring of its ever-shifting composition and informs more effective public health policies.IMPORTANCEOur original article demonstrated the origin and spread in a short time of equine-like G3P[8] in Brazil and the world. Due to its segmented genome, it allows numerous mechanisms including genetic drift and reassortment contribute substantially to the genetic diversity of rotavirus. Although the effectiveness and increasing implementation of vaccination have not been questioned, a matter of concern is its impact on the emergence of escape mutants or even the spread of unusual strains of zoonotic transmission that could drive epidemic patterns worldwide. This research emphasizes the need for comprehensive rotavirus genomic surveillance, which could facilitate the formulation of public policies aimed at preventing and mitigating its transmission.
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Affiliation(s)
| | - Ighor Arantes
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Lúcia Helena Berto
- Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília, Brazil
| | - Leonardo Hermes Dutra
- Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília, Brazil
| | - Rodrigo Bentes Kato
- Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília, Brazil
| | - Tulio Machado Fumian
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
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5
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Sarmento SK, de Andrade JDSR, Malta FC, Fialho AM, Mello MDS, Burlandy FM, Fumian TM. Norovirus Epidemiology and Genotype Circulation during the COVID-19 Pandemic in Brazil, 2019-2022. Pathogens 2023; 13:3. [PMID: 38276149 PMCID: PMC10818385 DOI: 10.3390/pathogens13010003] [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: 11/23/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 01/27/2024] Open
Abstract
Norovirus stands out as a leading cause of acute gastroenteritis (AGE) worldwide, affecting all age groups. In the present study, we investigated fecal samples from medically attended AGE patients received from nine Brazilian states, from 2019 to 2022, including the COVID-19 pandemic period. Norovirus GI and GII were detected and quantified using RT-qPCR, and norovirus-positive samples underwent genotyping through sequencing the ORF1/2 junction region. During the four-year period, norovirus prevalence was 37.2%, varying from 20.1% in 2020 to 55.4% in 2021. GII genotypes dominated, being detected in 92.9% of samples. GII-infected patients had significantly higher viral concentrations compared to GI-infected patients (median of 3.8 × 107 GC/g and 6.7 × 105 GC/g, respectively); and patients aged >12-24 months showed a higher median viral load (8 × 107 GC/g) compared to other age groups. Norovirus sequencing revealed 20 genotypes by phylogenetic analysis of RdRp and VP1 partial regions. GII.4 Sydney[P16] was the dominant genotype (57.3%), especially in 2019 and 2021, followed by GII.2[P16] (14.8%) and GII.6[P7] (6.3%). The intergenogroup recombinant genotype, GIX.1[GII.P15], was detected in five samples. Our study is the first to explore norovirus epidemiology and genotype distribution in Brazil during COVID-19, and contributes to understanding the epidemiological dynamics of norovirus and highlighting the importance of continuing to follow norovirus surveillance programs in Brazil.
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Affiliation(s)
| | | | | | | | | | | | - Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21045-900, RJ, Brazil (F.M.B.)
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Abid I, Blanco A, Al-Otaibi N, Guix S, Costafreda MI, Pintó RM, Bosch A. Dynamic and Seasonal Distribution of Enteric Viruses in Surface and Well Water in Riyadh (Saudi Arabia). Pathogens 2023; 12:1405. [PMID: 38133289 PMCID: PMC10747075 DOI: 10.3390/pathogens12121405] [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: 10/02/2023] [Revised: 11/06/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Enteric viruses are the major cause of gastroenteritis and enteric hepatitis worldwide, but in some areas like Saudi Arabia, little is known about their presence in water sources. The available information from clinical samples is not enough to figure out their actual prevalence. The aim of this study was to gather information for the first time in Saudi Arabia on the presence of the Norovirus (NoV) genogroup GI and GII, hepatitis A virus (HAV), and hepatitis E virus (HEV) in water. For this purpose, thirteen monthly samples were collected from Lake Wadi Hanifa and surrounding wells from December 2014 to November 2015. Viruses were detected and quantified using real-time RT-qPCR. Despite HEV findings being anecdotic, our results highlight interesting behaviors of the other viruses. There was a higher prevalence of noroviruses in Wadi Hanifa samples than in well water samples (46.43% vs. 12.5% of NoV GI; 66.67% vs. 8.33% of NoV GII). On the contrary, similar levels of HAV positivity were observed (40.48% in surface water vs. 43.06% in well water). Also, a strong influence of flooding events on HAV and NoV GI occurrence was observed in both surface and well water samples, with NoV GII apparently not affected.
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Affiliation(s)
- Islem Abid
- Center of Excellence in Biotechnology Research, College of Applied Medical Science, King Saud University, Riyadh 11495, Saudi Arabia;
| | - Albert Blanco
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (A.B.); (S.G.); (M.I.C.); (R.M.P.)
- Research Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, 08921 Barcelona, Spain
| | - Nawal Al-Otaibi
- Department of Botany and Microbiology, Science College, King Saud University, Riyadh 11495, Saudi Arabia;
| | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (A.B.); (S.G.); (M.I.C.); (R.M.P.)
- Research Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, 08921 Barcelona, Spain
| | - Maria I. Costafreda
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (A.B.); (S.G.); (M.I.C.); (R.M.P.)
- Research Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, 08921 Barcelona, Spain
| | - Rosa M. Pintó
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (A.B.); (S.G.); (M.I.C.); (R.M.P.)
- Research Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, 08921 Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (A.B.); (S.G.); (M.I.C.); (R.M.P.)
- Research Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, 08921 Barcelona, Spain
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Bonura F, Filizzolo C, Pizzo M, Sanfilippo GL, Cacioppo F, Palazzotto E, Di Bernardo F, Collura A, Martella V, De Grazia S, Giammanco GM. Biological Specimen Banking as a Time Capsule to Explore the Temporal Dynamics of Norovirus Epidemiology. Viruses 2023; 15:2303. [PMID: 38140544 PMCID: PMC10747129 DOI: 10.3390/v15122303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Norovirus is recognised as a major cause of epidemic and sporadic acute gastroenteritis (AGE) in all age groups. Information on the genetic diversity of the noroviruses circulating in the 1980s and 1990s, before the development and adoption of dedicated molecular assays, is limited compared with the last decades. Between 1986 and 2020, uninterrupted viral surveillance was conducted in symptomatic children hospitalized with AGE in Palermo, Italy, providing a unique time capsule for exploring the epidemiological and evolutionary dynamics of enteric viruses. A total of 8433 stool samples were tested using real-time RT-PCR. All samples were stored at -20 or -80 °C until processing. In this 35-year long time span, noroviruses of genogroup II (GII) were detected in 15.6% of AGE requiring hospitalization, whilst GI noroviruses were detected in 1.4% of AGE. Overall, the predominant norovirus capsid (Cap) genotype was GII.4 (60.8%), followed by GII.3 (13.3%) and GII.2 (12.4%). Temporal replacement of the GII.4 Cap variants associated with different polymerase (Pol) types were observed over the study period. The chronology of emergence and circulation of the different GII.4 variants were consistent with data available in the literature. Also, for GII.3 and GII.2 NoVs, the circulation of different lineages/strains, differing in either the Cap or Pol genes or in both, was observed. This long-term study revealed the ability of noroviruses to continuously and rapidly modify their genomic makeup and highlights the importance of surveillance activities in vaccine design.
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Affiliation(s)
- Floriana Bonura
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Chiara Filizzolo
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Mariangela Pizzo
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Giuseppa L. Sanfilippo
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Federica Cacioppo
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Emilia Palazzotto
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Francesca Di Bernardo
- Unità Operativa di Microbiologia e Virologia, Ospedale Civico e di Cristina, ARNAS, 90129 Palermo, Italy; (F.D.B.); (A.C.)
| | - Antonina Collura
- Unità Operativa di Microbiologia e Virologia, Ospedale Civico e di Cristina, ARNAS, 90129 Palermo, Italy; (F.D.B.); (A.C.)
| | - Vito Martella
- Dipartimento di Sanità Pubblica e Zootecnia, Università Aldo Moro di Bari, 70010 Valenzano, Italy;
| | - Simona De Grazia
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
| | - Giovanni M. Giammanco
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università di Palermo, Via del Vespro 133, 90127 Palermo, Italy; (C.F.); (M.P.); (G.L.S.); (F.C.); (E.P.); (S.D.G.); (G.M.G.)
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Zhang P, Xu D, Liu T, Chen L, Ji L. Genetic characterization of rarely reported GII.3[P25] norovirus strain detected in patients with acute gastroenteritis in Huzhou, China, 2021. Virol Sin 2023; 38:646-649. [PMID: 37390869 PMCID: PMC10436046 DOI: 10.1016/j.virs.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 06/25/2023] [Indexed: 07/02/2023] Open
Abstract
•The first genome of GII.3 [P25] strain isolated in China was determined by NGS. •About 19 unique amino acid substitutions were identified in the VP1 region of GII.3 [P25]. •Antigenic variation may have contributed to the re-emerge of GII.3 [P25] strains.
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Affiliation(s)
- Peng Zhang
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China
| | - Deshun Xu
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China
| | - Teng Liu
- Wuxing District Center for Disease Control and Prevention of Huzhou, Huzhou, 313000, China
| | - Liping Chen
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China
| | - Lei Ji
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China.
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9
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Bai GH, Tsai MC, Lin SC, Hsu YH, Chen SY. Unraveling the interplay between norovirus infection, gut microbiota, and novel antiviral approaches: a comprehensive review. Front Microbiol 2023; 14:1212582. [PMID: 37485533 PMCID: PMC10359435 DOI: 10.3389/fmicb.2023.1212582] [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: 04/26/2023] [Accepted: 06/15/2023] [Indexed: 07/25/2023] Open
Abstract
Norovirus infection is a leading cause of acute gastroenteritis worldwide and can also cause harmful chronic infections in individuals with weakened immune systems. The role of the gut microbiota in the interactions between the host and noroviruses has been extensively studied. While most past studies were conducted in vitro or focused on murine noroviruses, recent research has expanded to human noroviruses using in vivo or ex vivo human intestinal enteroids culture studies. The gut microbiota has been observed to have both promoting and inhibiting effects on human noroviruses. Understanding the interaction between noroviruses and the gut microbiota or probiotics is crucial for studying the pathogenesis of norovirus infection and its potential implications, including probiotics and vaccines for infection control. Recently, several clinical trials of probiotics and norovirus vaccines have also been published. Therefore, in this review, we discuss the current understanding and recent updates on the interactions between noroviruses and gut microbiota, including the impact of norovirus on the microbiota profile, pro-viral and antiviral effects of microbiota on norovirus infection, the use of probiotics for treating norovirus infections, and human norovirus vaccine development.
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Affiliation(s)
- Geng-Hao Bai
- Department of Internal Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Meng-Chen Tsai
- Department of General Medicine, Taipei Medical University Hospital, Taipei, Taiwan
| | - Sheng-Chieh Lin
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Pediatrics, Division of Allergy, Asthma and Immunology, Shuang Ho Hospital, New Taipei, Taiwan
| | - Yi-Hsiang Hsu
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Shih-Yen Chen
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Pediatrics, Division of Pediatric Gastroenterology and Hepatology, Shuang Ho Hospital, New Taipei, Taiwan
- TMU Research Center for Digestive Medicine, Taipei Medical University, Taipei, Taiwan
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Lin SC, Bai GH, Lin PC, Chen CY, Hsu YH, Lee YC, Chen SY. Molecular and Genetics-Based Systems for Tracing the Evolution and Exploring the Mechanisms of Human Norovirus Infections. Int J Mol Sci 2023; 24:ijms24109093. [PMID: 37240438 DOI: 10.3390/ijms24109093] [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: 04/04/2023] [Revised: 05/09/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Human noroviruses (HuNoV) are major causes of acute gastroenteritis around the world. The high mutation rate and recombination potential of noroviruses are significant challenges in studying the genetic diversity and evolution pattern of novel strains. In this review, we describe recent advances in the development of technologies for not only the detection but also the analysis of complete genome sequences of noroviruses and the future prospects of detection methods for tracing the evolution and genetic diversity of human noroviruses. The mechanisms of HuNoV infection and the development of antiviral drugs have been hampered by failure to develop the infectious virus in a cell model. However, recent studies have demonstrated the potential of reverse genetics for the recovery and generation of infectious viral particles, suggesting the utility of this genetics-based system as an alternative for studying the mechanisms of viral infection, such as cell entry and replication.
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Affiliation(s)
- Sheng-Chieh Lin
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei City 11031, Taiwan
- Division of Allergy, Asthma, and Immunology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Geng-Hao Bai
- Department of Internal Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei City 10002, Taiwan
| | - Pei-Chun Lin
- Division of Pediatric Gastroenterology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Chung-Yung Chen
- Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan City 32023, Taiwan
- Center for Nanotechnology, Institute of Biomedical Technology, Chung Yuan Christian University, Taoyuan City 32023, Taiwan
| | - Yi-Hsiang Hsu
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yuan-Chang Lee
- Department of Infectious Diseases, School of Medicine, College of Medicine, Taipei Medical University, Taipei City 11031, Taiwan
- Department of Infectious Diseases, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Shih-Yen Chen
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei City 11031, Taiwan
- Division of Pediatric Gastroenterology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
- TMU Research Center for Digestive Medicine, Taipei Medical University, Taipei City 11031, Taiwan
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Zhang Q, Zhu S, Zhang X, Su L, Ni J, Zhang Y, Fang L. Recent insights into reverse genetics of norovirus. Virus Res 2023; 325:199046. [PMID: 36657615 DOI: 10.1016/j.virusres.2023.199046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 12/23/2022] [Accepted: 01/15/2023] [Indexed: 01/18/2023]
Abstract
Norovirus is the leading cause of viral gastroenteritis globally, and poses substantial threats to public health. Despite substantial progress made in preventing norovirus diseases, the lack of a robust virus culture system has hampered biological research and effective strategies to combat this pathogen. Reverse genetic system is the technique to generate infectious viruses from cloned genetic constructs, which is a powerful tool for the investigation of viral pathogenesis and for the development of novel drugs and vaccines. The strategies of reverse genetics include bacterial artificial chromosomes, vaccinia virus vectors, and entirely plasmid-based systems. Since each strategy has its pros and cons, choosing appropriate approaches will greatly improve the efficiency of virus rescue. Reverse genetic systems that have been employed for norovirus greatly extend its life cycle and facilitate the development of medical countermeasures. In this review, we summarize the current knowledge on the structure, transmission, genetic evolution and clinical manifestations of norovirus, and describe recent advances in the studies of norovirus reverse genetics as well as its future prospects for therapeutics and vaccine development.
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Affiliation(s)
- Qinyi Zhang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, China; Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Shuirong Zhu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | | | - Lingxuan Su
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jun Ni
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yanjun Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China.
| | - Lei Fang
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China.
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Gao J, Zhang Z, Xue L, Li Y, Cheng T, Meng L, Li Y, Cai W, Hong X, Zhang J, Wang J, Chen M, Ye Q, Ding Y, Wu Q. GII.17[P17] and GII.8[P8] noroviruses showed different RdRp activities associated with their epidemic characteristics. J Med Virol 2023; 95:e28216. [PMID: 36254681 DOI: 10.1002/jmv.28216] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/23/2022] [Accepted: 10/07/2022] [Indexed: 01/11/2023]
Abstract
Norovirus is the primary foodborne pathogenic agent causing viral acute gastroenteritis. It possesses broad genetic diversity and the prevalence of different genotypes varies substantially. However, the differences in RNA-dependent RNA polymerase (RdRp) activity among different genotypes of noroviruses remain unclear. In this study, the molecular mechanism of RdRp activity difference between the epidemic strain GII.17[P17] and the non-epidemic strain GII.8[P8] was characterized. By evaluating the evolutionary history of RdRp sequences with Markov Chain Monte Carlo method, the evolution rate of GII.17[P17] variants was higher than that of GII.8[P8] variants (1.22 × 10-3 nucleotide substitutions/site/year to 9.31 × 10-4 nucleotide substitutions/site/year, respectively). The enzyme catalytic reaction demonstrated that the Vmax value of GII.17[P17] RdRp was 2.5 times than that of GII.8[P8] RdRp. And the Km of GII.17[P17] and GII.8[P8] RdRp were 0.01 and 0.15 mmol/L, respectively. Then, GII.8[P8] RdRp fragment mutants (A-F) were designed, among which GII.8[P8]-A/B containing the conserved motif G/F were found to have significant effects on improving RdRp activity. The Km values of GII.8[P8]-A/B reached 0.07 and 0.06 mmol/L, respectively. And their Vmax values were 1.34 times than that of GII.8[P8] RdRp. In summary, our results suggested that RdRp activities were correlated with their epidemic characteristics. These findings will ultimately provide a better understanding in replication mechanism of noroviruses and development of antiviral drugs.
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Affiliation(s)
- Junshan Gao
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong, Guangzhou, China
| | - Zilei Zhang
- Inspection and Quarantine Technology Communication Department, Shanghai Customs College, Shanghai, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong, Guangzhou, China
| | - Ying Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong, Guangzhou, China
| | - Tong Cheng
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong, Guangzhou, China
| | - Luobing Meng
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong, Guangzhou, China
| | - Yijing Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong, Guangzhou, China
| | - Weicheng Cai
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong, Guangzhou, China
| | - Xiaojing Hong
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong, Guangzhou, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong, Guangzhou, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong, Guangzhou, China
| | - Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong, Guangzhou, China
| | - Yu Ding
- Department of Food Science & Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong, Guangzhou, China
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Pooled prevalence and genetic diversity of norovirus in Africa: a systematic review and meta-analysis. Virol J 2022; 19:115. [PMID: 35765033 PMCID: PMC9238157 DOI: 10.1186/s12985-022-01835-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/02/2022] [Indexed: 12/04/2022] Open
Abstract
Background Noroviruses are the leading cause of acute gastroenteritis in all age groups globally. The problem is magnified in developing countries including Africa. These viruses are highly prevalent with high genetic diversity and fast evolution rates. With this dynamicity, there are no recent review in the past five years in Africa. Therefore, this review and meta-analysis aimed to assess the prevalence and genetic diversity of noroviruses in Africa and tried to address the change in the prevalence and genetic diverisity the virus has been observed in Africa and in the world.
Methods Twenty-one studies for the pooled prevalence, and 11 out of the 21 studies for genetic characterization of norovirus were included. Studies conducted since 2006, among symptomatic cases of all age groups in Africa, conducted with any study design, used molecular diagnostic methods and reported since 2015, were included and considered for the main meta-analysis. PubMed, Cochrane Library, and Google Scholar were searched to obtain the studies. The quality the studies was assessed using the JBI assessment tool. Data from studies reporting both asymptomatic and symptomatic cases, that did not meet the inclusion criteria were reviewed and included as discussion points. Data was entered to excel and imported to STATA 2011 to compute the prevalence and genetic diversity. Heterogeneity was checked using I2 test statistics followed by subgroup and sensitivity analysis. Publication bias was assessed using a funnel plot and eggers test that was followed by trim and fill analysis. Result The pooled prevalence of norovirus was 20.2% (95% CI: 15.91, 24.4). The highest (36.3%) prevalence was reported in Ghana. Genogroup II noroviruses were dominant and reported as 89.5% (95% CI: 87.8, 96). The highest and lowest prevalence of this genogroup were reported in Ethiopia (98.3%), and in Burkina Faso (72.4%), respectively. Diversified genotypes had been identified with an overall prevalence of GII. 4 NoV (50.8%) which was followed by GII.6, GII.17, GI.3 and GII.2 with a pooled prevalence of 7.7, 5.1, 4.6, and 4.2%, respectively. Conclusion The overall pooled prevalence of norovirus was high in Africa with the dominance of genogroup II and GII.4 genotype. This prevalence is comparable with some reviews done in the same time frame around the world. However, in Africa, an in increasing trained of pooled prevalence had been reported through time. Likewise, a variable distribution of non-GII.4 norovirus genotypes were reported as compared to those studies done in the world of the same time frame, and those previous reviews done in Africa. Therefore, continuous surveillance is required in Africa to support future interventions and vaccine programs. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-022-01835-w.
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Kendra JA, Tohma K, Parra GI. Global and regional circulation trends of norovirus genotypes and recombinants, 1995-2019: A comprehensive review of sequences from public databases. Rev Med Virol 2022; 32:e2354. [PMID: 35481689 PMCID: PMC9542180 DOI: 10.1002/rmv.2354] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/16/2022] [Accepted: 04/01/2022] [Indexed: 12/25/2022]
Abstract
Human noroviruses are the leading global cause of viral gastroenteritis. Attempts at developing effective vaccines and treatments against norovirus disease have been stymied by the extreme genetic diversity and rapid geographic distribution of these viruses. The emergence and replacement of predominantly circulating norovirus genotypes has primarily been attributed to mutations on the VP1 capsid protein leading to genetic drift, and more recently to recombination events between the ORF1/ORF2 junction. However, large‐scale research into the historical and geographic distribution of recombinant norovirus strains has been limited in the literature. We performed a comprehensive historical analysis on 30,810 human norovirus sequences submitted to public databases between the years 1995 and 2019. During this time, 37 capsid genotypes and 56 polymerase types were detected across 90 different countries, and 97 unique recombinant genomes were also identified. GII.4, both capsid and polymerase, was the predominately circulating type worldwide for the majority of this time span, save for a brief swell of GII.17 and GII.2 capsid genotypes and a near‐total eclipse by GII.P16, GII.P21 and GII.P31 beginning in 2013. Interestingly, an analysis of 4067 recombinants found that 50.2% (N = 2039) of all recorded sequences belonged to three recently emerged recombinant strains: GII.2[P16], GII.4[P31], and GII.4[P16]. This analysis should provide an important historical foundation for future studies that evaluate the emergence and distribution of noroviruses, as well as the design of cross‐protective vaccines.
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Affiliation(s)
- Joseph A Kendra
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, USA
| | - Kentaro Tohma
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, USA
| | - Gabriel I Parra
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, USA
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15
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Zheng GL, Zhu ZX, Cui JL, Yu JM. Evolutionary Analyses of Emerging GII.2[P16] and GII.4 Sydney [P16] Noroviruses. Virus Evol 2022; 8:veac030. [PMID: 35450165 PMCID: PMC9019527 DOI: 10.1093/ve/veac030] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/22/2022] [Accepted: 03/30/2022] [Indexed: 11/14/2022] Open
Abstract
GII.2[P16] and GII.4 Sydney [P16] are currently the two predominant norovirus genotypes. This study sought to clarify their evolutionary patterns by analyzing the major capsid VP1 and RNA-dependent RNA polymerase (RdRp) genes. Sequence diversities were analyzed at both nucleotide and amino acid levels. Selective pressures were evaluated with the Hyphy package in different models. Phylogenetic trees were constructed by the maximum likelihood method from full VP1 sequences, and evolutionary rates were estimated by the Bayesian Markov Chain Monte Carlo approach. The results showed that (1) several groups of tightly linked mutations between the RdRp and VP1 genes were detected in the GII.2[P16] and GII.4[P16] noroviruses, and most of these mutations were synonymous, which may lead to a better viral fitness to the host; (2) although the pattern of having new GII.4 variants every 2–4 years has been broken, both the pre- and the post-2015 Sydney VP1 had comparable evolutionary rates to previously epidemic GII.4 variants, and half of the major antigenic sites on GII.4 Sydney had residue substitutions and several caused obvious changes in the carbohydrate-binding surface that may potentially alter the property of the virus; and (3) GII.4 Sydney variants during 2018–21 showed geographical specificity in East Asia, South Asia, and North America; the antigenic sites of GII.2 are strictly conserved, but the GII.2 VP1 chronologically evolved into nine different sublineages over time, with sublineage IX being the most prevalent one since 2018. This study suggested that both VP1 and RdRp of the GII.2[P16] and GII.4 Sydney [P16] noroviruses exhibited different evolutionary directions. GII.4[P16] is likely to generate potential novel epidemic variants by accumulating mutations in the P2 domain, similar to previously epidemic GII.4 variants, while GII.2[P16] has conserved predicted antigenicity and may evolve by changing the properties of nonstructural proteins, such as polymerase replicational fidelity and efficiency. This study expands the understanding of the evolutionary dynamics of GII.2[P16] and GII.4[P16] noroviruses and may predict the emergence of new variants.
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Affiliation(s)
- Guo-li Zheng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing 100044, China
| | - Zheng-xi Zhu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing 100044, China
| | - Jia-le Cui
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing 100044, China
| | - Jie-mei Yu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing 100044, China
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Xia X, Yang H, Cao J, Zhang J, He Q, Deng R. Isothermal nucleic acid amplification for food safety analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116641] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Genomic stratification and differential natural selection signatures among human norovirus genogroup II isolates. Arch Virol 2022; 167:1235-1245. [PMID: 35322317 PMCID: PMC8942050 DOI: 10.1007/s00705-022-05396-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/12/2022] [Indexed: 11/27/2022]
Abstract
Noroviruses (NoVs), which are members of the family Caliciviridae, are the most common cause of gastroenteritis in humans. Ten NoV genogroups have been reported so far. Of these, genogroup II (GII) is the most prevalent, and it causes serious infections worldwide. The complete genome sequences of NoV GII isolates from different geographical regions were retrieved from the public database. The model-based clustering approach, implemented in the STRUCTURE resource, was employed for assessment of genetic composition. The MEGA X and IQ Tree tools were used for phylogenetic analysis. Genome-wide natural selection analysis was performed using maximum-likelihood-based methods. The demographic features of NoV GII genome sequences were assessed using the BEAST package. All of the NoV GII sequences initially clustered into two main subpopulations at significant K = 2, where the genotype GII.4 samples clearly split from the rest of the genotypes. This indicates a marked genetic distinction between norovirus GII.4 and non-GII.4 samples. Phylogenetic analysis showed the presence of five distinct subclades for genotype GII.2 and seven subclades for GII.4 samples. Several isolates with admixed ancestry were identified that constituted distinct subclusters in the phylogenetic tree. No continental-specific genetic distinctions were observed among the NoV GII samples. Significant genomic signatures of both positive and negative natural selection were identified across the NoV GII genes. A differential pattern of positive selection signals was inferred between the GII.4 and non-GII.4 genotypes. The demographic analysis revealed an increase in the effective population size of NoV GII during 2009-2010, followed by a rapid fall in 2015.
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Epidemiological and Genetic Characterization of Norovirus Outbreaks That Occurred in Catalonia, Spain, 2017–2019. Viruses 2022; 14:v14030488. [PMID: 35336893 PMCID: PMC8955687 DOI: 10.3390/v14030488] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 01/27/2023] Open
Abstract
Molecular characterization of human norovirus (HuNoV) genotypes enhances the understanding of viral features and illustrates distinctive evolutionary patterns. The aim of our study was to describe the prevalence of the genetic diversity and the epidemiology of the genotypes involved in HuNoV outbreaks in Catalonia (Spain) between 2017 and 2019. A total of 100 HuNoV outbreaks were notified with the predominance of GII (70%), followed by GI (27%) and mixed GI/GII (3%). Seasonality was observed for GII outbreaks only. The most prevalent genotypes identified were GII.4[P31] Sydney 2012, GII.4[P16] Sydney 2012 and GII.2[P16]. As compared to person-to-person (P/P) transmitted outbreaks, foodborne outbreaks showed significantly higher attack rates and lower duration. The average attack rate was higher in youth hostel/campgrounds compared to nursing homes. Only genotypes GI.4[P4], GII.2[P16], GII.4[P16], GII.4[P31] and GII.17[P17] were consistently detected every year, and only abundance of GII.2[P16] showed a negative trend over time. GII.4 Sydney 2012 outbreaks were significantly associated to nursing homes, while GII.2[P16] and GI.3[P3] were most frequently identified in youth hostel/campgrounds. The average attack rate was significantly higher when comparing GII.2[P16] vs. GI.4[P4], GII.2[P16] vs. GII.4[P31] Sydney 2012, and GII.6[P7] vs. GII.4[P31] Sydney 2012. No correlations were found between genotype and outbreak duration or age of affected individuals.
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Du J, Wu G, Cui C, Yu C, Cui Y, Guo L, Liu Y, Liu Y, Wang W, Liu C, Fu Z, Li M, Guo S, Yu X, Yang Y, Duan M, Xu G, Wang L. Finger printing human norovirus-like particles by capillary isoelectric focusing with whole column imaging detection. Virus Res 2022; 311:198700. [DOI: 10.1016/j.virusres.2022.198700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 01/24/2023]
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Li W, Yan H, Liu B, Tian Y, Chen Y, Jia L, Gao Z, Wang Q. Epidemiological characteristics and genetic diversity of norovirus infections among outpatient children with diarrhea under 5 years of age in Beijing, China, 2011-2018. Gut Pathog 2021; 13:77. [PMID: 34952625 PMCID: PMC8709959 DOI: 10.1186/s13099-021-00473-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/07/2021] [Indexed: 11/10/2022] Open
Abstract
Background Human noroviruses are the leading cause of sporadic cases and outbreaks of viral acute gastroenteritis in all age groups worldwide. Methods Epidemiological data and fecal specimens were collected between January 2011 and December 2018 from 4911 children < 5 years of age with diarrhea in three districts of Beijing. From 2011 to 2013, One-Step Reverse Transcription Polymerase Chain Reaction (RT-PCR) was used to detect noroviruses, and from January 2014 to December 2018, norovirus GI and GII were screened using duplex quantitative real-time RT-PCR (qRT-PCR). One-Step RT-PCR and RT-seminested PCR were performed to amplify the RNA-dependent polymerase and capsid genes of noroviruses in positive sample. Amplified products were sequenced directly; norovirus was typed using the online Norovirus Genotyping Tool v2.0 and phylogenetic analyses were conducted using MEGA-X. Results From 2011 to 2018, noroviruses were detected in 16.5% of specimens from children with diarrhea. The highest prevalence was observed in children aged 12 to 23 months (22.4%, 319/1421), followed by children aged 6 to 11 months (17.6%, 253/1441). The highest prevalence of norovirus infections occurred in autumn followed by winter, spring, and summer. From 2011 to 2018, the most prevalent dual types (genotype and polymerase type) were GII.4 Sydney[P31] (51.6%, 239/463), followed by GII.3[P12] (24.0%, 111/463), GII.4 2006b[P4 2006b] (7.3%, 34/463), GII.2[P16] (5.0%, 23/463), GII.17[P17] (2.6%, 12/463) and GII.6[P7] (2.6%, 12/463). GII.4 2006b[P4 2006b] predominated in 2011 and 2012. GII.4 Sydney[P31] predominated from 2013 to 2018. In total, 15 genotypes, 15 P-types and 19 dual types were detected in this study, reflecting the genetic diversity. Conclusions There were significant epidemiological characteristics and genetic diversity among outpatient children with norovirus infections < 5 years of age in Beijing from 2011 to 2018. These characteristics differ from those of norovirus outbreaks in Beijing. The complete genome sequences of each genotype are needed to better understand norovirus evolutionary mechanisms.
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Affiliation(s)
- Weihong Li
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China
| | - Hanqiu Yan
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China
| | - Baiwei Liu
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China
| | - Yi Tian
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China
| | - Yanwei Chen
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China
| | - Lei Jia
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China
| | - Zhiyong Gao
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China.
| | - Quanyi Wang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China.
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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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22
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Fang Y, Dong Z, Liu Y, Wang W, Hou M, Wu J, Wang L, Zhao Y. Molecular epidemiology and genetic diversity of norovirus among hospitalized children with acute gastroenteritis in Tianjin, China, 2018-2020. BMC Infect Dis 2021; 21:682. [PMID: 34261441 PMCID: PMC8277986 DOI: 10.1186/s12879-021-06375-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/25/2021] [Indexed: 02/07/2023] Open
Abstract
Background Norovirus (NoV) is a major cause of viral acute gastroenteritis (AGE) in children worldwide. Epidemiological analysis with respect to the virus strains is limited in China. This study aimed to investigate the prevalence, patterns, and molecular characteristics of NoV infection among children with AGE in China. Methods A total 4848 stool samples were collected from children who were admitted with AGE in Tianjin Children’s Hospital from August 2018 to July 2020. NoV was preliminarily detected using real-time reverse transcription polymerase chain reaction (RT-PCR). Partial sequences of the RNA-dependent RNA polymerase (RdRp) and capsid genes of positive samples were amplified by conventional RT-PCR and then sequenced. The NoV genotype was determined by online Norovirus Typing Tool Version 2.0, and phylogenetic analysis was conducted using MEGA 6.0. Results The prevalence of NoV was 26.4% (1280/4848). NoV was detected in all age groups, with the 7–12 months group having the highest detection rate (655/2014, 32.5%). NoV was detected during most part of the year with higher frequency in winter than other seasons. Based on the genetic analysis of RdRp, GII. Pe was the most predominant genotype detected at 70.7% (381/539) followed by GII.P12 at 25.4% (137/539). GII.4 was the most predominant capsid genotype detected at 65.3% (338/518) followed by GII.3 at 26.8% (139/518). Based on the genetic analysis of RdRp and capsid sequences, the strains were clustered into 10 RdRp–capsid genotypes: GII.Pe-GII.4 Sydney 2012 (65.5%), GII.P12-GII.3 (27.2%), GII.P16-GII.2 (1.8%), GII.P12-GII.2 (0.2%), GII.P17-GII.17 (1.1%), GII.Pe-GII.3 (1.8%), GII.Pe-GII.2 (1.1%), GII.Pe-GII.1 (0.4%), GII.16-GII.4 Sydney 2012 (0.7%), and GII.P7-GII.6 (0.2%). The predominant NoV genotypes changed from GII.Pe-GII.4 Sydney 2012 and GII.P12-GII.3 between August 2018 and July 2019 to GII.Pe-GII.4 Sydney 2012 and GII.P16-GII.2 between August 2019 and July 2020. The patients with GII.Pe-GII.4 Sydney 2012 genotype were more likely to suffer from vomiting symptom than those with GII.P12-GII.3. Conclusions NoV is an important pathogen responsible for viral AGE among children in China. GII.Pe-GII.4 Sydney 2012 and GII.P12-GII.3 were major recombinant genotypes. Knowledge of circulating genotypes and seasonal trends is of great importance for disease prevention and surveillance.
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Affiliation(s)
- Yulian Fang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, No.238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Zhaoying Dong
- Department of Neurology, Tianjin Union Medical Centre, No. 190 Jieyuan Road, Hongqiao District, Tianjin, 300121, China
| | - Yan Liu
- Clinical Pediatric College of Tianjin Medical University, No.238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Wei Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, No.238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Mengzhu Hou
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, No.238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Jinying Wu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, No.238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Lu Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, No.238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Yu Zhao
- Department of Digestion, Tianjin Children's Hospital (Children's Hospital of Tianjin University), No.238 Longyan Road, Beichen District, Tianjin, 300134, China.
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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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24
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Misumi M, Nishiura H. Long-term dynamics of Norovirus transmission in Japan, 2005-2019. PeerJ 2021; 9:e11769. [PMID: 34306831 PMCID: PMC8280881 DOI: 10.7717/peerj.11769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/22/2021] [Indexed: 11/20/2022] Open
Abstract
Norovirus continues to evolve, adjusting its pathogenesis and transmissibility. In the present study, we systematically collected datasets on Norovirus outbreaks in Japan from 2005 to 2019 and analyzed time-dependent changes in the asymptomatic ratio, the probability of virus detection, and the probability of infection given exposure. Reports of 1,728 outbreaks were published, and feces from all involved individuals, including those with asymptomatic infection, were tested for virus in 434 outbreaks. We found that the outbreak size did not markedly change over this period, but the variance in outbreak size increased during the winter (November–April). Assuming that natural history parameters did not vary over time, the asymptomatic ratio, the probability of virus detection, and the probability of infection given exposure were estimated to be 18.6%, 63.3% and 84.5%, respectively. However, a model with time-varying natural history parameters yielded better goodness-of-fit and suggested that the asymptomatic ratio varied by year. The asymptomatic ratio was as high as 25.8% for outbreaks caused by genotype GII.4 noroviruses. We conclude that Norovirus transmissibility has not changed markedly since 2005, and that yearly variation in the asymptomatic ratio could potentially be explained by the circulating dominant genotype.
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Affiliation(s)
- Megumi Misumi
- Graduate School of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan.,Rumoi City Hospital, Rumoi, Hokkaido, Japan
| | - Hiroshi Nishiura
- Graduate School of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan.,School of Public Health, Kyoto University, Kyoto, Japan
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25
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Abstract
The evolution of many microbes and pathogens, including circulating viruses such as seasonal influenza, is driven by immune pressure from the host population. In turn, the immune systems of infected populations get updated, chasing viruses even farther away. Quantitatively understanding how these dynamics result in observed patterns of rapid pathogen and immune adaptation is instrumental to epidemiological and evolutionary forecasting. Here we present a mathematical theory of coevolution between immune systems and viruses in a finite-dimensional antigenic space, which describes the cross-reactivity of viral strains and immune systems primed by previous infections. We show the emergence of an antigenic wave that is pushed forward and canalized by cross-reactivity. We obtain analytical results for shape, speed, and angular diffusion of the wave. In particular, we show that viral-immune coevolution generates an emergent timescale, the persistence time of the wave's direction in antigenic space, which can be much longer than the coalescence time of the viral population. We compare these dynamics to the observed antigenic turnover of influenza strains, and we discuss how the dimensionality of antigenic space impacts the predictability of the evolutionary dynamics. Our results provide a concrete and tractable framework to describe pathogen-host coevolution.
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Kondapi DS, Ramani S, Estes MK, Atmar RL, Okhuysen PC. Norovirus in Cancer Patients: A Review. Open Forum Infect Dis 2021; 8:ofab126. [PMID: 34189156 PMCID: PMC8232388 DOI: 10.1093/ofid/ofab126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/10/2021] [Indexed: 12/15/2022] Open
Abstract
Norovirus (NoV) is the leading cause of viral-related diarrhea in cancer patients, in whom it can be chronic, contributing to decreased quality of life, interruption of cancer care, malnutrition, and altered mucosal barrier function. Immunosuppressed cancer patients shed NoV for longer periods of time than immunocompetent hosts, favoring quasispecies development and emergence of novel NoV variants. While nucleic acid amplification tests (NAATs) for NoV diagnosis have revolutionized our understanding of NoV burden of disease, not all NAATs provide information on viral load or infecting genotype. There is currently no effective antiviral or vaccine for chronic NoV infections. Screening for inhibitors of NoV replication in intestinal organoid culture models and creation of NoV-specific adoptive T cells are promising new strategies to develop treatments for chronic NoV in immunosuppressed patients. Herein we summarize data on the epidemiology, clinical manifestations, diagnostic challenges, and treatment of NoV infection in patients with cancer.
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Affiliation(s)
- Divya Samantha Kondapi
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Section of Infectious Diseases, Baylor College of Medicine, Houston, Texas, USA
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Robert L Atmar
- Section of Infectious Diseases, Baylor College of Medicine, Houston, Texas, USA
| | - Pablo C Okhuysen
- Infection Control and Employee Health, Division of Internal Medicine, Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Ma H, Yue H, Luo Y, Li S, Tang C. First detection of canine norovirus in dogs and a complete GVI.2 genome in mainland China. INFECTION GENETICS AND EVOLUTION 2021; 92:104879. [PMID: 33901686 DOI: 10.1016/j.meegid.2021.104879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/28/2020] [Accepted: 04/16/2021] [Indexed: 11/25/2022]
Abstract
Canine norovirus (CNV) is a diarrhea-causing pathogen in canines. In this study, 268 canine diarrheic fecal samples were collected from 13 pet hospitals across three provinces in China between March 2017 and May 2019, and 7.8% (21/268) samples were detected as CNV-positive by RT-PCR. Phylogenetic analysis of twenty-one CNV RdRp fragments showed that eighteen of the strains clustered in GVI.2, two clustered in GVI.1 and one clustered in GIV.2. The complete RdRp, VP1, and VP2 genes of four GVI.2 strains obtained from three provinces were successfully sequenced. Phylogenetic analyses based on the RdRp, VP1, and VP2 genes showed that the GVI.2 strains from this study were closely related to USA GVI.2 strains. The complete genome of GVI.2 strain Dog/M9/18/CH was successfully sequenced, it was 7905 nucleotides (nt) in length and shared 95.9% nt identity with the sole available, nearly full-length genome of GVI.2 strain genome. To our knowledge, this is first description of the molecular prevalence of CNV in mainland China, and the first report of a complete GVI.2 genome. These findings will extend our understanding of epidemics and the genetic evolution of CNV.
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Affiliation(s)
- Huiqiang Ma
- College of Life Science and Technology, Southwest Minzu University, Chengdu, China
| | - Hua Yue
- College of Life Science and Technology, Southwest Minzu University, Chengdu, China; Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Chengdu, China
| | - Yingying Luo
- College of Life Science and Technology, Southwest Minzu University, Chengdu, China
| | - Siyi Li
- College of Life Science and Technology, Southwest Minzu University, Chengdu, China
| | - Cheng Tang
- College of Life Science and Technology, Southwest Minzu University, Chengdu, China; Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Chengdu, China.
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28
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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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29
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Walker FC, Hassan E, Peterson ST, Rodgers R, Schriefer LA, Thompson CE, Li Y, Kalugotla G, Blum-Johnston C, Lawrence D, McCune BT, Graziano VR, Lushniak L, Lee S, Roth AN, Karst SM, Nice TJ, Miner JJ, Wilen CB, Baldridge MT. Norovirus evolution in immunodeficient mice reveals potentiated pathogenicity via a single nucleotide change in the viral capsid. PLoS Pathog 2021; 17:e1009402. [PMID: 33705489 PMCID: PMC7987144 DOI: 10.1371/journal.ppat.1009402] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 03/23/2021] [Accepted: 02/17/2021] [Indexed: 02/06/2023] Open
Abstract
Interferons (IFNs) are key controllers of viral replication, with intact IFN responses suppressing virus growth and spread. Using the murine norovirus (MNoV) system, we show that IFNs exert selective pressure to limit the pathogenic evolutionary potential of this enteric virus. In animals lacking type I IFN signaling, the nonlethal MNoV strain CR6 rapidly acquired enhanced virulence via conversion of a single nucleotide. This nucleotide change resulted in amino acid substitution F514I in the viral capsid, which led to >10,000-fold higher replication in systemic organs including the brain. Pathogenicity was mediated by enhanced recruitment and infection of intestinal myeloid cells and increased extraintestinal dissemination of virus. Interestingly, the trade-off for this mutation was reduced fitness in an IFN-competent host, in which CR6 bearing F514I exhibited decreased intestinal replication and shedding. In an immunodeficient context, a spontaneous amino acid change can thus convert a relatively avirulent viral strain into a lethal pathogen.
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Affiliation(s)
- Forrest C. Walker
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Ebrahim Hassan
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Stefan T. Peterson
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Rachel Rodgers
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Lawrence A. Schriefer
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Cassandra E. Thompson
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Yuhao Li
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Gowri Kalugotla
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Carla Blum-Johnston
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Dylan Lawrence
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Broc T. McCune
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Vincent R. Graziano
- Departments of Laboratory Medicine & Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Larissa Lushniak
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sanghyun Lee
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Alexa N. Roth
- Department of Molecular Genetics & Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Stephanie M. Karst
- Department of Molecular Genetics & Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Timothy J. Nice
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Jonathan J. Miner
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Craig B. Wilen
- Departments of Laboratory Medicine & Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Megan T. Baldridge
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
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Epidemiology of norovirus gastroenteritis in hospitalized children under five years old in western China, 2015-2019. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2021; 54:918-925. [PMID: 33531203 DOI: 10.1016/j.jmii.2021.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/30/2020] [Accepted: 01/06/2021] [Indexed: 02/08/2023]
Abstract
OBJECTIVES Norovirus is associated with one-fifth of all gastroenteritis cases, but basic epidemiological data is lacking, especially in developing countries. As long-term surveillance on norovirus gastroenteritis is scarce in western China, this study aims to update the epidemiological knowledge of norovirus gastroenteritis and to characterize the genotypes of norovirus strains. METHODS Stool samples were collected from hospitalized children under 5 years old with gastroenteritis in Chengdu, China. All samples were tested for norovirus as well as rotavirus, sapovirus, enteric adenovirus, and astrovirus by real-time RT-PCR. RdRp and VP1 genes were sequenced in norovirus-positive samples to investigate viral phylogenies. RESULTS Of the 1181 samples collected from 2015 to 2019, 242 (20.5%) were positive for norovirus. Among norovirus-positive cases, 65 cases had co-infection with another virus; norovirus/enteric adenovirus was most frequently detected (50.8%, 33/65). The highest positive rate was observed in children aged 13-18 months (23.7%, 68/287). Norovirus infection peaked in autumn (36.6%, 91/249), followed by summer (20.3%, 70/345). Pearson correlation analysis showed significant correlation between the norovirus-positive rate and humidity (r = 0.773, P < 0.05). GII.4 Sydney 2012 [P31] (48.5%, 79/163) and GII.3 [P12] (35.6%, 58/163) were the dominant norovirus strains. CONCLUSIONS Norovirus has become one of the most common causes of viral gastroenteritis in children under 5 years old in western China. Continuous monitoring is imperative for predicting the emergence of new epidemic strains and for current vaccine development.
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Pairing of Parental Noroviruses with Unequal Competitiveness Provides a Clear Advantage for Emergence of Progeny Recombinants. Appl Environ Microbiol 2021; 87:AEM.02015-20. [PMID: 33187997 PMCID: PMC7848925 DOI: 10.1128/aem.02015-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/02/2020] [Indexed: 11/20/2022] Open
Abstract
Genetic recombination plays a pivotal role in the appearance of human norovirus recombinants that cause global epidemics. However, the factors responsible for the appearance of these recombinants remains largely unknown. In this study, we revealed a selective pressure that restricts parental combinations leading to the emergence of norovirus recombinants. To investigate traces of emerging novel recombinants and their parents in the human population, we isolated mass nucleotide sequence clones of human norovirus genogroups I and II in sewage-affected waters over a 4-year sampling period. Fourteen different phylogenetic combinations of recombinants and their parents were defined from the dozens of phylogenetic lineages circulating in the human population. To evaluate the probability of these combinations, parental lineages of each recombinant were categorized into two groups as HP (relatively higher-competitiveness parents) and LP (relatively lower-competitiveness parents), according to their relative detection frequency. Strong categorization of HP and LP was confirmed by tests with modified data and additional variables. An algorithm that was developed in this study to visualize the chance of mixed infection between parents revealed that HP lineages have a higher chance of mixed infection than LP lineages in the human population. Three parental pairing types in recombinants were defined: HP-HP, HP-LP, and LP-LP. Among these, most recombinants were identified as HP-LP, despite the prediction of dominant emergence of HP-HP-type recombinants. These results suggest that nature favors recombinants of human norovirus that originate from parental pairing of heterogeneous competitiveness.IMPORTANCE Novel recombinants, generated from inter- and intraspecies recombination of norovirus lineages, often emerge and pose a threat to public health. However, the factors determining emergence of these particular recombinants from all possible combinations of parental lineages remain largely unknown. Therefore, current investigations on these recombinants are inevitably limited to postepidemic analyses, which merely identify genetic or phenotypic changes in the newly emerged recombinants compared to their parents. Here, we provide a new theoretical concept that emergence of novel recombinants could be explained by a combination of parental noroviruses thriving in the human population and those circulating at lower levels. This study could provide an additional and important rationale for the proactive environmental monitoring of potential future epidemics due to viral recombinants.
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Xie D, Chen J, Yu J, Pei F, Koroma MM, Wang L, Qiu M, Hou Y, Yu D, Zhang XF, Dai YC. Characterization of Antigenic Relatedness Among GI Norovirus Genotypes Using Serum Samples From Norovirus-Infected Patients and Mouse Sera. Front Microbiol 2020; 11:607723. [PMID: 33363528 PMCID: PMC7752868 DOI: 10.3389/fmicb.2020.607723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/11/2020] [Indexed: 12/03/2022] Open
Abstract
Characterizing diversity and the antigenic relatedness of norovirus remains a primary focus in understanding its biological properties and vaccine designs. The precise antigenic and serological features of GI genotypes have not been studied. The study represented an investigation on a gastroenteritis outbreak related to GI.3 norovirus and the three most detected GI genotypes, GI.2 (belonging to immunotype B), GI.3 and GI.9 (belonging to immunotype C), were selected to characterize their phylogenetic relationship, HBGA binding profiles and antigenic relatedness within (intra-immunotype), and between (inter-immunotypes) genotypes using mouse sera and patient’s serum samples from the GI.3 related outbreak. Wide HBGA binding profiles and evolution of binding affinity were observed in the three GI genotypes studied. A low specific blockade antibody to GI.3 in the population generated the pool of susceptible individuals and supported virus spread in the outbreak. We found strong blockade immune response in homologous strains, moderate intra-immunotype blockade but weak inter-immunotypes blockade in humans following GI.3 norovirus infections. These findings further support the immunotypes grouping and will be valuable for optimizing the design of norovirus vaccine.
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Affiliation(s)
- Dongjie Xie
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Junrui Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Jingrong Yu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Fuyu Pei
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mark Momoh Koroma
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Lu Wang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Mengsi Qiu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yuzhen Hou
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Dexian Yu
- Guangzhou Military Command Center for Disease Control and Prevention, Guangzhou, China
| | - Xu-Fu Zhang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Ying-Chun Dai
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
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Yan Y, Li Y, Shi W, Kong X, Li H, Zhang Q, Pang L, Jiang L, Liu J, Jin M, Li Y, Duan Z. An outbreak of gastroenteritis associated with a novel GII.8 sapovirus variant-transmitted by vomit in Shenzhen, China, 2019. BMC Infect Dis 2020; 20:911. [PMID: 33261582 PMCID: PMC7706173 DOI: 10.1186/s12879-020-05643-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/22/2020] [Indexed: 12/27/2022] Open
Abstract
Background Human Sapoviruses (SaVs) has been reported as one of the causative agents of acute gastroenteritis (AGE) worldwide. An outbreak of SaVs affected 482 primary school students during spring activities from February 24 to March 11, 2019 in Shenzhen City, China. Our study was aimed at determining the epidemiology of the outbreak, investigating its origins, and making a clear identification of the SaVs genetic diversity. Methods Epidemiological investigation was conducted for this AGE outbreak. Stool samples were collected for laboratory tests of causative agents. Real-time reverse-transcription polymerase chain reaction (rRT-PCR) and conventional RT-PCR were used for detecting and genotyping of SaVs. The nearly complete genome of GII.8 SaV strains were amplified and sequenced by using several primer sets designed in this study. Phylogenetic analysis was performed to characterize the genome of GII.8 SaV strains. Results The single factor analysis showed that the students who were less than 1.5 m away from the vomitus in classroom or playgroundwere susceptible (P < 0.05). Seven of 11 fecal samples from patients were positive for GII.8 SaV genotype. In this study, we obtained the genome sequence of a SaV GII.8 strain Hu/SaV/2019008Shenzhen/2019 /CHN (SZ08) and comprehensively analyzed the genetic diversity. The phylogenetic analysis showed that the GII.8 strain SZ08 formed an independent branch and became a novel variant of GII.8 genotype. Strain SZ08 harbored 11 specific amino acid variations compared with cluster A-D in full-length VP1. Conclusions This study identified SaVs as the causative agents for the AGE outbreak. Strain Hu SZ08 was clustered as independent branch and there was no recombination occurred in this strain SZ08. Further, it might become the predominant strain in diarrhea cases in the near future. Constant surveillance is required to monitor the emerging variants which will improve our knowledge of the evolution of SaVs among humans.
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Affiliation(s)
- Yuxiao Yan
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, 730000, Gansu, China.,Department of Viral Diarrhea, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Chang-ping District, Beijing, 102206, China
| | - Yuan Li
- Shenzhen Baoan Center for Disease Control and Prevention, Baoan District, Shenzhen, Guangdong Province, China
| | - Wen Shi
- Yingkou Center for Disease Control and Prevention, Yingkou, Liaoning, China
| | - Xiangyu Kong
- Department of Viral Diarrhea, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Chang-ping District, Beijing, 102206, China
| | - Huiying Li
- Department of Viral Diarrhea, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Chang-ping District, Beijing, 102206, China
| | - Qing Zhang
- Department of Viral Diarrhea, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Chang-ping District, Beijing, 102206, China
| | - Lili Pang
- Department of Viral Diarrhea, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Chang-ping District, Beijing, 102206, China
| | - Li Jiang
- The First Hospital of Lanzhou University, Donggang-xi Rd, Cheng-guan District, Lanzhou, 730000, Gansu, China
| | - Junying Liu
- Central Hospital of Zhoukou, Zhoukou, 466000, Henan, China
| | - Miao Jin
- Department of Viral Diarrhea, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Chang-ping District, Beijing, 102206, China.
| | - Yuning Li
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, 730000, Gansu, China. .,The First Hospital of Lanzhou University, Donggang-xi Rd, Cheng-guan District, Lanzhou, 730000, Gansu, China.
| | - Zhaojun Duan
- Department of Viral Diarrhea, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Chang-ping District, Beijing, 102206, China
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Nonthabenjawan N, Boonyos P, Phattanawiboon B, Towayunanta W, Chuntrakool K, Ngaopravet K, Ruchusatsawat K, Uppapong B, Sangkitporn S, Mekada E, Matsuura Y, Tatsumi M, Mizushima H. Identification of GII.14[P7] norovirus and its genomic mutations from a case of long-term infection in a post-symptomatic individual. INFECTION GENETICS AND EVOLUTION 2020; 86:104612. [PMID: 33137471 DOI: 10.1016/j.meegid.2020.104612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/24/2020] [Accepted: 10/27/2020] [Indexed: 11/17/2022]
Abstract
Norovirus is a leading cause of acute gastroenteritis worldwide. Norovirus shedding typically lasts one week to one month after the onset of diarrhea in immunocompetent hosts. The occurrence of mutations in the genome during infection has contributed to the evolution of norovirus. It has been suggested that genomic mutations in the P2-domain of capsid protein VP1, the major antigenic site for virus clearance, are involved in the evasion of host immunity and prolonged shedding of norovirus. In our previous study, we found a case of long-term shedding of GII.14 norovirus in a post-symptomatic immunocompetent individual that lasted about three months. In this study, we characterized the genomic sequence of the GII.14 strain to gain insight into the context of long-term shedding. By sequencing a 4.8 kb region of the genome corresponding to half of ORF1 and the entire ORF2 and ORF3, which encode several non-structural proteins and the structural proteins VP1 and VP2, the GII.14 strain was found to be classified as recombinant GII.14[P7]. Six point-mutations occurred during the three-month period of infection in a time-dependent manner in the genomic regions encoding RNA-dependent RNA polymerase, VP1, and VP2. Three of the six mutations were sense mutations, but no amino acid substitution was identified in the P2-domain of VP1. These results suggest that there is a mechanism by which long-term shedding of norovirus occurs in immunocompetent individuals independent of P2-domain mutations.
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Affiliation(s)
- Nutthawan Nonthabenjawan
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Patcharaporn Boonyos
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Benjarat Phattanawiboon
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | | | | | | | - Kriangsak Ruchusatsawat
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Ballang Uppapong
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Somchai Sangkitporn
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Eisuke Mekada
- Research and Education Promotion Foundation, Bangkok, Thailand
| | - Yoshiharu Matsuura
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Masashi Tatsumi
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Hiroto Mizushima
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand.
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Phattanawiboon B, Nonthabenjawan N, Boonyos P, Jetsukontorn C, Towayunanta W, Chuntrakool K, Ngaopravet K, Ruchusatsawat K, Uppapong B, Sangkitporn S, Mekada E, Matsuura Y, Tatsumi M, Mizushima H. Norovirus transmission mediated by asymptomatic family members in households. PLoS One 2020; 15:e0236502. [PMID: 32702014 PMCID: PMC7377487 DOI: 10.1371/journal.pone.0236502] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
The transmission of human norovirus excreted from infected persons occasionally causes sporadic infections and outbreaks. Both symptomatic patients and asymptomatic carriers have been reported to contribute to norovirus transmission, but little is known about the magnitude of the contribution of asymptomatic carriers. We carried out a 1-year survey of residents of a district of Bangkok, Thailand to determine the percentage of norovirus transmissions originating from asymptomatic individuals. We screened 38 individuals recruited from 16 families from May 2018 to April 2019 for GI and GII genotypes. Norovirus was detected every month, and 101 of 716 stool samples (14.1%) from individuals with no symptoms of acute gastroenteritis were norovirus-positive. The average infection frequency was 2.4 times per person per year. Fourteen genotypes were identified from the positive samples, with GII.4 being detected most frequently. Notably, 89.1% of the norovirus-positive samples were provided by individuals with no diarrhea episode. Similar to cases of symptomatic infections in Thailand, asymptomatic infections were observed most frequently in December. We detected 4 cases of NV infection caused by household transmission, and 3 of the 4 transmissions originated from asymptomatic individuals. We also identified a case in which norovirus derived from an asymptomatic individual caused diarrhea in a family member. These results suggest that asymptomatic individuals play a substantial role in both the maintenance and spreading of norovirus in a community through household transmission.
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Affiliation(s)
- Benjarat Phattanawiboon
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Nutthawan Nonthabenjawan
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Patcharaporn Boonyos
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Chanya Jetsukontorn
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | | | | | | | - Kriangsak Ruchusatsawat
- Department of Medical Sciences, National Institute of Health, Ministry of Public Health, Nonthaburi, Thailand
| | - Ballang Uppapong
- Department of Medical Sciences, National Institute of Health, Ministry of Public Health, Nonthaburi, Thailand
| | - Somchai Sangkitporn
- Department of Medical Sciences, National Institute of Health, Ministry of Public Health, Nonthaburi, Thailand
| | - Eisuke Mekada
- Research and Education Promotion Foundation, Bangkok, Thailand
| | - Yoshiharu Matsuura
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Masashi Tatsumi
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Hiroto Mizushima
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
- * E-mail:
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Interaction between norovirus and Histo-Blood Group Antigens: A key to understanding virus transmission and inactivation through treatments? Food Microbiol 2020; 92:103594. [PMID: 32950136 DOI: 10.1016/j.fm.2020.103594] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/27/2020] [Accepted: 07/02/2020] [Indexed: 02/06/2023]
Abstract
Human noroviruses (HuNoVs) are a main cause of acute gastroenteritis worldwide. They are frequently involved in foodborne and waterborne outbreaks. Environmental transmission of the virus depends on two main factors: the ability of viral particles to remain infectious and their adhesion capacity onto different surfaces. Until recently, adhesion of viral particles to food matrices was mainly investigated by considering non-specific interactions (e.g. electrostatic, hydrophobic) and there was only limited information about infectious HuNoVs because of the absence of a reliable in vitro HuNoV cultivation system. Many HuNoV strains have now been described as having specific binding interactions with human Histo-Blood Group Antigens (HBGAs) and non-HBGA ligands found in food and the environment. Relevant approaches to the in vitro replication of HuNoVs were also proposed recently. On the basis of the available literature data, this review discusses the opportunities to use this new knowledge to obtain a better understanding of HuNoV transmission to human populations and better evaluate the hazard posed by HuNoVs in foodstuffs and the environment.
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Ruis C, Lindesmith LC, Mallory ML, Brewer-Jensen PD, Bryant JM, Costantini V, Monit C, Vinjé J, Baric RS, Goldstein RA, Breuer J. Preadaptation of pandemic GII.4 noroviruses in unsampled virus reservoirs years before emergence. Virus Evol 2020; 6:veaa067. [PMID: 33381305 PMCID: PMC7751145 DOI: 10.1093/ve/veaa067] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The control of re-occurring pandemic pathogens requires understanding the origins of new pandemic variants and the factors that drive their global spread. This is especially important for GII.4 norovirus, where vaccines under development offer promise to prevent hundreds of millions of annual gastroenteritis cases. Previous studies have hypothesized that new GII.4 pandemic viruses arise when previously circulating pandemic or pre-pandemic variants undergo substitutions in antigenic regions that enable evasion of host population immunity, as described by conventional models of antigenic drift. In contrast, we show here that the acquisition of new genetic and antigenic characteristics cannot be the proximal driver of new pandemics. Pandemic GII.4 viruses diversify and spread over wide geographical areas over several years prior to simultaneous pandemic emergence of multiple lineages, indicating that the necessary sequence changes must have occurred before diversification, years prior to pandemic emergence. We confirm this result through serological assays of reconstructed ancestral virus capsids, demonstrating that by 2003, the ancestral 2012 pandemic strain had already acquired the antigenic characteristics that allowed it to evade prevailing population immunity against the previous 2009 pandemic variant. These results provide strong evidence that viral genetic changes are necessary but not sufficient for GII.4 pandemic spread. Instead, we suggest that it is changes in host population immunity that enable pandemic spread of an antigenically preadapted GII.4 variant. These results indicate that predicting future GII.4 pandemic variants will require surveillance of currently unsampled reservoir populations. Furthermore, a broadly acting GII.4 vaccine will be critical to prevent future pandemics.
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Affiliation(s)
- Christopher Ruis
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Lisa C Lindesmith
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Michael L Mallory
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | | | - Josephine M Bryant
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Veronica Costantini
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Christopher Monit
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Richard A Goldstein
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children, London, UK
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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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39
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Atmar RL, Baehner F, Cramer JP, Lloyd E, Sherwood J, Borkowski A, Mendelman PM. Persistence of Antibodies to 2 Virus-Like Particle Norovirus Vaccine Candidate Formulations in Healthy Adults: 1-Year Follow-up With Memory Probe Vaccination. J Infect Dis 2020; 220:603-614. [PMID: 31001633 DOI: 10.1093/infdis/jiz170] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 04/09/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND We previously reported the tolerability and immunogenicity 1 month after intramuscular administration of 2 bivalent virus-like particle (VLP)-based candidate norovirus vaccine formulations in adults. We now describe the persistence of immunity and responses to a memory probe vaccination 1 year later. METHODS A total of 454 healthy men and women aged 18-49 years in 3 equal groups received placebo (saline) or 15/50 or 50/50 vaccine formulations (ie, 15 or 50 µg of GI.1 genotype VLPs, respectively, and 50 µg of GII.4c VLPs) with MPL and Al(OH)3. Immunogenicity and safety were assessed up to day 365, when 351 participants received a memory probe vaccination of 15 µg each of GI.1 and GII.4c VLPs with Al(OH)3. RESULTS No safety signals were detected up to 1 year after the first vaccination. Pan-immunoglobulin, immunoglobulin A, and histo-blood group antigen-blocking (HBGA) antibody levels among vaccinees waned but remained higher than levels before vaccination and levels in placebo recipients on days 180 and 365. Memory probe vaccination increased all antibody titers. Levels of HBGA antibodies to GI.1 but not GII.4c were higher after the first vaccination in candidate vaccine groups, compared with those in the placebo group. CONCLUSION Levels of antibodies to both candidate norovirus VLP formulations persisted above baseline levels for at least 1 year after primary vaccination. HBGA-blocking responses to the memory probe for GI.1 but not GII.4c displayed characteristics of immune memory. CLINICAL TRIALS REGISTRATION NCT02142504.
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Affiliation(s)
- Robert L Atmar
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Frank Baehner
- Takeda Pharmaceuticals International, Zurich, Switzerland
| | - Jakob P Cramer
- Takeda Pharmaceuticals International, Zurich, Switzerland
| | | | - James Sherwood
- Takeda Pharmaceuticals International, Zurich, Switzerland
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Saito M, Tsukagoshi H, Ishigaki H, Aso J, Ishii H, Okayama K, Ryo A, Ishioka T, Kuroda M, Saruki N, Katayama K, Kimura H. Molecular evolution of the capsid ( VP1) region in human norovirus genogroup II genotype 3. Heliyon 2020; 6:e03835. [PMID: 32395646 PMCID: PMC7205756 DOI: 10.1016/j.heliyon.2020.e03835] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 11/07/2019] [Accepted: 04/21/2020] [Indexed: 12/13/2022] Open
Abstract
Norovirus GII.3 has been suggested to be a prevalent genotype in patients with acute gastroenteritis. However, the genetic properties of the VP1 region encoding the major GII.3 antigen remain unclear. Here, we performed molecular evolutionary analyses of the GII.3 VP1 region detected in various countries. We performed time-scaled phylogenetic analyses, selective pressure analyses, phylogenetic distance analyses, and conformational epitope analyses. The time-scaled phylogenetic tree showed that an ancestor of the GII.3 VP1 region diverged from the common ancestors of the GII.6, GII.11, GII.18, and GII.19 approximately 70 years ago with relatively low divergence. The evolutionary rate of the GII.3 VP1 region was rapid (4.82 × 10−3 substitutions/site/year). Furthermore, one positive site and many negative selection sites were observed in the capsid protein. These results suggest that the GII.3 VP1 region rapidly evolved with antigenic variations.
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Affiliation(s)
- Mariko Saito
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Hirotaka Ishigaki
- Department of Health Science, Gunma Paz University Graduate School of Health Sciences, 1-7-1 Tonyamachi, Takasaki-shi, Gunma 370-0006, Japan
| | - Jumpei Aso
- Department of Health Science, Gunma Paz University Graduate School of Health Sciences, 1-7-1 Tonyamachi, Takasaki-shi, Gunma 370-0006, Japan
- Kyorin University Hospital, 6-20-2 Shinkawa, Mitaka-shi, Tokyo 181-8611, Japan
| | - Haruyuki Ishii
- Kyorin University Hospital, 6-20-2 Shinkawa, Mitaka-shi, Tokyo 181-8611, Japan
| | - Kaori Okayama
- Department of Health Science, Gunma Paz University Graduate School of Health Sciences, 1-7-1 Tonyamachi, Takasaki-shi, Gunma 370-0006, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, 3-9 Fukuura, Yokohama-shi, Kanagawa 236-0004, Japan
| | - Taisei Ishioka
- Department of Health Science, Gunma Paz University Graduate School of Health Sciences, 1-7-1 Tonyamachi, Takasaki-shi, Gunma 370-0006, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Nobuhiro Saruki
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Kitasato Institute for Life Sciences Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Hirokazu Kimura
- Department of Health Science, Gunma Paz University Graduate School of Health Sciences, 1-7-1 Tonyamachi, Takasaki-shi, Gunma 370-0006, Japan
- Department of Microbiology, Yokohama City University School of Medicine, 3-9 Fukuura, Yokohama-shi, Kanagawa 236-0004, Japan
- Corresponding author.
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41
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Ahmed K, Dony JJF, Mori D, Haw LY, Giloi N, Jeffree MS, Iha H. An outbreak of gastroenteritis by emerging norovirus GII.2[P16] in a kindergarten in Kota Kinabalu, Malaysian Borneo. Sci Rep 2020; 10:7137. [PMID: 32346119 PMCID: PMC7189370 DOI: 10.1038/s41598-020-64148-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 04/08/2020] [Indexed: 11/09/2022] Open
Abstract
Outbreaks of diarrhea in kindergartens are underreported and frequently go unnoticed in developing countries. To better understand the etiology this study was performed during an outbreak of diarrhea in a kindergarten in Sabah, Malaysia. Outbreak investigation was performed according to the standard procedures. In this outbreak a total of 34 (36.5%) children and 4 (30.8%) teachers suffered from gastroenteritis. Stool samples from seven children and 13 teachers were tested for rotavirus and norovirus. During the investigation stool samples were collected and sent in cold chain to the laboratory. The samples were subjected to rotavirus enzyme linked immunosorbent assay, and reverse transcription PCR for norovirus. All samples were negative for rotavirus but positive for norovirus. To determine the genogroup and genotype of norovirus, nucleotide sequencing of the amplicons was performed. All norovirus from the outbreak was of genotype GII.2[16]. To determine the relatedness of the strains phylogenetic analysis was done using neighbor-joining method. Phylogenetically these strains were highly related to GII.2[P16] noroviruses from China and Japan. This study provided evidence that a diarrheal outbreak in a kindergarten was caused by GII.2[P16] norovirus which is an emerging strain in East Asia and Europe.
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Affiliation(s)
- Kamruddin Ahmed
- Borneo Medical and Health Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, 88400, Sabah, Malaysia. .,Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, 88400, Sabah, Malaysia.
| | | | - Daisuke Mori
- Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, 88400, Sabah, Malaysia
| | - Liaw Yun Haw
- KPJ Sabah Specialist Hospital, Kota Kinabalu, 88300, Sabah, Malaysia
| | - Nelbon Giloi
- Department of Community Medicine and Public Health, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, 88400, Sabah, Malaysia
| | - Mohammad Saffree Jeffree
- Department of Community Medicine and Public Health, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, 88400, Sabah, Malaysia
| | - Hidekatsu Iha
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, 879-5593, Oita, Japan
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42
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Todd KV, Tripp RA. Vero Cells as a Mammalian Cell Substrate for Human Norovirus. Viruses 2020; 12:E439. [PMID: 32295124 PMCID: PMC7232407 DOI: 10.3390/v12040439] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/06/2020] [Accepted: 04/11/2020] [Indexed: 12/13/2022] Open
Abstract
Human norovirus (HuNoV) is a principal cause of acute gastroenteritis worldwide, particularly in developing countries. Its global prevalence is underscored by more serious morbidity and some mortality in the young (<5 years) and the elderly. To date, there are no licensed vaccines or approved therapeutics for HuNoV, mostly because there are limited cell culture systems and small animal models available. Recently described cell culture systems are not ideal substrates for HuNoV vaccine development because they are not clonal or only support a single strain. In this study, we show Vero cell-based replication of two pandemic GII.4 HuNoV strains and one GII.3 strain and confirm exosome-mediated HuNoV infection in Vero cells. Lastly, we show that trypsin addition to virus cultures or disruption of Vero cell host genes can modestly increase HuNoV replication. These data provide support for Vero cells as a cell culture model for HuNoV.
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Affiliation(s)
| | - Ralph A. Tripp
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
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43
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Environmental and Adaptive Changes Necessitate a Paradigm Shift for Indicators of Fecal Contamination. Microbiol Spectr 2020. [DOI: 10.1128/microbiolspec.erv-0001-2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
ABSTRACT
Changes in the occurrence, distribution, and seasonal variation of waterborne pathogens due to global climate change may increase the risk of human exposure to these microorganisms, thus heightening the need for more reliable surveillance systems. Routine monitoring of drinking water supplies and recreational waters is performed using fecal indicator microorganisms, such as
Escherichia coli
,
Enterococcus
spp., and coliphages. However, the presence and numbers of these indicators, especially
E. coli
and
Enterococcus
spp., do not correlate well with those of other pathogens, especially enteric viruses, which are a major cause of waterborne outbreaks associated with contaminated water and food, and recreational use of lakes, ponds, rivers, and estuarine waters. For that reason, there is a growing need for a surveillance system that can detect and quantify viral pathogens directly in water sources to reduce transmission of pathogens associated with fecal transmission. In this review, we present an updated overview of relevant waterborne enteric viruses that we believe should be more commonly screened to better evaluate water quality and to determine the safety of water use and reuse and of epidemiological data on viral outbreaks. We also discuss current methodologies that are available to detect and quantify these viruses in water resources. Finally, we highlight challenges associated with virus monitoring. The information presented in this review is intended to aid in the assessment of human health risks due to contact with water sources, especially since current environmental and adaptive changes may be creating the need for a paradigm shift for indicators of fecal contamination.
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Abstract
Norovirus, a major cause of gastroenteritis in people of all ages worldwide, was first reported in South Korea in 1999. The most common causal agents of pediatric acute gastroenteritis are norovirus and rotavirus. While vaccination has reduced the pediatric rotavirus infection rate, norovirus vaccines have not been developed. Therefore, prediction and prevention of norovirus are very important. Norovirus is divided into genogroups GI-GVII, with GII.4 being the most prevalent. However, in 2012-2013, GII.17 showed a higher incidence than GII.4 and a novel variant, GII.P17-GII.17, appeared. In this study, 204 stool samples collected in 2013-2014 were screened by reverse transcriptase-polymerase chain reaction; 11 GI (5.39%) and 45 GII (22.06%) noroviruses were identified. GI.4, GI.5, GII.4, GII.6 and GII.17 were detected. The whole genomes of the three norovirus GII.17 were sequenced. The whole genome of GII.17 consists of three open reading frames of 5109, 1623 and 780 bp. Compared with 20 GII.17 strains isolated in other countries, we observed numerous changes in the protruding P2 domain of VP1 in the Korean GII.17 viruses. Our study provided genome information that might aid in epidemic prevention, epidemiology studies and vaccine development.
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45
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Quantitative PCR Detection of Enteric Viruses in Wastewater and Environmental Water Sources by the Lisbon Municipality: A Case Study. WATER 2020. [DOI: 10.3390/w12020544] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Current regulations and legislation require critical revision to determine safety for alternative water sources and water reuse as part of the solution to global water crisis. In order to fulfill those demands, Lisbon municipality decided to start water reuse as part of a sustainable hydric resources management, and there was a need to confirm safety and safeguard for public health for its use in this context. For this purpose, a study was designed that included a total of 88 samples collected from drinking, superficial, underground water, and wastewater at three different treatment stages. Quantitative Polimerase Chain Reaction (PCR) detection (qPCR) of enteric viruses Norovirus (NoV) genogroups I (GI) and II (GII) and Hepatitis A (HepA) was performed, and also FIB (E. coli, enterococci and fecal coliforms) concentrations were assessed. HepA virus was only detected in one untreated influent sample, whereas NoV GI/ NoV GI were detected in untreated wastewater (100/100%), secondary treated effluent (47/73%), and tertiary treated effluent (33/20%). Our study proposes that NoV GI and GII should be further studied to provide the support that they may be suitable indicators for water quality monitoring targeting wastewater treatment efficiency, regardless of the level of treatment.
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46
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Fu J, Bao C, Huo X, Hu J, Shi C, Lin Q, Zhang J, Ai J, Xing Z. Increasing Recombinant Strains Emerged in Norovirus Outbreaks in Jiangsu, China: 2015-2018. Sci Rep 2019; 9:20012. [PMID: 31882797 PMCID: PMC6934623 DOI: 10.1038/s41598-019-56544-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 12/02/2019] [Indexed: 11/19/2022] Open
Abstract
From January 2015 to December 2018, 213 norovirus outbreaks with 3,951 patients were reported in Jiangsu, China. Based on viral RdRp and VP1 genes, eight genotypes, GII.2[P16] (144, 67.6%), GII.3[P12] (21, 9.9%), GII.6[P7] (5, 2.3%), GII.14[P7] (4, 1.9%), GII.4 Sydney[P31] (3, 1.4%), GII.1[P33] (1, 0.5%), GII.2[P2] (3, 1.4%), and GII.17[P17] (16, 7.5%) were identified throughout the study period. These genotypes were further regrouped as GII.R (Recombinant) and GII.Non-R (Non-recombinant) strains. In this report we showed that GII.R strains were responsible for at least 178 (83.6%) of 213 norovirus-positive outbreaks with a peak in 2017 and 2018. Most norovirus outbreaks occurred in primary schools and 94 of 109 (86.2%) outbreaks in primary schools were caused by GII.R, while GII.Non-R and GII.NT (not typed) strains accounted for 6 (5.5%) and 9 (8.3%) norovirus outbreaks, respectively. The SimPlot analysis showed recombination breakpoints near the ORF1/2 junction for all six recombinant strains. The recombination breakpoints were detected at positions varying from nucleotides 5009 to 5111, localized in the ORF1 region for four strains (GII.2[P16], GII.3[P12], GII.6[P7], and GII.14[P7]) and in the ORF2 region for the other (GII.4 Sydney[P31] and GII.1[P33]). We identified four clusters, Cluster I through IV, in the GII.P7 RdRp gene by phylogenetic analysis and the GII.14[P7] variants reported here belonged to Cluster IV in the RdRp tree. The HBGA binding site of all known GII.14 strains remained conserved with several point mutations found in the predicted conformational epitopes. In conclusion, gastroenteritis outbreaks caused by noroviruses increased rapidly in the last years and these viruses were classified into eight genotypes. Emerging recombinant noroviral strains have become a major concern and challenge to public health.
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Affiliation(s)
- Jianguang Fu
- Medical School and the Jiangsu Provincial Key Laboratory of Medicine, Nanjing University, Nanjing, China.,Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Changjun Bao
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Xiang Huo
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Jianli Hu
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Chao Shi
- Wuxi Center for Disease Control and Prevention, Wuxi, China
| | - Qin Lin
- Changzhou Center for Disease Control and Prevention, Changzhou, China
| | - Jun Zhang
- Yangzhou Center for Disease Control and Prevention, Yangzhou, China
| | - Jing Ai
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China.
| | - Zheng Xing
- Medical School and the Jiangsu Provincial Key Laboratory of Medicine, Nanjing University, Nanjing, China. .,College of Veterinary Medicine, Department of Veterinary Biomedical Sciences, University of Minnesota at Twin Cities, Saint Paul, Minnesota, 55108, USA.
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Abstract
Noroviruses are a very diverse group of viruses that infect different mammalian species. In humans, norovirus is a major cause of acute gastroenteritis. Multiple norovirus infections can occur in a lifetime as the result of limited duration of acquired immunity and cross-protection among different strains. A combination of advances in sequencing methods and improvements on surveillance has provided new insights into norovirus diversification and emergence. The generation of diverse norovirus strains has been associated with (1) point mutations on two different genes: ORF1, encoding the non-structural proteins, and ORF2, encoding the major capsid protein (VP1); and (2) recombination events that create chimeric viruses. While both mechanisms are exploited by all norovirus strains, individual genotypes utilize each mechanism differently to emerge and persist in the human population. GII.4 noroviruses (the most prevalent genotype in humans) present an accumulation of amino acid mutations on VP1 resulting in the chronological emergence of new variants. In contrast, non-GII.4 noroviruses present co-circulation of different variants over long periods with limited changes on their VP1. Notably, genetic diversity of non-GII.4 noroviruses is mostly related to the high number of recombinant strains detected in humans. While it is difficult to determine the precise mechanism of emergence of epidemic noroviruses, observations point to multiple factors that include host-virus interactions and changes on two regions of the genome (ORF1 and ORF2). Larger datasets of viral genomes are needed to facilitate comparison of epidemic strains and those circulating at low levels in the population. This will provide a better understanding of the mechanism of norovirus emergence and persistence.
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Affiliation(s)
- Gabriel I Parra
- Division of Viral Products, Food and Drug Administration, 10903 New Hampshire Avenue, Building 52/72, Room 1308, Silver Spring, MD 20993, USA
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48
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Abstract
BACKGROUND Based on the impact public health of norovirus and the current progress in norovirus vaccine development, it is necessary to continuously monitor the epidemiology of norovirus infection, especially in children who are more susceptible to norovirus. OBJECTIVES To monitor the activity and genotypes of norovirus infection in sporadic diarrhea in Shanghainese children during 2014-2018. STUDY DESIGN Acute diarrheal cases were prospectively enrolled in the outpatient setting. Real-time reverse transcription-polymerase chain reaction was used for screening norovirus GI and GII genogroups. Dual norovirus genotypes were identified based on the partial capsid and polymerase gene sequences. RESULTS Of the 3422 children with diarrhea, 510 (14.9%) were positive for noroviruses with 13 (2.5%) strains being GI genogroup and 497 (97.5%) strains being GII genogroup. Five distinct capsid GII genotypes were identified, including GII.4-Sydney/2012 (71.8%), GII.3 (13.8%), GII.17 (7.8%), GII.2 (6.0%), GII.6 (0.3%) and GII.8 (0.3%). Seven polymerase GII genotypes were identified, including GII.Pe (77.0%), GII.P12 (11.0%), GII.P17 (9.0%), GII.P16 (2.1%), and GII.P7, GII.P8 and GII.P2 in each (0.3%). Eleven distinct polymerase/capsid genotypes were identified with GII.Pe/GII.4-Sydney/2012 (74.2%), GII.P12/GII.3 (11.7%) and GII.P17/GII.17 (7.7%) being common. GII.P17/GII.17 strains were detected since September 2014. Recombinant GII.P16/GII.2 strains were detected since December 2016. CONCLUSIONS Norovirus is a major pathogen causing diarrhea in Shanghainese children. GII.Pe/GII.4-Sydney/2012 strains remained the predominant genotype. The emergence of GII.P17/GII.17 and GII.P16/GII.2 strains in sporadic diarrhea was consistent with norovirus-associated outbreaks attributable to these 2 novel variants in China. Continuous monitoring norovirus genotypes circulating in pediatric population is needed for current vaccine development.
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49
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Wang Y, Yue H, Tang C. Prevalence and complete genome of bovine norovirus with novel VP1 genotype in calves in China. Sci Rep 2019; 9:12023. [PMID: 31427703 PMCID: PMC6700072 DOI: 10.1038/s41598-019-48569-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/07/2019] [Indexed: 12/21/2022] Open
Abstract
Bovine norovirus (BNoV) is a diarrhea-causing pathogen of calves. In this study, 211 diarrheic fecal samples were collected from 25 farms across six provinces in China, between November 2017 and September 2018. 20.4% of the samples were detected as BNoV-positive by RT-PCR. Phylogenetic analyses based on RdRp, VP1, and VP2 fragments revealed these BNoV strains had unique evolutionary characteristics. The complete genome of strain Bo/BET-17/18/CH was successfully sequenced. It was 7321 nucleotides (nt) in length, shared 79.4-80.9% nt identity with all five BNoV genomes, clustered on a separate branch of the phylogenetic tree, suggesting that strain Bo/BET-17/18/CH could represent a novel BNoV strain. Two interesting characteristics were found in the genome: (i) the VP1 sequence differed greatly from known BNoV VP1 sequences; (ii) a recombination event is predicted within the ORF1-ORF2 overlap. Moreover 16.3% (7/43) of the BNoV were identified as the novel VP1 genotype, which were distributed on four farms across two provinces, indicating that the novel VP1 genotype strain has spread. To our knowledge, this is first description of the molecular and genomic characteristics of BNoV in China. These findings extend our understanding of the genetic evolution and epidemics of BNoV.
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Affiliation(s)
- Yuelin Wang
- College of Life Science and Technology, Southwest Minzu University, Chengdu, China
| | - Hua Yue
- College of Life Science and Technology, Southwest Minzu University, Chengdu, China. .,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China.
| | - Cheng Tang
- College of Life Science and Technology, Southwest Minzu University, Chengdu, China. .,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China.
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50
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Guo Z, He Q, Zhang B, Yue H, Tang C. First detection of neboviruses in yak (Bos grunniens) and identification of a novel neboviruses based on complete genome. Vet Microbiol 2019; 236:108388. [PMID: 31500726 PMCID: PMC7127790 DOI: 10.1016/j.vetmic.2019.108388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 08/08/2019] [Accepted: 08/08/2019] [Indexed: 12/29/2022]
Abstract
This is the first detection of neboviruses in yak (Bos grunniens). Neboviruses has been widely circulated among yak in Qinghai-Tibet Plateau, China. A novel neboviruses was identified, and it has spread in local region. New insights about the prevalence and evolution of neboviruses.
Neboviruses (NeVs) is an important causative agent of calf diarrhea. Here, 354 diarrhoeic samples were collected from yak on 55 farms in the Qinghai-Tibet Plateau, China. 22.0% of the diarrhoeic samples were detected as NeVs-positive by RT–PCR assay. Phylogenetic analysis of 78 NeVs RdRp fragments showed that 69 strains were closely related to NB-like strains, and the remaining 9 strains were clustered into an independent branch, which may represent a novel RdRp genotype. Two complete NeVs genomes (YAK/NRG-17/17/CH and YAK/HY1-2/18/CH) were successfully sequenced with 7459 nt and 7460 nt in length, respectively. The genomes of the two strains only shared 68.1%–69.3% nt identity with all six known NeVs genomes, and phylogenetic trees based on its genome, VP1, RdRp, VP2, P34, NTPase, P30, VPg and 3CLpro proteins suggested that the two strains may represent a novel NeVs strain with novel VP1 genotype and novel RdRp genotype. Notably, 11.5% NeVs strains were screened as the novel NeVs strains based VP1 and RdRp sequences. These novel NeVs strains were detected from 6 farms in two counties, indicating that the novel NeVs has spread in local region. To best of our knowledge, this is the first detection of NeVs in yak. Moreover, a novel NeVs strain was identified based on complete genome. These results contribute to further understand the prevalence and genetic evolution of NeVs.
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Affiliation(s)
- Zijing Guo
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China
| | - Qifu He
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China
| | - Bin Zhang
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China; Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China
| | - Hua Yue
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China; Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China.
| | - Cheng Tang
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China; Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China.
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