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Xiong H, Ma F, Tang D, Liu D. Measures for preventing norovirus outbreaks on campus in economically underdeveloped areas and countries: evidence from rural areas in Western China. Front Public Health 2024; 12:1406133. [PMID: 38894991 PMCID: PMC11183813 DOI: 10.3389/fpubh.2024.1406133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Background The outbreak of norovirus represents a significant public health emergency within densely populated, impoverished, and underdeveloped areas and countries. Our objective is to conduct an epidemiology study of a norovirus outbreak that occurred in a kindergarten located in rural western China. We aim to raise awareness and garner increased attention towards the prevention and control of norovirus, particularly in economically underdeveloped regions. Methods Retrospective on-site epidemiological investigation results, including data on school layout, case symptoms, onset time, disposal methods and sample testing results, questionnaire surveys, and case-control study were conducted in a kindergarten to analyze the underlying causes of the norovirus outbreak. Results A total of 15 cases were identified, with an attack rate of 44.12% (15/34). Among them, 10 cases were diagnosed through laboratory tests, and 5 cases were diagnosed clinically. Vomiting (100%, 15/15) and diarrhea (93.33%, 14/15) were the most common symptoms in the outbreak. Case control study revealed that cases who had close contact (<1 m) with the patient's vomitus (OR = 5.500) and those who had close contact with similar patients (OR = 8.000) had significantly higher ORs compared to the control participants. The current study demonstrated that improper handling of vomitus is positively associated with norovirus outbreak. The absence of standardized disinfection protocols heightens the risk of norovirus outbreaks. Conclusion To our knowledge, this study represents the first investigation into a norovirus outbreak in rural areas of western China. We aspire that amidst rapid economic development, a greater emphasis will be placed on the prevention and control of infectious diseases in economically underdeveloped areas and countries.
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Affiliation(s)
- Huali Xiong
- Department of Public Health, Health Commission of Rongchang District, Chongqing, China
- Center for Mental Health of Rongchang District, Chongqing, China
| | - Fengxun Ma
- Department of Public Health, The People's Hospital of Rongchang District, Chongqing, China
| | - Dayi Tang
- First Clinical College, Mudanjiang Medical College, Mudanjiang, Heilongjiang, China
| | - Daiqiang Liu
- Department of Hospital Information, The People's Hospital of Rongchang District, Chongqing, China
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2
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Brodmerkel MN, Thiede L, De Santis E, Uetrecht C, Caleman C, Marklund EG. Collision induced unfolding and molecular dynamics simulations of norovirus capsid dimers reveal strain-specific stability profiles. Phys Chem Chem Phys 2024; 26:13094-13105. [PMID: 38628116 DOI: 10.1039/d3cp06344e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Collision induced unfolding (CIU) is a method used with ion mobility mass spectrometry to examine protein structures and their stability. Such experiments yield information about higher order protein structures, yet are unable to provide details about the underlying processes. That information can however be provided using molecular dynamics simulations. Here, we investigate the gas-phase unfolding of norovirus capsid dimers from the Norwalk and Kawasaki strains by employing molecular dynamics simulations over a range of temperatures, representing different levels of activation, together with CIU experiments. The dimers have highly similar structures, but their CIU reveals different stability that can be explained by the different dynamics that arises in response to the activation seen in the simulations, including a part of the sequence with previously observed strain-specific dynamics in solution. Our findings show how similar protein variants can be examined using mass spectrometric techniques in conjunction with atomistic molecular dynamics simulations to reveal differences in stability as well as differences in how and where unfolding takes place upon activation.
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Affiliation(s)
- Maxim N Brodmerkel
- Department of Chemistry - BMC, Uppsala University, 75123 Uppsala, Sweden.
| | - Lars Thiede
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Leibniz Institute of Virology (LIV), Notkestrasse 85, 22607 Hamburg, Germany
- Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Emiliano De Santis
- Department of Chemistry - BMC, Uppsala University, 75123 Uppsala, Sweden.
- Department of Physics and Astronomy, Uppsala University, 75120 Uppsala, Sweden
| | - Charlotte Uetrecht
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Leibniz Institute of Virology (LIV), Notkestrasse 85, 22607 Hamburg, Germany
- Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, 75120 Uppsala, Sweden
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, 75123 Uppsala, Sweden.
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3
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Lo M, Doan YH, Mitra S, Saha R, Miyoshi SI, Kitahara K, Dutta S, Oka T, Chawla-Sarkar M. Comprehensive full genome analysis of norovirus strains from eastern India, 2017-2021. Gut Pathog 2024; 16:3. [PMID: 38238807 PMCID: PMC10797879 DOI: 10.1186/s13099-023-00594-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/20/2023] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Worldwide, noroviruses are the leading cause of acute gastroenteritis (AGE) in people of all age groups. In India, norovirus rates between 1.4 to 44.4% have been reported. Only a very few complete norovirus genome sequences from India have been reported. OBJECTIVE To perform full genome sequencing of noroviruses circulating in India during 2017-2021, identify circulating genotypes, assess evolution including detection of recombination events. METHODOLOGY Forty-five archived norovirus-positive samples collected between October 2017 to July 2021 from patients with AGE from two hospitals in Kolkata, India were processed for full genome sequencing. Phylogenetic analysis, recombination breakpoint analysis and comprehensive mutation analysis were also performed. RESULTS Full genome analysis of norovirus sequences revealed that strains belonging to genogroup (G)I were genotyped as GI.3[P13]. Among the different norovirus capsid-polymerase combinations, GII.3[P16], GII.4 Sydney[P16], GII.4 Sydney[P31], GII.13[P16], GII.16[P16] and GII.17 were identified. Phylogenetic analysis confirmed phylogenetic relatedness with previously reported norovirus strains and all viruses were analyzed by Simplot. GII[P16] viruses with multiple residue mutations within the non-structural region were detected among circulating GII.4 and GII.3 strains. Comprehensive mutation analysis and selection pressure analysis of GII[P16] viruses showed positive as well as negative selection sites. A GII.17 strain (NICED-BCH-11889) had an untypeable polymerase type, closely related to GII[P38]. CONCLUSION This study highlights the circulation of diverse norovirus strains in eastern India. These findings are important for understanding norovirus epidemiology in India and may have implications for future vaccine development.
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Affiliation(s)
- Mahadeb Lo
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Rd, Scheme-XM, Beliaghata, Kolkata, 700010, West Bengal, India
| | - Yen Hai Doan
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-Murayama, Tokyo, Japan
| | - Suvrotoa Mitra
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Rd, Scheme-XM, Beliaghata, Kolkata, 700010, West Bengal, India
| | - Ritubrita Saha
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Rd, Scheme-XM, Beliaghata, Kolkata, 700010, West Bengal, India
| | - Shin-Ichi Miyoshi
- Collaborative Research Center of Okayama University for Infectious Diseases in India, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Kei Kitahara
- Collaborative Research Center of Okayama University for Infectious Diseases in India, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Regional Virus Research and Diagnostic Laboratory, ICMR-National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, West Bengal, India
| | - Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-Murayama, Tokyo, Japan.
| | - Mamta Chawla-Sarkar
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Rd, Scheme-XM, Beliaghata, Kolkata, 700010, West Bengal, India.
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Siafakas N, Anastassopoulou C, Lafazani M, Chronopoulou G, Rizos E, Pournaras S, Tsakris A. Predominance of Recombinant Norovirus Strains in Greece, 2016-2018. Microorganisms 2023; 11:2885. [PMID: 38138029 PMCID: PMC10745620 DOI: 10.3390/microorganisms11122885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/17/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
GII.4 noroviruses have caused the overwhelming majority of norovirus-related gastroenteritis cases during the past two decades. However, a trend towards the emergence of new genotypes and novel GII.4 variants provided the impetus to explore further the changing patterns in norovirus epidemiology during the present study. Genotyping of 60 norovirus strains detected during a period of 33 months (January 2016-October 2018) was performed on the basis of the capsid VP1-coding ORF2 gene sequence. All norovirus strains detected were classified into seven genotypes, six of which belonged to genogroup GII. GII.2 was the dominant genotype till February 2017, whereas GII.4 prevailed thereafter. Most of the GII.4 strains were of the Sydney_2012 variant, whereas five strains could not be classified. Further recombination analysis at the ORF1/ORF2 gene junction revealed that 23 out of 24 strains were recombinant, thereby showcasing the significant role of genetic recombination in norovirus evolution and epidemiology. Continuous genomic surveillance and molecular characterization are essential for tracking norovirus evolution, which could contribute to the elucidation of new aspects of virus-host interactions that potentially affect host morbidity and epidemiology.
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Affiliation(s)
- Nikolaos Siafakas
- Clinical Microbiology Laboratory, ATTIKON University Hospital, 12462 Athens, Greece; (M.L.); (S.P.)
| | - Cleo Anastassopoulou
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (C.A.); (A.T.)
| | - Maria Lafazani
- Clinical Microbiology Laboratory, ATTIKON University Hospital, 12462 Athens, Greece; (M.L.); (S.P.)
| | - Genovefa Chronopoulou
- Biopathology Department, Athens Medical Center, 5-7 Distomou Str., 15125 Marousi, Greece;
| | - Emmanouil Rizos
- 2nd Department of Psychiatry, ATTIKON University Hospital, 12462 Athens, Greece;
| | - Spyridon Pournaras
- Clinical Microbiology Laboratory, ATTIKON University Hospital, 12462 Athens, Greece; (M.L.); (S.P.)
| | - Athanasios Tsakris
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (C.A.); (A.T.)
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Fumian TM, Malta FC, Sarmento SK, Fernandes SB, Negri CM, Belettini SADA, Machado MH, Guimarães MAAM, de Assis RMS, Baduy GA, Fialho AM, Burlandy FM. Acute gastroenteritis outbreak associated with multiple and rare norovirus genotypes after storm events in Santa Catarina, Brazil. J Med Virol 2023; 95:e29205. [PMID: 37933896 DOI: 10.1002/jmv.29205] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023]
Abstract
Norovirus is a major cause of acute diarrheal disease (ADD) outbreaks worldwide. In the present study, we investigated an ADD outbreak caused by norovirus in several municipalities of Santa Catarina state during the summer season, southern Brazil in 2023. As of the 10th epidemiological week of 2023, approximately 87 000 ADD cases were reported, with the capital, Florianópolis, recording the highest number of cases throughout the weeks. By using RT-qPCR and sequencing, we detected 10 different genotypes, from both genogroups (G) I and II. Some rare genotypes were also identified. Additionally, rotavirus and human adenovirus were sporadically detected among the ADD cases. Several features of the outbreak suggest that sewage-contaminated water could played a role in the surge of ADD cases. Storm events in Santa Catarina state that preceded the outbreak likely increased the discharge of contaminated wastewater and stormwater into water bodies, such as rivers and beaches during a high touristic season in the state. Climate change-induced extreme weather events, including intensified rainfall and frequent floods, can disturb healthcare and sanitation systems. Implementing public policies for effective sanitation, particularly during peak times, is crucial to maintain environmental equilibrium and counter marine pollution.
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Affiliation(s)
- Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Fábio Correia Malta
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
- Department of Infectious and Parasitic Diseases, School of Medicine, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sylvia Kahwage Sarmento
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | - Cynthia Maria Negri
- Central Laboratory of Public Health-LACEN, Florianópolis, Santa Catarina, Brazil
| | | | | | - Maria Angelica Arpon Marandino Guimarães
- Department of Infectious and Parasitic Diseases, School of Medicine, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rosane Maria Santos de Assis
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Gabriel Assad Baduy
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Alexandre Madi Fialho
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Fernanda Marcicano Burlandy
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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6
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Sun Z, Niu P, Jin M, Zhang R, Gao Q, Wang H, Ma X, Wang J. Genotyping and traceability analysis of norovirus in Yantai between 2017 and 2019. J Med Virol 2023; 95:e29220. [PMID: 37947460 DOI: 10.1002/jmv.29220] [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: 03/13/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023]
Abstract
To investigate the diversity and evolution of noroviruses in Yantai in recent years, this study focused on the coat protein regions of norovirus-positive samples with nucleic acid detection (cycle threshold) values below 30 between 2017 and 2019. A total of 81 sequences were obtained for genotyping. Initially, a high-throughput sequencing approach was established to perform the whole-genome sequencing of multiple typical diarrheal strains. Using bioinformatics software such as BEAST, recombinant variant analysis was performed for each genotype of the norovirus strains, and genetic evolutionary analysis was conducted for the dominant strain GII.4, as well as the rare variant GII.21. The results showed that there were multiple genotypes such as GI.3, GI.6, GI.7, GII.1, GII.2, GII.3, GII.4, GII.6, GII.13, GII.17, GII.21, and GIX.1 in the positive samples of norovirus from 2017 to 2019. GII.4 is characterized by diverse genotypes, with new changes in antigenic epitopes occurring during the course of the epidemic. This may have led to the emergence of a new pandemic. This suggests a need to strengthen surveillance. The results of this study suggest that attention should be paid to the predominant genotypes prevalent in neighboring countries and regions, and the safety supervision of imported food should be strengthened to aid in the prevention and control of related viruses.
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Affiliation(s)
- Zhenlu Sun
- Yantai Center for Disease Control and Prevention, Yantai, Shandong, China
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Peihua Niu
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Miao Jin
- Department of Viral Diarrhea, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruiqing Zhang
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Qiao Gao
- Yantai Center for Disease Control and Prevention, Yantai, Shandong, China
| | - Hongtao Wang
- Yantai Center for Disease Control and Prevention, Yantai, Shandong, China
| | - Xuejun Ma
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Ji Wang
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
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Mai CTN, Ly LTK, Doan YH, Oka T, Mai LTP, Quyet NT, Mai TNP, Thiem VD, Anh LT, Van Sanh L, Hien ND, Anh DD, Parashar UD, Tate JE, Van Trang N. Prevalence and Characterization of Gastroenteritis Viruses among Hospitalized Children during a Pilot Rotavirus Vaccine Introduction in Vietnam. Viruses 2023; 15:2164. [PMID: 38005842 PMCID: PMC10675811 DOI: 10.3390/v15112164] [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: 09/08/2023] [Revised: 10/16/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Rotavirus (RV), norovirus (NoV), sapovirus (SaV), and human astrovirus (HAstV) are the most common viral causes of gastroenteritis in children worldwide. From 2016 to 2021, we conducted a cross-sectional descriptive study to determine the prevalence of these viruses in hospitalized children under five years old in Nam Dinh and Thua Thien Hue provinces in Vietnam during the pilot introduction of the RV vaccine, Rotavin-M1 (POLYVAC, Hanoi, Vietnam). We randomly selected 2317/6718 (34%) acute diarrheal samples from children <5 years of age enrolled at seven sentinel hospitals from December 2016 to May 2021; this period included one year surveillance pre-vaccination from December 2016 to November 2017. An ELISA kit (Premier Rotaclone®, Meridian Bioscience, Inc., Cincinnati, OH, USA) was used to detect RV, and two multiplex real-time RT-PCR assays were used for the detection of NoV, SaV and HAstV. The prevalence of RV (single infection) was reduced from 41.6% to 22.7% (p < 0.0001) between pre- and post-vaccination periods, while the single NoV infection prevalence more than doubled from 8.8% to 21.8% (p < 0.0001). The SaV and HAstV prevalences slightly increased from 1.9% to 3.4% (p = 0.03) and 2.1% to 3.3% (p = 0.09), respectively, during the same period. Viral co-infections decreased from 7.2% to 6.0% (p = 0.24), mainly due to a reduction in RV infection. Among the genotypeable samples, NoV GII.4, SaV GI.1, and HAstV-1 were the dominant types, representing 57.3%, 32.1%, and 55.0% among the individual viral groups, respectively. As the prevalence of RV decreases following the national RV vaccine introduction in Vietnam, other viral pathogens account for a larger proportion of the remaining diarrhea burden and require continuing close monitoring.
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Affiliation(s)
- Chu Thi Ngoc Mai
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (C.T.N.M.); (L.T.K.L.); (T.N.P.M.); (V.D.T.)
| | - Le Thi Khanh Ly
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (C.T.N.M.); (L.T.K.L.); (T.N.P.M.); (V.D.T.)
| | - Yen Hai Doan
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Le Thi Phuong Mai
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (C.T.N.M.); (L.T.K.L.); (T.N.P.M.); (V.D.T.)
| | - Nguyen Tu Quyet
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (C.T.N.M.); (L.T.K.L.); (T.N.P.M.); (V.D.T.)
| | - Tran Ngoc Phuong Mai
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (C.T.N.M.); (L.T.K.L.); (T.N.P.M.); (V.D.T.)
| | - Vu Dinh Thiem
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (C.T.N.M.); (L.T.K.L.); (T.N.P.M.); (V.D.T.)
| | - Lai Tuan Anh
- Nam Dinh Center for Disease Control, Nam Dinh 420000, Vietnam
| | - Le Van Sanh
- TT Hue Center for Disease Control, Hue, Thua Thien Hue 530000, Vietnam
| | - Nguyen Dang Hien
- Center for Research and Production of Vaccines and Biologicals, Hanoi 100000, Vietnam
| | - Dang Duc Anh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (C.T.N.M.); (L.T.K.L.); (T.N.P.M.); (V.D.T.)
| | | | | | - Nguyen Van Trang
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (C.T.N.M.); (L.T.K.L.); (T.N.P.M.); (V.D.T.)
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Li TT, Xu Q, Liu MC, Wang T, Che TL, Teng AY, Lv CL, Wang GL, Hong F, Liu W, Fang LQ. Prevalence and Etiological Characteristics of Norovirus Infection in China: A Systematic Review and Meta-Analysis. Viruses 2023; 15:1336. [PMID: 37376635 DOI: 10.3390/v15061336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/04/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
Norovirus is a common cause of sporadic cases and outbreaks of gastroenteritis worldwide, although its prevalence and the dominant genotypes responsible for gastroenteritis outbreaks remain obscure. A systematic review was conducted on norovirus infection in China between January 2009 and March 2021. A meta-analysis and beta-binomial regression model were used to explore the epidemiological and clinical characteristics of norovirus infection and the potential factors contributing to the attack rate of the norovirus outbreaks, respectively. A total of 1132 articles with 155,865 confirmed cases were included, with a pooled positive test rate of 11.54% among 991,786 patients with acute diarrhea and a pooled attack rate of 6.73% in 500 norovirus outbreaks. GII.4 was the predominant genotype in both the etiological surveillance and outbreaks, followed by GII.3 in the etiological surveillance, and GII.17 in the outbreaks, with the proportion of recombinant genotypes increasing in recent years. A higher attack rate in the norovirus outbreaks was associated with age group (older adults), settings (nurseries, primary schools, etc.) and region (North China). The nation-wide pooled positive rate in the etiological surveillance of norovirus is lower than elsewhere in the global population, while the dominant genotypes are similar in both the etiological surveillance and the outbreak investigations. This study contributes to the understanding of norovirus infection with different genotypes in China. The prevention and control of norovirus outbreaks during the cold season should be intensified, with special attention paid to and enhanced surveillance performed in nurseries, schools and nursing homes from November to March.
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Affiliation(s)
- Ting-Ting Li
- School of Public Health, Guizhou Medical University, Guiyang 550025, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Qiang Xu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Mei-Chen Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
- School of Public Health, Anhui Medical University, Hefei 230032, China
| | - Tao Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Tian-Le Che
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Ai-Ying Teng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Chen-Long Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Guo-Lin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Feng Hong
- School of Public Health, Guizhou Medical University, Guiyang 550025, China
| | - Wei Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
- School of Public Health, Anhui Medical University, Hefei 230032, China
| | - Li-Qun Fang
- School of Public Health, Guizhou Medical University, Guiyang 550025, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
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9
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Li J, Zhang L, Zou W, Yang Z, Zhan J, Cheng J. Epidemiology and genetic diversity of norovirus GII genogroups among children in Hubei, China, 2017-2019. Virol Sin 2023; 38:351-362. [PMID: 37030436 PMCID: PMC10311278 DOI: 10.1016/j.virs.2023.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 04/03/2023] [Indexed: 04/10/2023] Open
Abstract
Norovirus (NoV) is an important cause of viral acute gastroenteritis (AGE). To gain insights into the epidemiological characteristics and genetic diversity of NoV among children in Hubei, 1216 stool samples from children (≤ 5 years) obtained under AGE surveillance from January 2017 to December 2019 were analyzed. The results showed that NoV was responsible for 14.64% of AGE cases, with the highest detection rate in children aged 7-12 months (19.76%). Statistically significant differences were found between male and female infection rates (χ2 = 8.108, P = 0.004). Genetic analysis of RdRp and VP1 sequences showed that NoV GII genotypes were GII.4 Sydney [P31] (34.35%), GII.3 [P12] (25.95%), GII.2 [P16] (22.90%), GII.4 Sydney [P16] (12.98%), GII.17 [P17] (2.29%), GII.6 [P7] and GII.3 [P16] (each at 0.76%). GII.17 [P17] variants were divided into the Kawasaki323-like lineage and the Kawasaki308-like lineage. A unique recombination event was detected between strains of GII.4 Sydney 2012 and GII.4 Sydney 2016. Significantly, all GII.P16 sequences associated with GII.4/GII.2 obtained in Hubei were correlated with novel GII.2 [P16] variants that re-emerged in Germany in 2016. Antigenic site analysis of complete VP1 sequences from all GII.4 variants from Hubei identified notable variable residues of antibody epitopes. Genotyping under continuous AGE surveillance and observation of the antigenic sites of VP1 are important monitoring strategies for emerging NoV strains.
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Affiliation(s)
- Jing Li
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430079, China
| | - Lingyao Zhang
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430079, China
| | - Wenjing Zou
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430079, China
| | - Zhaohui Yang
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430079, China
| | - Jianbo Zhan
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430079, China.
| | - Jing Cheng
- Wuhan University of Science and Technology, Wuhan, 430065, China.
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10
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Dinu S, Oprea M, Iordache RI, Rusu LC, Usein CR. Genome characterisation of norovirus GII.P17-GII.17 detected during a large gastroenteritis outbreak in Romania in 2021. Arch Virol 2023; 168:116. [PMID: 36947248 DOI: 10.1007/s00705-023-05741-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 03/23/2023]
Abstract
Norovirus (NoV) is one of the leading causes of acute gastroenteritis worldwide. Genotype GII.P17-G.II.17 emerged in Asia between 2013 and 2015 and transiently replaced the GII.4 Sydney 2012 variant circulating at that time. We present the genome characterisation of a GII.P17-GII.17 strain causing a large outbreak in Romania in 2021. Our study shows that the 2021 strain belongs to a novel cluster of genotype GII.17, different from the two previously recognised P.17 clusters. Distinctive substitutions in predicted conformational epitopes of VP1 were identified for this new cluster. Also, our phylogenetic analysis showed the existence of another P.17 cluster grouping strains from France and Canada.
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Affiliation(s)
- Sorin Dinu
- Molecular Epidemiology for Communicable Diseases Laboratory, Cantacuzino National Military Medical Institute for Research and Development, 103 Splaiul Independenței, Bucharest, 050096, Romania.
| | - Mihaela Oprea
- Molecular Epidemiology for Communicable Diseases Laboratory, Cantacuzino National Military Medical Institute for Research and Development, 103 Splaiul Independenței, Bucharest, 050096, Romania
| | - Ramona-Ionela Iordache
- Molecular Epidemiology for Communicable Diseases Laboratory, Cantacuzino National Military Medical Institute for Research and Development, 103 Splaiul Independenței, Bucharest, 050096, Romania
| | - Lavinia-Cipriana Rusu
- National Institute of Public Health, National Center for Surveillance and Control of Communicable Diseases, 1-3 Doctor Leonte Anastasievici, Bucharest, 050463, Romania
| | - Codruța-Romanița Usein
- Molecular Epidemiology for Communicable Diseases Laboratory, Cantacuzino National Military Medical Institute for Research and Development, 103 Splaiul Independenței, Bucharest, 050096, Romania
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11
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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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12
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Phengma P, Khamrin P, Jampanil N, Yodmeeklin A, Ushijima H, Maneekarn N, Kumthip K. The emergence of recombinant norovirus GII.12[P16] and predominance of GII.3[P12] strains in pediatric patients with acute gastroenteritis in Thailand, 2019-2020. J Med Virol 2023; 95:e28321. [PMID: 36397269 DOI: 10.1002/jmv.28321] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/17/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022]
Abstract
Norovirus (NoV) and sapovirus (SaV) are important pathogens that cause acute gastroenteritis (AGE) in all age groups, commonly in children worldwide. Recently, a number of studies have reported a wide variety of NoV recombinant strains. This study aimed to investigate the distribution of NoV and SaV recombinant strains circulating in Chiang Mai, Thailand, during 2019-2020. One hundred and twenty-four NoV and seven SaV strains detected in children admitted to the hospital with AGE were included in this study. The partial RNA-dependent RNA-polymerase (RdRp)/VP1 regions of these NoV and SaV strains were analyzed by phylogenetic analysis, Simplot, and RDP software. Overall, eight recombination patterns of NoV were detected. NoV GII.4[P16] was the most common strain detected (39.1%), followed by GII.3[P12] (25.0%), GII.4[P31] (17.2%), and other recombinant strains were detected at a lower rate. NoV GII.12[P16] strains were detected for the first time in Thailand. For SaV, none of the recombinant strains was detected. All SaV strains, GI.1/GI.1, GI.2/GI.2, and GII.5/GII.5, exhibited VP1 genotype corresponded to RdRp genotype. In conclusion, this study demonstrates the distribution and diversity of NoV and SaV recombinant strains circulating in pediatric patients with AGE in Chiang Mai, during 2019-2020 with the emergence of NoV GII.3[P12] and GII.12[P16].
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Affiliation(s)
- Phitchakorn Phengma
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence (Emerging and Re-Emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
| | - Nutthawadee Jampanil
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Arpaporn Yodmeeklin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence (Emerging and Re-Emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence (Emerging and Re-Emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence (Emerging and Re-Emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
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13
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Lactobacilli as a Vector for Delivery of Nanobodies against Norovirus Infection. Pharmaceutics 2022; 15:pharmaceutics15010063. [PMID: 36678692 PMCID: PMC9863548 DOI: 10.3390/pharmaceutics15010063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
Passive administration of neutralizing antibodies (Abs) is an attractive strategy for the control of gastrointestinal infections. However, an unanswered practical concern is the need to assure the stability of sufficient amounts of orally administered neutralizing Abs against intestinal pathogens (e.g., norovirus) in the harsh environment of the gastrointestinal tract. To this end, we expressed a single-domain Ab (VHH, nanobody) against norovirus on the cell surface of Lactobacillus, a natural and beneficial commensal component of the gut microbiome. First, we used intestinal epithelial cells generated from human induced pluripotent stem cells to confirm that VHH 1E4 showed neutralizing activity against GII.17 norovirus. We then expressed VHH 1E4 as a cell-wall-anchored form in Lactobacillus paracasei BL23. Flow cytometry confirmed the expression of VHH 1E4 on the surface of lactobacilli, and L. paracasei that expressed VHH 1E4 inhibited the replication of GII.17 norovirus in vitro. We then orally administered VHH 1E4-expressing L. paracasei BL23 to germ-free BALB/c mice and confirmed the presence of lactobacilli with neutralizing activity in the intestine for at least 10 days after administration. Thus, cell-wall-anchored VHH-displaying lactobacilli are attractive oral nanobody deliver vectors for passive immunization against norovirus infection.
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14
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Mabasa VV, van Zyl WB, Ismail A, Allam M, Taylor MB, Mans J. Multiple Novel Human Norovirus Recombinants Identified in Wastewater in Pretoria, South Africa by Next-Generation Sequencing. Viruses 2022; 14:v14122732. [PMID: 36560736 PMCID: PMC9788511 DOI: 10.3390/v14122732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/25/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The genogroup II genotype 4 (GII.4) noroviruses are a major cause of viral gastroenteritis. Since the emergence of the Sydney_2012 variant, no novel norovirus GII.4 variants have been reported. The high diversity of noroviruses and periodic emergence of novel strains necessitates continuous global surveillance. The aim of this study was to assess the diversity of noroviruses in selected wastewater samples from Pretoria, South Africa (SA) using amplicon-based next-generation sequencing (NGS). Between June 2018 and August 2020, 200 raw sewage and final effluent samples were collected fortnightly from two wastewater treatment plants in Pretoria. Viruses were recovered using skimmed milk flocculation and glass wool adsorption-elution virus recovery methods and screened for noroviruses using a one-step real-time reverse-transcription PCR (RT-PCR). The norovirus BC genotyping region (570-579 bp) was amplified from detected norovirus strains and subjected to Illumina MiSeq NGS. Noroviruses were detected in 81% (162/200) of samples. The majority (89%, 89/100) of raw sewage samples were positive for at least one norovirus, compared with 73% (73/100) of final effluent samples. Overall, a total of 89 different GI and GII RdRp-capsid combinations were identified, including 51 putative novel recombinants, 34 previously reported RdRp-capsid combinations, one emerging novel recombinant and three Sanger-sequencing confirmed novel recombinants.
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Affiliation(s)
- Victor Vusi Mabasa
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
| | - Walda Brenda van Zyl
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
- National Health Laboratory Service, Tshwane Academic Division, Pretoria 0002, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2192, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2192, South Africa
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Maureen Beatrice Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
| | - Janet Mans
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
- Correspondence: ; Tel.: +27-12-319-2660
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15
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Chen Y, Wu Q, Li G, Li H, Li W, Li H, Qin L, Zheng H, Liu C, Hou M, Liu L. Identification and genetic characterization of a minor norovirus genotype, GIX.1[GII.P15], from China. BMC Genom Data 2022; 23:50. [PMID: 35794533 PMCID: PMC9261040 DOI: 10.1186/s12863-022-01066-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
Background Human noroviruses, single-stranded RNA viruses in the family Caliciviridae, are a leading cause of nonbacterial acute gastroenteritis in people of all ages worldwide. Despite three decades of genomic sequencing and epidemiological norovirus studies, full-length genome analyses of the non-epidemic or minor norovirus genotypes are rare and genomic regions other than ORF2 and 3′-end of ORF1 have been largely understudied, which hampers a better understanding of the evolutionary mechanisms of emergence of new strains. In this study, we detected a rare norovirus genotype, GIX.1[GII.P15], in a vomit sample of a 60 year old woman with acute gastroenteritis using Raji cells and sequenced the complete genome. Results Using electron microscopy, a morphology of spherical and lace-like appearance of norovirus virus particles with a diameter of approximately 30 nm were observed. Phylogenetic analysis of VP1 and the RdRp region indicated that the KMN1 strain could be genotyped as GIX.1[GII.P15]. In addition, the VP1 region of KMN1 strain had 94.15% ± 3.54% percent nucleotide identity (PNI) compared to 26 genomic sequences available in GenBank, indicating a higher degree similarity between KMN1 and other GIX.1[GII.P15] strains. Further analysis of the full genome sequence of KMN1 strain showed that a total of 96 nucleotide substitutions (63 in ORF1, 25 in ORF2, and 8 in ORF3) were found across the genome compared with the consensus sequence of GIX.1[GII.P15] genome, and 6 substitutions caused amino acid changes (4 in ORF1, 1 in ORF2, and 1 in ORF3). However, only one nucleotide substitution results in the amino acid change (P302S) in the VP1 protein and the site was located near one of the predicted conformational B epitopes on the dimer structure. Conclusions The genomic information of the new GIX.1[GII.P15] strain KMN1, which was identified in Kunming, China could provide helpful insights for the study of the genetic evolution of the virus. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01066-6.
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16
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Honjo S, Kuronuma K, Fujiya Y, Nakae M, Ukae S, Nihira H, Yamamoto M, Akane Y, Kondo K, Takahashi S, Kimura H, Tsutsumi H, Kawasaki Y, Tsugawa T. Genotypes and transmission routes of noroviruses causing sporadic acute gastroenteritis among adults and children, Japan, 2015-2019. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 104:105348. [PMID: 35952938 DOI: 10.1016/j.meegid.2022.105348] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Noroviruses (NoVs) are major causes of acute viral gastroenteritis at all ages worldwide. The molecular epidemiology of sporadic cases remains poorly understood, especially in adults. Additionally, no studies have analyzed the transmission route in sporadic acute gastroenteritis. In this study, we investigated cases of very mild sporadic NoV acute gastroenteritis in adults (medical staff) who do not visit the outpatient clinic and child outpatients. We also evaluated genotype differences between adults and children and possible transmission routes in adults during 5 years. The number of NoV positives were 58 in adults and 124 in children. In adults, the NoV positivity rate in this study was higher (64.4%) than that in previous reports of outpatients (10%) and inpatients (5%) in the United State. This finding suggested that the NoV positivity rate might be high in adults with very mild acute gastroenteritis. In adults, human-to-human transmission rates from children and food-borne transmission (raw oysters) were 21.6% (11/51) and 19.6% (10/51), respectively. Among adults, GII.2, GII.4, and GII.17 were the predominant genotypes, with rates of 32.7%, 30.9%, and 21.8%, respectively. Among children, GII.4 and GII.2 were the predominant genotypes, with rates of 45.5% and 40.6%, respectively. GII.17 was only detected in 0.8% (1/123) of children. Trends in NoV genotypes are expected to differ depending on the patient's age. Investigating sporadic cases including the patient's background (age and transmission route) may be helpful to monitor the trend of NoV strains, forecast prevalent NoV GII genotypes, and develop NoV vaccines.
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Affiliation(s)
- Saho Honjo
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Koji Kuronuma
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yoshihiro Fujiya
- Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Mami Nakae
- Division of Infection Control, Sapporo Medical University Hospital, Sapporo, Japan
| | - Susumu Ukae
- Department of Pediatrics, Motomachi Children's Clinic, Sapporo, Japan
| | - Hiroshi Nihira
- Department of Pediatrics, Nihira Children's Clinic, Sapporo, Japan
| | - Masaki Yamamoto
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yusuke Akane
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kenji Kondo
- Department of Pediatrics, Sunagawa City Hospital, Sunagawa, Japan
| | - Satoshi Takahashi
- Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hirokazu Kimura
- Graduate School of Health Science, Gunma Paz University, Takasaki, Japan
| | - Hiroyuki Tsutsumi
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yukihiko Kawasaki
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan.
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17
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Epifanova NV, Sashina TA, Morozova OV, Oparina SV, Novikova NA. An increase in prevalence of recombinant GII.3[P12] norovirus in sporadic acute diarrhea in children in Nizhny Novgorod, Russia, 2018-2021. Virus Genes 2022; 58:467-472. [PMID: 35680691 DOI: 10.1007/s11262-022-01919-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/25/2022] [Indexed: 11/25/2022]
Abstract
Noroviruses are important etiological agents causing acute intestinal infection in humans. In the last decades, the most common norovirus genotype was GII.4 despite a significant genetic diversity among strains, while the active circulation of noroviruses with other genotypes was observed periodically. This study shows an increase in the detection rate of recombinant GII.3[P12] norovirus in Nizhny Novgorod, Russia, from 6.8% in 2018-2019 to 34.9% in 2020-2021. We performed a phylogenetic analysis based on the nucleotide sequences of noroviruses possessing this genotype obtained in this work, as well as presented in the GenBank database. It has been shown that the circulation of GII.3[P12] noroviruses in the study area was the result of several independent introductions, either directly from the Western Pacific region, or through the Asian part of Russia. The polyphyletic origin, the geographical expansion, and the growth of the epidemic significance of the recombinant GII.3[P12] noroviruses were noted.
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Affiliation(s)
- N V Epifanova
- I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - T A Sashina
- I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - O V Morozova
- I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia.
| | - S V Oparina
- I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - N A Novikova
- I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
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18
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Estienney M, Tarris G, Abou-Hamad N, Rouleau A, Boireau W, Chassagnon R, Ayouni S, Daval-Frerot P, Martin L, Bouyer F, Le Pendu J, de Rougemont A, Belliot G. Epidemiological Impact of GII.17 Human Noroviruses Associated With Attachment to Enterocytes. Front Microbiol 2022; 13:858245. [PMID: 35572680 PMCID: PMC9094630 DOI: 10.3389/fmicb.2022.858245] [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: 01/19/2022] [Accepted: 03/23/2022] [Indexed: 01/19/2023] Open
Abstract
For the last 30 years, molecular surveys have shown that human norovirus (HuNoV), predominantly the GII.4 genotype, is one of the main causative agents of gastroenteritis. However, epidemiological surveys have revealed the worldwide emergence of GII.17 HuNoVs. Genetic analysis confirmed that GII.17 strains are distributed into three variants (i.e., Kawasaki 308, Kawasaki 323, and CS-E1). Here, virus-like particles (VLPs) were baculovirus-expressed from these variants to study putative interactions with HBGA. Qualitative analysis of the HBGA binding profile of each variant showed that the most recent and predominant GII.17 variant, Kawasaki 308, possesses a larger binding spectrum. The retrospective study of GII.17 strains documented before the emergence of the dominant Kawasaki 308 variant showed that the emergence of a new GII.17 variant could be related to an increased binding capacity toward HBGA. The use of duodenal histological sections confirmed that recognition of enterocytes involved HBGA for the three GII.17 variants. Finally, we observed that the relative affinity of recent GII.17 VLPs for HBGA remains lower than that of the GII.4-2012 variant. These observations suggest a model whereby a combination of virological factors, such as polymerase fidelity and increased affinity for HBGA, and immunological factors was responsible for the incomplete and non-persistent replacement of GII.4 by new GII.17 variants.
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Affiliation(s)
- Marie Estienney
- National Reference Centre for Gastroenteritis Viruses, Laboratory of Virology, University Hospital of Dijon, Dijon, France.,UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, Université de Bourgogne, Franche-Comté/AgroSup Dijon, Dijon, France
| | - Georges Tarris
- Department of Pathology, University Hospital of Dijon, Dijon, France.,Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Dijon, France
| | - Nicole Abou-Hamad
- National Reference Centre for Gastroenteritis Viruses, Laboratory of Virology, University Hospital of Dijon, Dijon, France.,UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, Université de Bourgogne, Franche-Comté/AgroSup Dijon, Dijon, France.,Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS 6303, Université Bourgogne Franche-Comté, Dijon, France
| | - Alain Rouleau
- FEMTO-ST Institute, CNRS UMR-6174, Université de Bourgogne Franche-Comté, Besançon, France
| | - Wilfrid Boireau
- FEMTO-ST Institute, CNRS UMR-6174, Université de Bourgogne Franche-Comté, Besançon, France
| | - Rémi Chassagnon
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS 6303, Université Bourgogne Franche-Comté, Dijon, France
| | - Siwar Ayouni
- National Reference Centre for Gastroenteritis Viruses, Laboratory of Virology, University Hospital of Dijon, Dijon, France
| | - Philippe Daval-Frerot
- National Reference Centre for Gastroenteritis Viruses, Laboratory of Virology, University Hospital of Dijon, Dijon, France
| | - Laurent Martin
- Department of Pathology, University Hospital of Dijon, Dijon, France.,Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Dijon, France
| | - Frédéric Bouyer
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS 6303, Université Bourgogne Franche-Comté, Dijon, France
| | | | - Alexis de Rougemont
- National Reference Centre for Gastroenteritis Viruses, Laboratory of Virology, University Hospital of Dijon, Dijon, France.,UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, Université de Bourgogne, Franche-Comté/AgroSup Dijon, Dijon, France
| | - Gael Belliot
- National Reference Centre for Gastroenteritis Viruses, Laboratory of Virology, University Hospital of Dijon, Dijon, France.,UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, Université de Bourgogne, Franche-Comté/AgroSup Dijon, Dijon, France
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Changing Predominance of Norovirus Recombinant Strains GII.2[P16] to GII.4[P16] and GII.4[P31] in Thailand, 2017 to 2018. Microbiol Spectr 2022; 10:e0044822. [PMID: 35546545 PMCID: PMC9241750 DOI: 10.1128/spectrum.00448-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Human norovirus is a major virus that causes acute gastroenteritis in all age groups. Recently, norovirus recombinant strains have been reported as the cause of norovirus outbreaks. This study has investigated the distribution of norovirus genotypes and recombinant strains circulating in children hospitalized with diarrhea in Chiang Mai, Thailand from 2017 to 2018. A total of 882 stool specimens were tested for the presence of norovirus GI and GII by reverse transcription-PCR (RT-PCR) assay. Genotypes of the viruses were assessed by partial VP1 nucleotide sequencing and the representative strains were further characterized for norovirus recombinant strains by amplification of ORF1 (RdRp)/ORF2 (VP1 capsid) junction region. From a total of 882 stool samples, 131 (14.9%) were positive for norovirus, of which the majority of norovirus genogroups were norovirus GII, and only one was identified as norovirus GI. A wide variety of norovirus genotypes were detected in this study, including GI.5, GII.2, GII.3, GII.4, GII.6, GII.7, GII.13, GII.14, and GII.17 with the predominance of GII.2 (62.5%) in 2017 and GII.4 (57.0%) in 2018. Nevertheless, it should be noted that GII.4 remained the most predominant genotype (50.4%) in overall prevalence. Analysis of norovirus recombination revealed that several norovirus recombinant strains (GII.2[P16], GII.3[P16], GII.4[P16], GII.4[P31], GII.6[P7], GII.13[P16], and GII.14[P7]) had been identified with the predominance of GII.2[P16] in 2017 and changed to GII.4[P16] and GII.4[P31] in 2018. In conclusion, this study reported the detection of a wide variety of norovirus genotypes and several norovirus recombinant strains in Chiang Mai, Thailand from 2017 to 2018. IMPORTANCE In the present study, the prevalence of norovirus infection in children with acute gastroenteritis in Chiang Mai, Thailand between 2017 and 2018 was 14.9%. A variety of norovirus genotypes were detected, including GI.5, GII.2, GII.3, GII.4, GII.6, GII.7, GII.13, GII.14, and GII.17 with the predominance of GII.4 genotype. In addition, several norovirus recombinant strains (GII.2[P16], GII.3[P16], GII.4[P16], GII.4[P31], GII.6[P7], GII.13[P16], and GII.14[P7]) had been identified. Our results revealed that GII.2[P16] was a predominant strain till the end of 2017 and then was replaced by GII.4[P16] and GII.4[P31] in 2018. The findings imply that norovirus recombinant strains emerged in Chiang Mai, Thailand and that circulating strains changes over time.
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20
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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: 30] [Impact Index Per Article: 15.0] [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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21
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Li Q, Yao P, Jiang J, Mao X, Wang F, Zhang W. Genetic diversity of norovirus associated with outbreaks in school children with acute gastroenteritis in Changzhou, China, 2018-2019. J Med Virol 2022; 94:4005-4011. [PMID: 35383971 DOI: 10.1002/jmv.27743] [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: 07/21/2021] [Revised: 03/15/2022] [Accepted: 03/26/2022] [Indexed: 11/10/2022]
Abstract
OBJECTIVE Norovirus is one of the major causes of outbreaks and sporadic cases of acute gastroenteritis in school children. Obtaining local genotype diversity information regarding norovirus is important for developing and evaluating prevention strategies of the transmission of this virus in school children. METHODS Clinical specimens, obtained from the routine acute gastroenteritis surveillance network from 2018 to 2019, were primarily tested using commercial real-time PCR Kit. Samples with Ct value less than 25 were selected and used for complete genome sequencing and those with Ct value between 25 and 30 were selected and used for he partial VP1 and RdRp regions sequencing. Phylogenetic trees of the viral genome were constructed by using the neighbor-joining method with bootstrap analysis of 1,000 replicates in MEGA 6.0 RESULTS: Epidemiological surveillance of acute intestinal infections (n=384) showed high-level detection (73.18%) of human norovirus in school endemic acute gastroenteritis events in Changzhou, with obvious epidemic characteristics in autumn and winter. Through genotyping, it was found that 93.12% of norovirus were GII, including GII.2, GII.3, GII.4, GII.6, GII.7 and GII.17. By October 2019, two norovirus genotypes, GII.4[P31] and GII.17[P17], became the preponderant epidemic strains. Phylogenetic analysis of the new GII.17[P17] complete genomes showed close relationship with Miyagi strain identified in Japan in 2015, and GII.4[P31] showed close relationship with Jinan strain indentified in China in 2017. CONCLUSION The study highlights the emerging role of GII.4[P31] and GII.17[P17] in causing endemic acute gastroenteritis outbreaks at school children, in Changzhou, China in 2019. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Qiong Li
- Changzhou Center for Disease Prevention and Control, Changzhou, China, 213002
| | - Ping Yao
- Changzhou Center for Disease Prevention and Control, Changzhou, China, 213002
| | - Jingyi Jiang
- Changzhou Center for Disease Prevention and Control, Changzhou, China, 213002
| | - Xujian Mao
- Changzhou Center for Disease Prevention and Control, Changzhou, China, 213002
| | - Fengming Wang
- Changzhou Center for Disease Prevention and Control, Changzhou, China, 213002
| | - Wanju Zhang
- Microbiology Laboratory, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China, 200336
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22
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Huang Y, Zhou N, Zhang S, Yi Y, Han Y, Liu M, Han Y, Shi N, Yang L, Wang Q, Cui T, Jin H. Norovirus detection in wastewater and its correlation with human gastroenteritis: a systematic review and meta-analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:22829-22842. [PMID: 35048346 PMCID: PMC8769679 DOI: 10.1007/s11356-021-18202-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Norovirus (NoV) is a major cause of sporadic cases and outbreaks of acute gastroenteritis (AGE), thereby imposing threat to health globally. It is unclear how quantitation of wastewater NoV reflects the incidence of human AGE infections; therefore, we conducted this systematic review and meta-analysis of published NoV wastewater surveillance studies. A literature search was performed, and all studies on NoV wastewater surveillance were identified. Quantitative results were evaluated. The results showed that the overall detection rate of NoV in wastewater was 82.10% (95% confidence interval [CI]: 74.22-89.92%); NoV concentration was statistically significant in terms of season (P < 0.001), with higher concentration in spring and winter. There were positive correlations between NoV GII concentration in wastewater and GII AGE cases (rs = 0.51, 95% CI: 0.18-0.74, I2 = 0%), total AGE cases (rs = 0.40, 95% CI: 0.15-0.61, I2 = 23%) and NoV outbreaks (rs = 0.47, 95% CI: 0.30-0.62, I2 = 0%). Results of cross-correlation analysis of partial data indicated that variations in GII concentration were consistent with or ahead of those in the number of AGE cases. The diversity of NoV genotypes in wastewater was elucidated, and the dominant strains in wastewater showed a consistent temporal distribution with those responsible for human AGE. Our study demonstrated the potential association of NoV detected in wastewater with AGE infections, and further studies are needed to confirm this conclusion.
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Affiliation(s)
- Yue Huang
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, 210009, China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Nan Zhou
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, 210009, China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Shihan Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, 210009, China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Youqin Yi
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, 210009, China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Ying Han
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, 210009, China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Minqi Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, 210009, China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Yue Han
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, 210009, China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Naiyang Shi
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, 210009, China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Liuqing Yang
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, 210009, China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Qiang Wang
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, 210009, China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Tingting Cui
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, 210009, China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Hui Jin
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, 210009, China.
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
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Kittigul L, Pombubpa K, Rupprom K, Thasiri J. Detection of Norovirus Recombinant GII.2[P16] Strains in Oysters in Thailand. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:59-68. [PMID: 35075605 DOI: 10.1007/s12560-022-09508-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Human norovirus causes sporadic and epidemic acute gastroenteritis worldwide, and the predominant strains are genotype GII.4 variants. Recently, a novel GII.17[P17] and a recombinant GII.2[P16] strain have been reported as the causes of gastroenteritis outbreaks. Outbreaks of norovirus are frequently associated with foodborne illness. In this study, each of 75 oyster samples processed by a proteinase K extraction method and an adsorption-elution method were examined for noroviruses using RT-nested PCR with capsid primers. Thirteen (17.3%) samples processed by either method tested positive for norovirus genogroup II (GII). PCR amplicons were characterized by DNA sequencing and phylogenetic analysis as GII.2 (n = 6), GII.4 (n = 1), GII.17 (n = 3), and GII.unclassified (n = 3). Norovirus-positive samples were further amplified by semi-nested RT-PCR targeting the polymerase-capsid genes. One nucleotide sequence revealed GII.17[P17] Kawasaki strain. Five nucleotide sequences were identified as belonging to the recombinant GII.2[P16] strains by recombination analysis. The collected oyster samples were quantified for norovirus GII genome copy number by RT-quantitative PCR. Using the proteinase K method, GII was found in 13/75 (17.3%) of samples with a range of 8.83-1.85 × 104 genome copies/g of oyster. One sample (1/75, 1.3%) processed by the adsorption-elution method was positive for GII at 5.00 × 101 genome copies/g. These findings indicate the circulation of a new variant GII.17 Kawasaki strain and the recombinant GII.2[P16] in oyster samples corresponding to the circulating strains reported at a global scale during the same period of time. The detection of the recombinant strains in oysters emphasizes the need for continuing systematic surveillance for control and prevention of norovirus gastroenteritis.
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Affiliation(s)
- Leera Kittigul
- Department of Microbiology, Faculty of Public Health, Mahidol University, 420/1 Ratchawithi Road, Bangkok, 10400, Thailand.
| | - Kannika Pombubpa
- Department of Microbiology, Faculty of Public Health, Mahidol University, 420/1 Ratchawithi Road, Bangkok, 10400, Thailand
| | - Kitwadee Rupprom
- Department of Clinical Pathology, Faculty of Medicine Vajira Hospital, Navamindradhiraj University, Bangkok, Thailand
| | - Jinthapha Thasiri
- Department of Microbiology, Faculty of Public Health, Mahidol University, 420/1 Ratchawithi Road, Bangkok, 10400, Thailand
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24
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Abstract
Human noroviruses are the most common viral cause of acute gastroenteritis worldwide. Currently, there are no approved vaccines or specific therapeutics to treat the disease. Some obstacles delaying the development of a norovirus vaccine are: (i) the extreme diversity presented by noroviruses; (ii) our incomplete understanding of immunity to noroviruses; and (iii) the lack of a robust cell culture system or animal model for human noroviruses. Recent advances in in vitro cultivation of norovirus, novel approaches applied to viral genomics and immunity, and completion of vaccine trials and birth cohort studies have provided new information toward a better understanding of norovirus immunity. Here, we will discuss the complex relationship between norovirus diversity and correlates of protection for human noroviruses, and how this information could be used to guide the development of cross-protective vaccines.
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Affiliation(s)
- Lauren A. Ford-Siltz
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States
| | - Kentaro Tohma
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States
| | - Gabriel I. Parra
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States,CONTACT Gabriel I. Parra Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Building 52/72, Room 1308, Silver Spring, MD20993, United States
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25
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Nagarajan V, Chen J, Hsu B, Hsu G, Wang J, Hussain B. Prevalence, Distribution, and Genotypes of Adenovirus and Norovirus in the Puzi River and Its Tributaries and the Surrounding Areas in Taiwan. GEOHEALTH 2021; 5:e2021GH000465. [PMID: 34977444 PMCID: PMC8686652 DOI: 10.1029/2021gh000465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 11/18/2021] [Accepted: 11/27/2021] [Indexed: 05/04/2023]
Abstract
This study investigated the prevalence, distribution, and genotypes of adenoviruses (AdVs) and noroviruses (NoVs) in the Puzi River and surrounding areas in Taiwan. The viruses in the water samples were isolated using the membrane filtration method and the viral nucleic acids were extracted. The RNA of NoVs was reverse-transcribed into complementary DNA using reverse transcriptase-polymerase chain reaction. AdVs and NoVs were detected using nested PCR. Genotyping and phylogenetic analyses were performed to identify the various viral genotypes in the water samples. Human adenovirus (HAdVs) and porcine adenovirus (PAdVs) were the predominant genotypes in the water samples. The prevalence of F species HAdVs serotype 41 (79.2%) and C species PAdVs serotype 5 (18.1%) was higher than that of other serotypes. Among NoVs, genogroup GII was more prevalent than GI. In particular, GII.4 (21.2%) and GII.17 (18.2%) were the predominant genotypes, which was consistent with the clinical findings. The prevalence of both AdVs and NoVs was higher in the winter than spring, summer and autumn seasons. AdVs and NoVs detection results were statistically analyzed by investigating their association with water quality indicators. The results revealed that the presence of AdVs was significantly correlated with the heterotrophic bacterial count, total coliform Escherichia coli, turbidity, salinity, and dissolved oxygen. Meanwhile, the presence of NoVs was only significantly correlated with temperature, pH, and dissolved oxygen. Microbial pollution sources may include urban runoff and discharge of water from livestock farms situated near the river and tributaries within this region of Taiwan. Future studies should include comparisons of the presence of AdVs and NoVs in these known pollution sources and water quality monitoring of these watersheds, as this will allow potential identification of pollution sources. Additionally, remediation strategies must be developed to minimize viral contamination in the river ecosystem.
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Affiliation(s)
- Viji Nagarajan
- Department of Earth and Environmental SciencesNational Chung Cheng UniversityChiayi CountyTaiwan
| | | | - Bing‐Mu Hsu
- Department of Earth and Environmental SciencesNational Chung Cheng UniversityChiayi CountyTaiwan
| | - Gwo‐Jong Hsu
- Division of Infectious DiseasesDitmanson Medical FoundationChia‐Yi Christian HospitalChiayi CountyTaiwan
| | - Jiun‐Ling Wang
- Department of Internal MedicineNational Cheng Kung University HospitalTainanTaiwan
| | - Bashir Hussain
- Department of Earth and Environmental SciencesNational Chung Cheng UniversityChiayi CountyTaiwan
- Department of Biomedical SciencesNational Chung Cheng UniversityChiayi CountyTaiwan
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26
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Dynamics of norovirus genotype change and early characterization of variants in children with diarrhea in central Tunisia, 2001-2012. Arch Virol 2021; 167:99-107. [PMID: 34741201 DOI: 10.1007/s00705-021-05290-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/20/2021] [Indexed: 01/22/2023]
Abstract
Human noroviruses (HuNoVs), especially GII.4 strains, are a major cause of gastroenteritis epidemics in both children and adults. Stool samples were collected from 113 Tunisian children with acute gastroenteritis in 2001 and 2002 and were retrospectively tested for HuNoVs. Fifteen (13.2%) of the 113 samples were positive for HuNoVs, all of which were genogroup II strains, and the GII.4-2004/Hunter variant was predominant (67%). We reconstituted the temporal circulation of HuNoV strains in central Tunisia between 2003 and 2012 using HuNoV isolates reported in our previous studies. A comparative analysis showed a dynamic change in the molecular profile of the HuNoV strains over a 12-year period. We found that GII.4-2004/Hunter strains were circulating as early as June 2002 and that GIX.1[GII.P15] HuNoVs were already circulating four years before this genotype was first reported in Japan in 2006. Our data suggest that epidemic strains of HuNoV circulate for several years in the pediatric population before becoming predominant. This study suggests that children from low-income countries with poor sanitation may play a significant role in the molecular evolution of noroviruses and the global emergence of new epidemic strains.
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27
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Jeong MH, Song YH, Ju SY, Kim SH, Kwak HS, An ES. Surveillance To Prevent the Spread of Norovirus Outbreak from Asymptomatic Food Handlers during the PyeongChang 2018 Olympics. J Food Prot 2021; 84:1819-1823. [PMID: 34115864 DOI: 10.4315/jfp-21-136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/09/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Human noroviruses are major causes of nonbacterial gastroenteritis and are transmitted by both food and water, as well as person-to-person. Asymptomatic norovirus infection of food handlers may play a role in transmission. The outbreak of norovirus infections was recognized in the PyeongChang Winter Olympics, starting with security staff on 3 February 2018. The Ministry of Food and Drug Safety in the Republic of Korea conducted norovirus surveillance from asymptomatic food handlers of food-catering facilities related to the Olympics to prevent the spread of noroviruses. Rectal swab samples (707) from food handlers were collected and examined for noroviruses by using real-time reverse transcription PCR and conventional reverse transcription PCR. Five of 707 samples were identified as noroviruses. Genotypes of the norovirus-positive samples were determined with sequencing analysis. Identified genotypes of norovirus in asymptomatic food handlers included GI.3, GII.4, and GII.17. The GII.17 strain was prevalent among the genotypes, accounting for three of five detections. Food handlers with noroviruses detected in rectal swabs were excluded from cooking, and all food handled by infected food handlers was discarded. Surveillance of norovirus infection for food handlers contributed to preventing norovirus spread. HIGHLIGHTS
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Affiliation(s)
- Min Hee Jeong
- Food Microbiology Division, Food Safety Evaluation Department, National Institute of Food and Drug Safety Evaluation, 187 Osongsaengmyeong 2-ro, Osong, Cheongju, Chungbuk, 28159, Republic of Korea
| | - Yun-Hee Song
- Food Microbiology Division, Food Safety Evaluation Department, National Institute of Food and Drug Safety Evaluation, 187 Osongsaengmyeong 2-ro, Osong, Cheongju, Chungbuk, 28159, Republic of Korea
| | - Si Yeon Ju
- Food Microbiology Division, Food Safety Evaluation Department, National Institute of Food and Drug Safety Evaluation, 187 Osongsaengmyeong 2-ro, Osong, Cheongju, Chungbuk, 28159, Republic of Korea
| | - Soon Han Kim
- Food Microbiology Division, Food Safety Evaluation Department, National Institute of Food and Drug Safety Evaluation, 187 Osongsaengmyeong 2-ro, Osong, Cheongju, Chungbuk, 28159, Republic of Korea
| | - Hyo-Sun Kwak
- Food Microbiology Division, Food Safety Evaluation Department, National Institute of Food and Drug Safety Evaluation, 187 Osongsaengmyeong 2-ro, Osong, Cheongju, Chungbuk, 28159, Republic of Korea
| | - Eun Sook An
- Food Microbiology Division, Food Safety Evaluation Department, National Institute of Food and Drug Safety Evaluation, 187 Osongsaengmyeong 2-ro, Osong, Cheongju, Chungbuk, 28159, Republic of Korea
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28
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Virological and Epidemiological Features of Norovirus Infections in Brazil, 2017-2018. Viruses 2021; 13:v13091724. [PMID: 34578304 PMCID: PMC8472875 DOI: 10.3390/v13091724] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 12/19/2022] Open
Abstract
Noroviruses are considered an important cause of acute gastroenteritis (AGE) across all age groups. Here, we investigated the incidence of norovirus, genotypes circulation, and norovirus shedding in AGE stool samples from outpatients in Brazil. During a two-year period, 1546 AGE stool samples from ten Brazilian states were analyzed by RT-qPCR to detect and quantify GI and GII noroviruses. Positive samples were genotyped by dual sequencing using the ORF1/2 junction region. Overall, we detected norovirus in 32.1% of samples, with a massive predominance of GII viruses (89.1%). We also observed a significant difference between the median viral load of norovirus GI (3.4×105 GC/g of stool) and GII (1.9×107 GC/g). The most affected age group was children aged between 6 and 24 m old, and norovirus infection was detected throughout the year without marked seasonality. Phylogenetic analysis of partial RdRp and VP1 regions identified six and 11 genotype combinations of GI and GII, respectively. GII.4 Sydney[P16] was by far the predominant genotype (47.6%), followed by GII.2[P16], GII.4 Sydney[P31], and GII.6[P7]. We detected, for the first time in Brazil, the intergenogroup recombinant genotype GIX.1[GII.P15]. Our study contributes to the knowledge of norovirus genotypes circulation at the national level, reinforcing the importance of molecular surveillance programs for future vaccine designs.
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29
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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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Lu J, Peng J, Fang L, Zeng L, Lin H, Xiong Q, Liu Z, Jiang H, Zhang C, Yi L, Song T, Ke C, Li C, Ke B, He G, Zhu G, He J, Sun L, Li H, Zheng H. Capturing noroviruses circulating in the population: sewage surveillance in Guangdong, China (2013-2018). WATER RESEARCH 2021; 196:116990. [PMID: 33725645 DOI: 10.1016/j.watres.2021.116990] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
Noroviruses (NoVs) are the leading cause of acute gastroenteritis (AGE) outbreaks. Since 2014, novel genetic variants of NoV have been continuously identified and have caused a sharp increase in the number of AGE outbreaks. The specific geographical distribution and expanding genetic diversity of NoV has posed a challenge to conventional surveillance. Here, we describe the long-term dynamic correlation between NoV distribution in sewage and in the local population through the molecular surveillance of NoV in Guangdong, 2013-2018. The relative viral loads of the GI and GII genotypes in sewage were calculated through RT-PCR. A high-throughput sequencing method and operational taxonomic unit (OTU) clustering pipeline were developed to illustrate the abundances of different genotypes and genetic variants in sewage. Our results showed that the NoV viral loads and the emergence of new variants in sewage were closely associated with NoV outbreak risks in the population. Compared with the outbreaks surveillance, the dominance of the newly emerged variants, GII.P17-GII.17 and GII.P16-GII.2, could be detected one or two months ahead in sewage of a hub city. In addition, the dynamics of pre-epidemic variants, which were rarely detected in clinics, could be captured through sewage surveillance, thus improving our understanding of the origin and evolution of these novel epidemic variants. Our data highlight that sewage surveillance could provide nearly real-time and high-throughput data on NoV circulation in the community. With the advances in sequencing techniques, the sewage surveillance system could also be extended to other related infectious diseases.
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Affiliation(s)
- Jing Lu
- Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; School of Public Health, Southern Medical University, Guangzhou, China.
| | - Jinju Peng
- School of Public Health, Southern Medical University, Guangzhou, China; Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Ling Fang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Lilian Zeng
- Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Huifang Lin
- Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Qianling Xiong
- School of Public Health, Southern Medical University, Guangzhou, China; Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Zhe Liu
- Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Huimin Jiang
- School of Public Health, Southern Medical University, Guangzhou, China; Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Chaozheng Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Lina Yi
- Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Tie Song
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Changwen Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Caixia Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Bixia Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Guanhao He
- Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Guanghu Zhu
- School of Mathematics and Computing Science, Guilin University of Electronic Technology, Guilin 541004, China
| | - Jianfeng He
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Limei Sun
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Hui Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Huanying Zheng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
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31
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Barsoum Z. Pediatric Norovirus Gastroenteritis in Ireland: Seasonal Trends, Correlation with Disease Severity, Nosocomial Acquisition and Viral Co-Infection. Indian J Pediatr 2021; 88:463-468. [PMID: 33085042 DOI: 10.1007/s12098-020-03540-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 10/07/2020] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To determine norovirus frequency, seasonal trends, disease severity and nosocomial acquisition in a region of Ireland. METHODS From November 18th 2016 to November 18th 2017, all children up to 3 y of age who presented to Mayo University Hospital with vomiting and diarrhea, had their stool tested for norovirus and other viruses. Each week of the year was studied in relation to the total number of stool samples requested for norovirus testing, the number of positive stool samples, the calculated median of positive stool samples in two consecutive weeks and their calculated median percentage of positive stool samples in each two consecutive week period. RESULTS During the study period, norovirus was the third leading cause of gastroenteritis (12%), norovirus G2 was the predominant strain; 61% were male; 56% older than 1 y, 78% of cases were severe. No nosocomial disease was detected. The fifth week of January was the week peak. Viral Co- infection was confirmed in four cases of which astrovirus was confirmed in two cases. Three seasons of norovirus gastroenteritis and four short episodes of norovirus infection were noted during 2016/2017. CONCLUSIONS Norovirus is a predominant cause of gastroenteritis. Co- infection with other viruses, mainly astrovirus may occur. Norovirus infections occur throughout the year with a peak in winter.
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Affiliation(s)
- Zakaria Barsoum
- Department of Pediatrics, South West Acute Hospital, Enniskillen, Northern Ireland.
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Yi Y, Wang X, Wang S, Xiong P, Liu Q, Zhang C, Yin F, Huang Z. Identification of a blockade epitope of human norovirus GII.17. Emerg Microbes Infect 2021; 10:954-963. [PMID: 33929932 PMCID: PMC8143627 DOI: 10.1080/22221751.2021.1925162] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human noroviruses are the dominant causative agent of acute viral gastroenteritis worldwide. During the winter of 2014-2015, genotype GII.17 cluster IIIb strains emerged as the leading cause of norovirus infection in Asia and later spread to other parts of the world. It is speculated that mutation at blockade epitopes may have resulted in virus escape from herd immunity, leading to the emergence of GII.17 cluster IIIb variants. Here, we identify a GII.17 cluster IIIb-specific blockade epitope by monoclonal antibody (mAb)-based epitope mapping. Four mAbs (designated as M1 to M4) were generated from mice immunized with virus-like particle (VLP) of a GII.17 cluster IIIb strain. Among them, M1 and M3 reacted specifically with the cluster IIIb VLP but not with the VLPs from clusters II or IIIa. Moreover, M1 and M3 dose-dependently blocked cluster IIIb VLP binding with its ligand, histo-blood group antigens (HBGAs). Epitope mapping revealed that M1 and M3 recognized the same highly exposed epitope consisting of residues 293-296 and 299 in the capsid protein VP1. Sequence alignment showed that the M1/M3 epitope sequence is highly variable among different GII.17 clusters whereas it is identical for cluster IIIIb strains. These data define a dominant blockade epitope of GII.17 norovirus and provide evidence that blockade epitope evolution contributes to the emergence of GII.17 cluster IIIb strains.
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Affiliation(s)
- Yufang Yi
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, People's Republic of China.,Hainan Medical University - The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, People's Republic of China
| | - Xiaoli Wang
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Shuxia Wang
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Pei Xiong
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Qingwei Liu
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Chao Zhang
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Feifei Yin
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, People's Republic of China.,Hainan Medical University - The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, People's Republic of China
| | - Zhong Huang
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, People's Republic of China
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Zuo Y, Xue L, Gao J, Liao Y, Liang Y, Jiang Y, Cai W, Qin Z, Yang J, Zhang J, Wang J, Chen M, Ding Y, Wu Q. Evolutionary Mechanism of Immunological Cross-Reactivity Between Different GII.17 Variants. Front Microbiol 2021; 12:653719. [PMID: 33889144 PMCID: PMC8055840 DOI: 10.3389/fmicb.2021.653719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/09/2021] [Indexed: 11/25/2022] Open
Abstract
Human norovirus is regarded as the leading cause of epidemic acute gastroenteritis with GII.4 being the predominant genotype during the past decades. In the winter of 2014/2015, the GII.17 Kawasaki 2014 emerged as the predominant genotype, surpassing GII.4 in several East Asian countries. Hence, the influence of host immunity response on the continuous evolution of different GII.17 variants needs to be studied in depth. Here, we relate the inferences of evolutionary mechanisms of different GII.17 variants with the investigation of cross-reactivity and cross-protection of their respective antisera using the expression of norovirus P particles in Escherichia coli. The cross-reactivity assay showed that the antisera of previous strains (GII.17 A and GII.17 B) reacted with recent variants (GII.17 C and GII.17 D) at high OD values from 0.8 to 1.16, while recent variant antisera cross-reacting with previous strains were weak with OD values between 0.26 and 0.56. The cross-protection assay indicated that the antisera of previous strains had no inhibitory effect on recent variants. Finally, mutations at amino acids 353–363, 373–384, 394–404, and 444–454 had the greatest impact on cross-reactivity. These data indicate that the recent pandemic variants GII.17 C and GII.17 D avoided the herd immunity effect of previous GII.17 A and GII.17 B strains through antigenic variation.
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Affiliation(s)
- Yueting Zuo
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 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, Guangzhou, China
| | - 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, Guangzhou, China
| | - Yingyin Liao
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yanhui Liang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yueting Jiang
- Department of Laboratory Medicine, First Affiliated Hospital of Guangzhou Medical University, 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, Guangzhou, China
| | - Zhiwei Qin
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jiale Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 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, Guangzhou, China
| | - Juan Wang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 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, Guangzhou, China
| | - Yu Ding
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 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, Guangzhou, China
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Tohma K, Lepore CJ, Degiuseppe JI, Stupka JA, Saito M, Mayta H, Zimic M, Ford-Siltz LA, Gilman RH, Parra GI. Recombinant Nontypeable Genotype II Human Noroviruses in the Americas. Emerg Infect Dis 2021; 26:157-159. [PMID: 31855537 PMCID: PMC6924879 DOI: 10.3201/eid2601.190626] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We report multiple nontypeable genotype II noroviruses circulating in South America; nucleotides differed by >25% from those of other genotypes. These viruses have been circulating in the Americas for ≈20 years and show recombination with other genotypes. Clues to norovirus natural history can guide development of treatment and prevention plans.
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Wang L, Xie D, Yu J, Koroma MM, Qiu M, Duan W, Zhang XF, Dai YC. Serological surveillance of noroviruses in a community-based prospective cohort: a study protocol. BMJ Open 2021; 11:e043228. [PMID: 33664074 PMCID: PMC7934767 DOI: 10.1136/bmjopen-2020-043228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
INTRODUCTION Noroviruses are the leading cause of viral acute gastroenteritis affecting all age groups. Since 2014, the previous rarely reported GII.P17-GII.17 and recombinant GII.P16-GII.2 norovirus emerged, replacing GII.4 predominant genotype, causing increased outbreaks in China and other countries. Meanwhile, GII.4/2012 Sydney strain has re-emerged as the dominant variant in many places in 2015-2018. The role of herd immunity as the driving force during these new emerging or re-emerging noroviruses is poorly defined. Serological surveillance studies on community-based prospective cohort on norovirus are highly needed. METHODS AND ANALYSES This study will include 1000 out of 9798 participants aged 18 years and above from Caofeidian district, Tangshan city, northern China. Baseline data on sociodemographic characteristics and blood samples were collected in 2013-2014. Blood collection will be replicated annually throughout the cohort until 2023. Saliva samples were also collected in 2016. The seroprevalence and seroincidence of blockade antibodies against norovirus genotypes of GII.P17-GII.17, GII.P16-GII.2, the re-emerged GII.4/2012 and potential novel pandemic variants will be evaluated by ELISA. Associations between genotype blockade antibodies and sociodemographic factors and human histo-blood group antigens will be evaluated using univariate and multivariate analysis. The dynamics of herd immunity duration will be estimated in this longitudinal surveillance. ETHICS AND DISSEMINATION The study has been approved by the Ethical Committees of the Staff Hospital of Jidong oil-field of China National Petroleum Corporation. This study will provide insight into the seroprevalence and seroincidence of noroviruses, and their relationships with sociodemographic characteristics and genetic susceptibility. It will also explain herd immunity of the emerged and re-emerged genotypes or variants. The study will further enable an understanding of the mechanism driving the replacement of norovirus genotypes. Research findings will be disseminated in peer-reviewed journals and at scientific meetings.
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Affiliation(s)
- Lu Wang
- Department of Epidemiology,Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Dongjie Xie
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Jingrong Yu
- Department of Epidemiology,Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Mark Momoh Koroma
- Department of Epidemiology,Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Mengsi Qiu
- Department of Epidemiology,Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Wentao Duan
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Xu-Fu Zhang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Ying-Chun Dai
- Department of Epidemiology,Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
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Norovirus strains in patients with acute gastroenteritis in rural and low-income urban areas in northern Brazil. Arch Virol 2021; 166:905-913. [PMID: 33462673 DOI: 10.1007/s00705-020-04944-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 11/13/2020] [Indexed: 01/24/2023]
Abstract
From 2010-2016, a total of 251 stool samples were screened for norovirus using next-generation sequencing (NGS) followed by phylogenetic analysis to investigate the genotypic diversity of noroviruses in rural and low-income urban areas in northern Brazil. Norovirus infection was detected in 19.9% (50/251) of the samples. Eight different genotypes were identified: GII.4_Sydney[P31] (64%, 32/50), GII.6[P7] (14%, 7/50), GII.17[P17] (6%, 3/50), GII.1[P33] (6%, 3/50), GII.3[P16] (4%, 2/50), GII.2[P16] (2%, 1/50), GII.2[P2] (2%, 1/50), and GII.4_New Orleans[P4] (2%, 1/50). Distinct GII.6[P7] variants were recognized, indicating the presence of different co-circulating strains. Elucidating norovirus genetic diversity will improve our understanding of their potential health burden, in particular for the GII.4_Sydney[P31] variant.
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Sasou A, Yuki Y, Kurokawa S, Sato S, Goda Y, Uchida M, Matsumoto N, Sagara H, Watanabe Y, Kuroda M, Sakon N, Sugiura K, Nakahashi-Ouchida R, Ushijima H, Fujihashi K, Kiyono H. Development of Antibody-Fragment-Producing Rice for Neutralization of Human Norovirus. FRONTIERS IN PLANT SCIENCE 2021; 12:639953. [PMID: 33868338 PMCID: PMC8047661 DOI: 10.3389/fpls.2021.639953] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Human norovirus is the leading cause of acute nonbacterial gastroenteritis in people of all ages worldwide. Currently, no licensed norovirus vaccine, pharmaceutical drug, or therapy is available for the control of norovirus infection. Here, we used a rice transgenic system, MucoRice, to produce a variable domain of a llama heavy-chain antibody fragment (VHH) specific for human norovirus (MucoRice-VHH). VHH is a small heat- and acid-stable protein that resembles a monoclonal antibody. Consequently, VHHs have become attractive and useful antibodies (Abs) for oral immunotherapy against intestinal infectious diseases. MucoRice-VHH constructs were generated at high yields in rice seeds by using an overexpression system with RNA interference to suppress the production of the major rice endogenous storage proteins. The average production levels of monomeric VHH (7C6) to GII.4 norovirus and heterodimeric VHH (7C6-1E4) to GII.4 and GII.17 noroviruses in rice seed were 0.54 and 0.28% (w/w), respectively, as phosphate buffered saline (PBS)-soluble VHHs. By using a human norovirus propagation system in human induced pluripotent stem-cell-derived intestinal epithelial cells (IECs), we demonstrated the high neutralizing activity of MucoRice expressing monomeric VHH (7C6) against GII.4 norovirus and of heterodimeric VHH (7C6-1E4) against both GII.4 and GII.17 noroviruses. In addition, MucoRice-VHH (7C6-1E4) retained neutralizing activity even after heat treatment at 90°C for 20 min. These results build a fundamental platform for the continued development of MucoRice-VHH heterodimer as a candidate for oral immunotherapy and for prophylaxis against GII.4 and GII.17 noroviruses in not only healthy adults and children but also immunocompromised patients and the elderly.
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Affiliation(s)
- Ai Sasou
- Division of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoshikazu Yuki
- Division of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Division of Mucosal Vaccines, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shiho Kurokawa
- Division of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shintaro Sato
- Division of Mucosal Vaccines, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Mucosal Vaccine Project, BIKEN Innovative Vaccine Research Alliance Laboratories, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Department of Immunology and Genomics, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Yuki Goda
- Division of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masao Uchida
- Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Japan
| | - Naomi Matsumoto
- Mucosal Vaccine Project, BIKEN Innovative Vaccine Research Alliance Laboratories, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Hiroshi Sagara
- Medical Proteomics Laboratory, The Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Yuji Watanabe
- Medical Proteomics Laboratory, The Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Masaharu Kuroda
- The National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Naomi Sakon
- Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Kotomi Sugiura
- Division of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Rika Nakahashi-Ouchida
- Division of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Division of Mucosal Vaccines, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Ushijima
- Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Kohtaro Fujihashi
- Division of Clinical Vaccinology, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Pediatric Dentistry, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Hiroshi Kiyono
- Division of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Division of Mucosal Vaccines, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
- Division of Gastroenterology, Department of Medicine, Chiba University – University of California San Diego Center for Mucosal Immunology, Allergy, and Vaccine, University of California, San Diego, San Diego, CA, United States
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Yuki Y, Kurokawa S, Sato S, Sasou A, Matsumoto N, Suzuki A, Sakon N, Goda Y, Takeyama N, Miyoshi T, Marcotte H, Tanaka T, Hammarstrom L, Kiyono H. A Heterodimeric Antibody Fragment for Passive Immunotherapy Against Norovirus Infection. J Infect Dis 2021; 222:470-478. [PMID: 32211769 DOI: 10.1093/infdis/jiaa115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/21/2020] [Indexed: 11/14/2022] Open
Abstract
Human noroviruses cause an estimated 685 million infections and 200 000 deaths annually worldwide. Although vaccines against GII.4 and GI.1 genotypes are under development, no information is available regarding vaccines or monoclonal antibodies to other noroviral genotypes. Here, we developed 2 variable-domain llama heavy-chain antibody fragment (VHHs) clones, 7C6 and 1E4, against GII.4 and GII.17 human noroviruses, respectively. Although 7C6 cross-reacted with virus-like particles (VLPs) of GII.17, GII.6, GII.3, and GII.4, it neutralized only GII.4 norovirus. In contrast, 1E4 reacted with and neutralized only GII.17 VLPs. Both VHHs blocked VLP binding to human induced pluripotent stem cell-derived intestinal epithelial cells and carbohydrate attachment factors. Using these 2 VHHs, we produced a heterodimeric VHH fragment that neutralized both GII.4 and GII.17 noroviruses. Because VHH fragments are heat- and acid-stable recombinant monoclonal antibodies, the heterodimer likely will be useful for oral immunotherapy and prophylaxis against GII.4 and GII.17 noroviruses in young, elderly, or immunocompromised persons.
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Affiliation(s)
- Yoshikazu Yuki
- Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Shiho Kurokawa
- Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Shintaro Sato
- Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,BIKEN Innovative Vaccine Research Alliance Laboratories, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,BIKEN Center for Innovative Vaccine Research and Development, Research Foundation for Microbial Diseases, Osaka University, Osaka, Japan.,Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Ai Sasou
- Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Naomi Matsumoto
- BIKEN Innovative Vaccine Research Alliance Laboratories, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Akio Suzuki
- BIKEN Center for Innovative Vaccine Research and Development, Research Foundation for Microbial Diseases, Osaka University, Osaka, Japan
| | - Naomi Sakon
- Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Yuki Goda
- Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Natsumi Takeyama
- Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | | | - Harold Marcotte
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | | | - Lennart Hammarstrom
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Hiroshi Kiyono
- Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Division of Mucosal Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Chiba University-University of California San Diego Center for Mucosal Immunology, Allergy, and Vaccine, University of California, San Diego, California, USA
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Molecular epidemiology and genetic diversity of norovirus infection in children hospitalized with acute gastroenteritis in East Java, Indonesia in 2015-2019. INFECTION GENETICS AND EVOLUTION 2021; 88:104703. [PMID: 33401005 DOI: 10.1016/j.meegid.2020.104703] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/02/2020] [Accepted: 12/30/2020] [Indexed: 12/12/2022]
Abstract
Noroviruses are recognized as a leading cause of outbreaks and sporadic cases of acute gastroenteritis (AGE) among individuals of all ages worldwide, especially in children <5 years old. We investigated the epidemiology of noroviruses among hospitalized children at two hospitals in East Java, Indonesia. Stool samples were collected from 966 children with AGE during September 2015-July 2019. All samples were analyzed by reverse transcription-polymerase chain reaction (RT-PCR) for the amplification of both the RNA-dependent RNA polymerase (RdRp) and the capsid genes of noroviruses. The genotypes were determined by phylogenetic analyses. In 2015-2019, noroviruses were detected in 12.3% (119/966) of the samples. Children <2 years old showed a significantly higher prevalence than those ≥2 years old (P = 0.01). NoV infections were observed throughout the year, with the highest prevalence in December. Based on our genetic analyses of RdRp, GII.[P31] (43.7%, 31/71) was the most prevalent RdRp genotype, followed by GII.[P16] (36.6%, 26/71). GII.[P31] was a dominant genotype in 2016 and 2018, whereas GII.[P16] was a dominant genotype in 2015 and 2017. Among the capsid genotypes, the most predominant norovirus genotype from 2015 to 2018 was GII.4 Sydney_2012 (33.6%, 40/119). The most prevalent genotype in each year was GII.13 in 2015, GII.4 Sydney_2012 in 2016 and 2018, and GII.3 in 2017. Based on the genetic analyses of RdRp and capsid sequences, the strains were clustered into 13 RdRp/capsid genotypes; 12 of them were discordant, e.g., GII.4 Sydney[P31], GII.3[P16], and GII.13[P16]. The predominant genotype in each year was GII.13[P16] in 2015, GII.4 Sydney[P31] in 2016, GII.3[P16] in 2017, and GII.4 Sydney[P31] in 2018. Our results demonstrate high detection rates and genetic diversity of norovirus GII genotypes in pediatric AGE samples from Indonesia. These findings strengthen the importance of the continuous molecular surveillance of emerging norovirus strains.
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Sun C, Zhao Y, Wang G, Huang D, He H, Sai L. Molecular epidemiology of GII noroviruses in outpatients with acute gastroenteritis in Shandong Province, China. Arch Virol 2020; 166:375-387. [PMID: 33226478 DOI: 10.1007/s00705-020-04883-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/03/2020] [Indexed: 11/26/2022]
Abstract
Noroviruses have been recognized as the most important causative agents of acute gastroenteritis. The present study was carried out to investigate the molecular epidemiological features of genotype II (GII) norovirus in outpatients with acute gastroenteritis in Shandong province in China from July 2017 to June 2018. In total, 151 (10.30%) samples were positive for NoV GII strains by RT-PCR. Eight genotypes were detected: GII.2, GII.3, GII.4, GII.6, GII.7, GII.12, GII.13 and GII.17. GII.4 (43.71%) was the most prevalent genotype, and the dominant strains belonged to the group of Sydney-2012 strains. GII.17 (27.15%), which has become the main cause of outbreaks of acute gastroenteritis in China, also accounted for a high proportion. Meanwhile, three recombinant types (GII.P17-GII.7, GII.P3-GII.4 and GII.P12-GII.4) were observed and authenticated using Simplot software. The results showed that GII norovirus was the main cause of acute gastroenteritis in Shandong province. GII.4 and GII.17 were the dominant genotypes. Continuous observation and identification of emerging genotypes are necessary for understanding the evolution of the virus, control of infection, and development of vaccines.
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Affiliation(s)
- Chengxi Sun
- Department of Clinical Laboratory, Cheeloo College of Medicine, Qilu Hospital, Shandong University, Wenhua Xi Road 107, Jinan, 250012, Shandong, China
| | - Yingjie Zhao
- Department of Rheumatology, Cheeloo College of Medicine, Qilu Hospital, Shandong University, Wenhua Xi Road 107, Jinan, 250012, Shandong, China
| | - Gang Wang
- Department of Infectious Diseases, Cheeloo College of Medicine, Qilu Hospital, Shandong University, Wenhua Xi Road 107, Jinan, 250012, Shandong, China
| | - Deyu Huang
- Department of Infectious Diseases, Affiliated Hospital of Qingdao University, Jiangsu Road 16, Qingdao, 266000, Shandong, China
| | - Hong He
- Department of Clinical Laboratory, Affiliated Hospital of Qingdao University, Jiangsu Road 16, Qingdao, 266000, Shandong, China
| | - Lintao Sai
- Department of Infectious Diseases, Cheeloo College of Medicine, Qilu Hospital, Shandong University, Wenhua Xi Road 107, Jinan, 250012, Shandong, China.
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41
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Devant JM, Hansman GS. Structural heterogeneity of a human norovirus vaccine candidate. Virology 2020; 553:23-34. [PMID: 33202318 DOI: 10.1016/j.virol.2020.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 11/30/2022]
Abstract
Human norovirus virus-like particles (VLPs) are assumed to be morphologically and antigenically similar to virion particles. The norovirus virion is assembled from 180 copies of the capsid protein (VP1) and exhibits T = 3 icosahedral symmetry. In this study, we showed that the vaccine candidate GII.4c VP1 formed T = 1 and T = 3 VLPs, but mainly assembled into T = 4 icosahedral particles that were composed of 240 VP1 copies. In contrast, another clinically important genotype, GII.17, almost exclusively folded into T = 3 VLPs. Interestingly, the GII.4c T = 1 particles had higher binding capacities to norovirus-specific Nanobodies than to GII.4c T = 3 and T = 4 particles. Our data indicated that the occluded Nanobody-binding epitopes on the T = 1 particles were more accessible compared to the larger T = 3 and T = 4 particles. Overall, this new data revealed that GII.4c VLPs had a preference for forming the T = 4 icosahedral symmetry and future studies with varied sized norovirus VLPs should take caution when examining antigenicity.
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Affiliation(s)
- Jessica M Devant
- Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg, Germany; Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Grant S Hansman
- Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg, Germany; Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany.
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42
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Hernandez JM, Silva LD, Sousa Junior EC, Cardoso JF, Reymão TKA, Portela ACR, de Lima CPS, Teixeira DM, Lucena MSS, Nunes MRT, Gabbay YB. Evolutionary and Molecular Analysis of Complete Genome Sequences of Norovirus From Brazil: Emerging Recombinant Strain GII.P16/GII.4. Front Microbiol 2020; 11:1870. [PMID: 32849456 PMCID: PMC7423841 DOI: 10.3389/fmicb.2020.01870] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/16/2020] [Indexed: 12/26/2022] Open
Abstract
Noroviruses (NoVs) are enteric viruses that cause acute gastroenteritis, and the pandemic GII.4 genotype is spreading and evolving rapidly. The recombinant GII.P16/GII.4_Sydney strain emerged in 2016, replacing GII.P31/GII.4_Sydney (GII.P31 formerly known as GII.Pe) in some countries. We analyzed the complete genome of 20 NoV strains (17 GII.P31/GII.4_ Sydney and 3 GII.P16/GII.4_Sydney) from Belém and Manaus, Brazil, collected from 2012 to 2016. Phylogenetic trees were constructed by maximum likelihood method from 191 full NoV-VP1 sequences, demonstrated segregation of the Sydney lineage in two larger clades, suggesting that GII.4 strains associated with GII.P16 already have modifications compared with GII.P31/GII.4. Additionally, the Bayesian Markov Chain Monte Carlo method was used to reconstruct a time-scaled phylogenetic tree formed by GII.P16 ORF1 sequences (n = 117) and three complete GII.P16 sequences from Belém. The phylogenetic tree indicated the presence of six clades classified into different capsid genotypes and locations. Evolutionary rates of the ORF1 gene of GII.P16 strains was estimated at 2.01 × 10-3 substitutions/site/year, and the most recent common ancestors were estimated in 2011 (2011-2012, 95% HPD). Comparing the amino acid (AA) sequence coding for ORF1 with the prototype strain GII.P16/GII.4, 36 AA changes were observed, mainly in the non-structural proteins p48, p22, and RdRp. GII.P16/GII.4 strains of this study presented changes in amino acids 310, 333, 373, and 393 of the antigenic sites in the P2 subdomain, and ML tree indicating the division within the Sydney lineage according to the GII.P16 and GII.P31 polymerases. Notably, as noroviruses have high recombination rates and the GII.4 genotype was prevalent for a long time in several locations, additional and continuous evolutionary analyses of this new genotype should be needed in the future.
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Affiliation(s)
- Juliana Merces Hernandez
- Postgraduate Program in Biology of Infectious and Parasitic Agents, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Luciana Damascena Silva
- Virology Section, Evandro Chagas Institute, Brazilian Ministry of Health, Ananindeua, Brazil
| | | | - Jedson Ferreira Cardoso
- Center for Technological Innovation, Evandro Chagas Institute, Brazilian Ministry of Health, Ananindeua, Brazil
| | - Tammy Kathlyn Amaral Reymão
- Postgraduate Program in Biology of Infectious and Parasitic Agents, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | | | | | | | | | | | - Yvone Benchimol Gabbay
- Virology Section, Evandro Chagas Institute, Brazilian Ministry of Health, Ananindeua, Brazil
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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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44
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Chen C, Wu B, Zhang H, Li KF, Liu R, Wang HL, Yan JB. Molecular evolution of GII.P17-GII.17 norovirus associated with sporadic acute gastroenteritis cases during 2013-2018 in Zhoushan Islands, China. Virus Genes 2020; 56:279-287. [PMID: 32065329 DOI: 10.1007/s11262-020-01744-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 02/10/2020] [Indexed: 12/13/2022]
Abstract
In this study, we investigated the molecular characteristics and spatio-temporal dynamics of GII.P17-GII.17 norovirus in Zhoushan Islands during 2013-2018. We collected 1849 samples from sporadic acute gastroenteritis patients between January 2013 and August 2018 in Zhoushan Islands, China. Among the 1849 samples, 134 (7.24%) samples were positive for human norovirus (HuNoV). The complete sequence of GII.17 VP1 gene was amplified from 31 HuNoV-positive samples and sequenced. A phylogenetic tree was constructed based on the full-length sequence of the VP1 gene. Phylogenetic analysis revealed that the GII.17 genotype detected during 2014-2018 belongs to the new GII.17 Kawasaki variant. Divergence analysis revealed that the time of the most recent common ancestor (TMRCA) of GII.17 in Zhoushan Islands was estimated to be between 1997 and 1998. The evolutionary rate of the VP1 gene of the GII.17 genotype norovirus was 1.14 × 10-3 (95% HPD: 0.62-1.73 × 10-3) nucleotide substitutions/site/year. The spatio-temporal diffusion analysis of the GII.17 genotype identified Hong Kong as the epicenter for GII.17 dissemination. The VP1 gene sequence of Zhoushan Island isolates correlated with that of Hong Kong and Japan isolates.
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Affiliation(s)
- Can Chen
- Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China.,Zhejiang Provincial Key Laboratory of Health Risk Factors for Seafood, Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China.,Jiangxi Province Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang, 330006, Jiangxi, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affifiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Bing Wu
- Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China.,Zhejiang Provincial Key Laboratory of Health Risk Factors for Seafood, Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China
| | - Hui Zhang
- Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China.,Zhejiang Provincial Key Laboratory of Health Risk Factors for Seafood, Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China
| | - Ke-Feng Li
- Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China.,Zhejiang Provincial Key Laboratory of Health Risk Factors for Seafood, Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China
| | - Rong Liu
- Jiangxi Province Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Hong-Ling Wang
- Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China. .,Zhejiang Provincial Key Laboratory of Health Risk Factors for Seafood, Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China.
| | - Jian-Bo Yan
- Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China. .,Zhejiang Provincial Key Laboratory of Health Risk Factors for Seafood, Zhoushan Center for Disease Control and Prevention, Zhoushan, Zhejiang Province, China. .,Jiangxi Province Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang, 330006, Jiangxi, China.
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Ozaki K, Matsushima Y, Nagasawa K, Aso J, Saraya T, Yoshihara K, Murakami K, Motoya T, Ryo A, Kuroda M, Katayama K, Kimura H. Molecular Evolution of the Protease Region in Norovirus Genogroup II. Front Microbiol 2020; 10:2991. [PMID: 31993031 PMCID: PMC6971112 DOI: 10.3389/fmicb.2019.02991] [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: 09/02/2019] [Accepted: 12/10/2019] [Indexed: 11/13/2022] Open
Abstract
Noroviruses are a major cause of viral epidemic gastroenteritis in humans worldwide. The protease (Pro) encoded in open reading frame 1 (ORF1) is an essential enzyme for proteolysis of the viral polyprotein. Although there are some reports regarding the evolutionary analysis of norovirus GII-encoding genes, there are few reports focused on the Pro region. We analyzed the molecular evolution of the Pro region of norovirus GII using bioinformatics approaches. A time-scaled phylogenetic tree of the Pro region constructed using a Bayesian Markov chain Monte Carlo method indicated that the common ancestor of GII diverged from GIV around 1680 CE [95% highest posterior density (HPD), 1607-1749]. The GII Pro region emerged around 1752 CE (95%HPD, 1707-1794), forming three further lineages. The evolutionary rate of GII Pro region was estimated at more than 10-3 substitutions/site/year. The distribution of the phylogenetic distances of each genotype differed, and showed genetic diversity. Mapping of the negative selection and substitution sites of the Pro structure showed that the substitution sites in the Pro protein were mostly produced under neutral selection in positions structurally adjacent to the active sites for proteolysis, whereas negative selection was observed in residues distant from the active sites. The phylodynamics of GII.P4, GII.P7, GII.P16, GII.P21, and GII.P31 indicated that their effective population sizes increased during the period from 2005 to 2016 and the increase in population size was almost consistent with the collection year of these genotypes. These results suggest that the Pro region of the norovirus GII evolved rapidly, but under no positive selection, with a high genetic divergence, similar to that of the RNA-dependent RNA polymerase (RdRp) region and the VP1 region of noroviruses.
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Affiliation(s)
- Keita Ozaki
- Graduate School of Health Sciences, Gunma Paz University, Takasaki, Japan
- Niitaka Co., Ltd., Osaka, Japan
| | - Yuki Matsushima
- Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Japan
| | | | - Jumpei Aso
- Department of Respiratory Medicine, Kyorin University School of Medicine, Mitaka, Japan
| | - Takeshi Saraya
- Department of Respiratory Medicine, Kyorin University School of Medicine, Mitaka, Japan
| | - Keisuke Yoshihara
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Koichi Murakami
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Takumi Motoya
- Ibaraki Prefectural Institute of Public Health, Mito, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjuku, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Graduate School of Infection Control Sciences, Kitasato Institute for Life Sciences, Kitasato University, Minato, Japan
| | - Hirokazu Kimura
- Graduate School of Health Sciences, Gunma Paz University, Takasaki, Japan
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Japan
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46
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Molecular Detection and Epidemiology of Etiologic Agents among Children with Acute Gastroenteritis at a Secondary Hospital from 2015 to 2018. ACTA ACUST UNITED AC 2020. [DOI: 10.14776/piv.2020.27.e13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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47
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das Neves Costa LCP, Teixeira DM, Portela ACR, de Lima ICG, da Silva Bandeira R, Sousa Júnior EC, Siqueira JAM, Resque HR, da Silva LD, Gabbay YB. Molecular and evolutionary characterization of norovirus GII.17 in the northern region of Brazil. BMC Infect Dis 2019; 19:1021. [PMID: 31791261 PMCID: PMC6889554 DOI: 10.1186/s12879-019-4628-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 11/11/2019] [Indexed: 01/06/2023] Open
Abstract
Background Currently, norovirus (NoV) is associated with one-fifth of all acute gastroenteritis (AGE) cases worldwide. The NoV GII.17_2014 variant has been associated with gastroenteritis outbreaks in several Asian countries, replacing the previously dominant Sydney 2012 variant. There is limited data about circulation of this new strain in Brazil. This study aimed to describe the phylogenetic and evolutionary characteristics of the GII.17_2014 strains in the Northern region of Brazil. Methods NoV was detected by enzyme immunoassay (EIA) in 645 stool samples of AGE cases that were reported in Pará and Amazonas states during 2015–2016. All positive samples were tested for NoV GI and GII by reverse transcription polymerase chain reaction (RT-PCR) and the amplicons were subjected to genome sequencing. The GII.17-positive samples were retested by PCR using different sets of designed primers, which target a highly conserved capsid gene region. Next, the amplicons were sequenced and phylogenetically analyzed using Bayesian inferences. Results Of the 645 samples tested, 208 (32.2%) tested were positive for NoV by EIA, among which 95 (45.7%) were genotyped. Among the genotyped samples, 12 (12.6%) were characterized as GII.17_2014 with the first case detected in November 2015 (1/30, 3.3%) and the others in 2016 (11/65, 16.9%). All strains found in our study were clustered in clade D (epidemic strain). The uncorrelated log-normal model estimations calculated the rate of evolution for GII-17 strains as 1.95 × 10− 3 (1.28 × 10− 3–2.63 × 10− 3). In total, 36 nucleotide changes were observed after analyzing the VP1 sequence, among which 28 occurred in the P2 region. Conclusions These data demonstrate the evolutionary dynamics in NoV GII.17_2014 strains, which indicated high mutation rates with nucleotide substitutions and indels that are related to the elevated levels of antigenic diversity. This partly explains the increase in viral prevalence.
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Affiliation(s)
- Larissa Cristina Prado das Neves Costa
- Postgraduate Program in Parasitic Biology in the Amazon, Universidade do Estado do Pará, Instituto Evandro Chagas, Belém, PA, Brazil. .,Virology Section, Evandro Chagas Institute, Brazilian Ministry of Health, Rodovia BR-316, Km 7 s/n, Levilândia, Ananindeua, Pará, 67030-000, Brazil.
| | - Dielle Monteiro Teixeira
- Postgraduate Program in Virology, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, PA, Brazil
| | - Ana Caroline Rodrigues Portela
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, PA, Brazil
| | - Ian Carlos Gomes de Lima
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, PA, Brazil
| | - Renato da Silva Bandeira
- Postgraduate Program in Virology, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, PA, Brazil
| | - Edivaldo Costa Sousa Júnior
- Postgraduate Program in Virology, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, PA, Brazil
| | | | - Hugo Reis Resque
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, PA, Brazil
| | - Luciana Damascena da Silva
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, PA, Brazil
| | - Yvone Benchimol Gabbay
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, PA, Brazil
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Strubbia S, Phan MVT, Schaeffer J, Koopmans M, Cotten M, Le Guyader FS. Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next-Generation Sequencing. FOOD AND ENVIRONMENTAL VIROLOGY 2019; 11:400-409. [PMID: 31446609 PMCID: PMC6848244 DOI: 10.1007/s12560-019-09402-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 08/17/2019] [Indexed: 05/06/2023]
Abstract
This study aimed to optimize a method to identify human enteric viruses in sewage and stool samples using random primed next-generation sequencing. We tested three methods, two employed virus enrichment based on the binding properties of the viral capsid using pig-mucin capture or by selecting viral RNA prior to library preparation through a capture using the SureSelect target enrichment. The third method was based on a non-specific biophysical precipitation with polyethylene glycol. Full genomes of a number of common human enteric viruses including norovirus, rotavirus, husavirus, enterovirus and astrovirus were obtained. In stool samples full norovirus genome were detected as well as partial enterovirus genome. A variety of norovirus sequences was detected in sewage samples, with genogroup II being more prevalent. Interestingly, the pig-mucin capture enhanced not only the recovery of norovirus and rotavirus but also recovery of astrovirus, sapovirus and husavirus. Documenting sewage virome using these methods provides information for molecular epidemiology and may be useful in developing strategies to prevent further spread of viruses.
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Affiliation(s)
- Sofia Strubbia
- Ifremer, Laboratoire de Microbiologie, LSEM-SG2M, BP 21105, 44311, Nantes Cedex 3, France
| | - My V T Phan
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Julien Schaeffer
- Ifremer, Laboratoire de Microbiologie, LSEM-SG2M, BP 21105, 44311, Nantes Cedex 3, France
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Matthew Cotten
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- London School of Hygiene and Tropical Medicine, London, UK
- Uganda Virus Research Institute, Entebbe, Uganda
- MRC-Centre for Virus Research, Glasgow, UK
| | - Françoise S Le Guyader
- Ifremer, Laboratoire de Microbiologie, LSEM-SG2M, BP 21105, 44311, Nantes Cedex 3, France.
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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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50
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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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