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Xu D, Li J, Han L, Chen D, Bao W, Li L, Wang H, Shui J, Liang R, Liu Y, Liu Y, Cai K, Chen W. Epidemics and diversity of norovirus variants with acute gastroenteritis outbreak in Hongshan District, Wuhan City, China, 2021-2023. J Infect Public Health 2024; 17:102499. [PMID: 39067200 DOI: 10.1016/j.jiph.2024.102499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/30/2024] Open
Abstract
BACKGROUND Norovirus is the predominant pathogen causing foodborne illnesses and acute gastroenteritis (AGE) outbreaks worldwide, imposing a significant disease burden. This study aimed to investigate the epidemiological characteristics and genotypic diversity of norovirus outbreaks in Hongshan District, Wuhan City. METHODS A total of 463 AGE cases from 39 AGE-related outbreaks in Hongshan District between January 1, 2021, and June 30, 2023, were included in the study. Reverse transcription-polymerase chain reaction (RT-PCR) was used to identify norovirus types GI and GII in anal swab samples from all cases. Norovirus-positive samples were sequenced and analyzed for the open reading frame (ORF) 1/ORF2 hinge region. RESULTS 26 norovirus infectious outbreaks were reported among 39 acute diarrheal outbreaks, including 14 outbreaks in kindergartens, 8 in elementary schools, and 4 in universities. Based on clinical symptoms and epidemiological investigations, a total of 1295 individuals were identified as having been exposed to norovirus, yielding an attack rate of 35.75 %. A higher proportion of outbreaks was observed during the winter and spring seasons (38.46 %). Additionally, norovirus-positive samples were subjected to sequencing and analysis of the open reading frame (ORF) 1/ORF2 hinge region. Genotypic data for norovirus was successfully obtained from 18 (69.23 %) of the infectious outbreaks, revealing 10 distinct recombinant genotypes. GII.4 Sydney 2012 [P31] and GII.17[P17] were the predominant strains in 2021 and 2022, GII.3 [P12] emerged as the dominant strain in 2023. CONCLUSION Norovirus outbreaks in Hongshan District predominantly occurred in crowded educational institutions, with peaks in the cold season and a high attack rate in universities. GII.3 [P12] has become the locally predominant strain.
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Affiliation(s)
- Dandan Xu
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Wuhan Hongshan Center for Disease Control and Prevention, Wuhan, Hubei 430065, China
| | - Jing Li
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, Hubei 430079, China
| | - Lingyan Han
- Wuhan Hongshan Center for Disease Control and Prevention, Wuhan, Hubei 430065, China
| | - Ding Chen
- Wuhan Hongshan Center for Disease Control and Prevention, Wuhan, Hubei 430065, China
| | - Wubo Bao
- Wuhan Hongshan Center for Disease Control and Prevention, Wuhan, Hubei 430065, China
| | - Li Li
- Wuhan Hongshan Center for Disease Control and Prevention, Wuhan, Hubei 430065, China
| | - Huawei Wang
- Wuhan Hongshan Center for Disease Control and Prevention, Wuhan, Hubei 430065, China
| | - Jinglin Shui
- Wuhan Hongshan Center for Disease Control and Prevention, Wuhan, Hubei 430065, China
| | - Ruyi Liang
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yang Liu
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yingle Liu
- The State Key Laboratory of Virology of China,Wuhan, Hubei 430072, China
| | - Kun Cai
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, Hubei 430079, China.
| | - Weihong Chen
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.
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Omatola CA, Mshelbwala PP, Okolo MLO, Onoja AB, Abraham JO, Adaji DM, Samson SO, Okeme TO, Aminu RF, Akor ME, Ayeni G, Muhammed D, Akoh PQ, Ibrahim DS, Edegbo E, Yusuf L, Ocean HO, Akpala SN, Musa OA, Adamu AM. Noroviruses: Evolutionary Dynamics, Epidemiology, Pathogenesis, and Vaccine Advances-A Comprehensive Review. Vaccines (Basel) 2024; 12:590. [PMID: 38932319 PMCID: PMC11209302 DOI: 10.3390/vaccines12060590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Noroviruses constitute a significant aetiology of sporadic and epidemic gastroenteritis in human hosts worldwide, especially among young children, the elderly, and immunocompromised patients. The low infectious dose of the virus, protracted shedding in faeces, and the ability to persist in the environment promote viral transmission in different socioeconomic settings. Considering the substantial disease burden across healthcare and community settings and the difficulty in controlling the disease, we review aspects related to current knowledge about norovirus biology, mechanisms driving the evolutionary trends, epidemiology and molecular diversity, pathogenic mechanism, and immunity to viral infection. Additionally, we discuss the reservoir hosts, intra-inter host dynamics, and potential eco-evolutionary significance. Finally, we review norovirus vaccines in the development pipeline and further discuss the various host and pathogen factors that may complicate vaccine development.
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Affiliation(s)
- Cornelius Arome Omatola
- Department of Microbiology, Kogi State University, Anyigba 272102, Kogi State, Nigeria; (C.A.O.)
| | | | | | - Anyebe Bernard Onoja
- Department of Virology, University College Hospital, Ibadan 211101, Oyo State, Nigeria
| | - Joseph Oyiguh Abraham
- Department of Microbiology, Kogi State University, Anyigba 272102, Kogi State, Nigeria; (C.A.O.)
| | - David Moses Adaji
- Department of Biotechnology Science and Engineering, University of Alabama, Huntsville, AL 35899, USA
| | - Sunday Ocholi Samson
- Department of Molecular Biology, Biotechnology, and Biochemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 29, 50-370 Wrocław, Poland
| | - Therisa Ojomideju Okeme
- Department of Biological Sciences, Federal University Lokoja, Lokoja 260101, Kogi State, Nigeria
| | - Ruth Foluke Aminu
- Department of Microbiology, Kogi State University, Anyigba 272102, Kogi State, Nigeria; (C.A.O.)
| | - Monday Eneojo Akor
- Department of Microbiology, Kogi State University, Anyigba 272102, Kogi State, Nigeria; (C.A.O.)
| | - Gideon Ayeni
- Department of Biochemistry, Kogi State University, Anyigba 272102, Kogi State, Nigeria
| | - Danjuma Muhammed
- Epidemiology and Public Health Unit, Department of Biology, Universiti Putra, Seri Kembangan 43300, Malaysia
| | - Phoebe Queen Akoh
- Department of Microbiology, Kogi State University, Anyigba 272102, Kogi State, Nigeria; (C.A.O.)
| | | | - Emmanuel Edegbo
- Department of Microbiology, Kogi State University, Anyigba 272102, Kogi State, Nigeria; (C.A.O.)
| | - Lamidi Yusuf
- Department of Microbiology, Kogi State University, Anyigba 272102, Kogi State, Nigeria; (C.A.O.)
| | | | - Sumaila Ndah Akpala
- Department of Microbiology, Kogi State University, Anyigba 272102, Kogi State, Nigeria; (C.A.O.)
- Department of Biotechnology, Federal University Lokoja, Lokoja 260101, Kogi State, Nigeria
| | - Oiza Aishat Musa
- Department of Microbiology, Kogi State University, Anyigba 272102, Kogi State, Nigeria; (C.A.O.)
| | - Andrew Musa Adamu
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville 4811, QLD, Australia
- College of Public Health Medical and Veterinary Sciences, James Cook University, Townsville 4811, QLD, Australia
- Centre for Tropical Biosecurity, James Cook University, Townsville 4811, QLD, Australia
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3
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Chandran S, Gibson KE. Improving the Detection and Understanding of Infectious Human Norovirus in Food and Water Matrices: A Review of Methods and Emerging Models. Viruses 2024; 16:776. [PMID: 38793656 PMCID: PMC11125872 DOI: 10.3390/v16050776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Human norovirus (HuNoV) is a leading global cause of viral gastroenteritis, contributing to numerous outbreaks and illnesses annually. However, conventional cell culture systems cannot support the cultivation of infectious HuNoV, making its detection and study in food and water matrices particularly challenging. Recent advancements in HuNoV research, including the emergence of models such as human intestinal enteroids (HIEs) and zebrafish larvae/embryo, have significantly enhanced our understanding of HuNoV pathogenesis. This review provides an overview of current methods employed for HuNoV detection in food and water, along with their associated limitations. Furthermore, it explores the potential applications of the HIE and zebrafish larvae/embryo models in detecting infectious HuNoV within food and water matrices. Finally, this review also highlights the need for further optimization and exploration of these models and detection methods to improve our understanding of HuNoV and its presence in different matrices, ultimately contributing to improved intervention strategies and public health outcomes.
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Affiliation(s)
| | - Kristen E. Gibson
- Department of Food Science, Center for Food Safety, University of Arkansas System Division of Agriculture, Fayetteville, AR 72704, USA;
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4
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Shirai T, Phadungsombat J, Ushikai Y, Yoshikaie K, Shioda T, Sakon N. Epidemiological Features of Human Norovirus Genotypes before and after COVID-19 Countermeasures in Osaka, Japan. Viruses 2024; 16:654. [PMID: 38675994 PMCID: PMC11055107 DOI: 10.3390/v16040654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/19/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
We investigated the molecular epidemiology of human norovirus (HuNoV) in all age groups using samples from April 2019 to March 2023, before and after the COVID-19 countermeasures were implemented. GII.2[P16] and GII.4[P31], the prevalent strains in Japan before COVID-19 countermeasures, remained prevalent during the COVID-19 pandemic, except from April to November 2020; in 2021, the prevalence of GII.2[P16] increased among children. Furthermore, there was an increase in the prevalence of GII.4[P16] after December 2022. Phylogenetic analysis of GII.P31 RdRp showed that some strains detected in 2022 belonged to a different cluster of other strains obtained during the present study period, suggesting that HuNoV strains will evolve differently even if they have the same type of RdRp. An analysis of the amino acid sequence of VP1 showed that some antigenic sites of GII.4[P16] were different from those of GII.4[P31]. The present study showed high infectivity of HuNoV despite the COVID-19 countermeasures and revealed changes in the prevalent genotypes and mutations of each genotype. In the future, we will investigate whether GII.4[P16] becomes more prevalent, providing new insights by comparing the new data with those analyzed in the present study.
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Affiliation(s)
- Tatsuya Shirai
- Department of Microbiology, Osaka Institute of Public Health, Osaka 537-0025, Japan; (T.S.)
| | | | - Yumi Ushikai
- Department of Microbiology, Osaka Institute of Public Health, Osaka 537-0025, Japan; (T.S.)
| | - Kunihito Yoshikaie
- Department of Microbiology, Osaka Institute of Public Health, Osaka 537-0025, Japan; (T.S.)
| | - Tatsuo Shioda
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan;
| | - Naomi Sakon
- Department of Microbiology, Osaka Institute of Public Health, Osaka 537-0025, Japan; (T.S.)
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Hayashi T, Kobayashi S, Hirano J, Murakami K. Human norovirus cultivation systems and their use in antiviral research. J Virol 2024; 98:e0166323. [PMID: 38470106 PMCID: PMC11019851 DOI: 10.1128/jvi.01663-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Human norovirus (HuNoV) is a major cause of acute gastroenteritis and foodborne diseases, affecting all age groups. Despite its clinical needs, no approved antiviral therapies are available. Since the discovery of HuNoV in 1972, studies on anti-norovirals, mechanism of HuNoV infection, viral inactivation, etc., have been hampered by the lack of a robust laboratory-based cultivation system for HuNoV. A recent breakthrough in the development of HuNoV cultivation systems has opened opportunities for researchers to investigate HuNoV biology in the context of de novo HuNoV infections. A tissue stem cell-derived human intestinal organoid/enteroid (HIO) culture system is one of those that supports HuNoV replication reproducibly and, to our knowledge, is most widely distributed to laboratories worldwide to study HuNoV and develop therapeutic strategies. This review summarizes recently developed HuNoV cultivation systems, including HIO, and their use in antiviral studies.
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Affiliation(s)
- Tsuyoshi Hayashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sakura Kobayashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Junki Hirano
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Kosuke Murakami
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo, Japan
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6
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Cavadini P, Trogu T, Velarde R, Lavazza A, Capucci L. Recombination between non-structural and structural genes as a mechanism of selection in lagoviruses: The evolutionary dead-end of an RHDV2 isolated from European hare. Virus Res 2024; 339:199257. [PMID: 38347757 PMCID: PMC10654597 DOI: 10.1016/j.virusres.2023.199257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 02/15/2024]
Abstract
The genus Lagovirus, belonging to the family Caliciviridae, emerged around the 1980s. It includes highly pathogenic species, rabbit hemorrhagic disease virus (RHDV/GI.1) and European brown hare syndrome virus (EBHSV/GII.1), which cause fatal hepatitis, and nonpathogenic viruses with enteric tropism, rabbit calicivirus (RCV/GI.3,4) and hare calicivirus (HaCV/GII.2). Lagoviruses have evolved along two independent genetic lineages: GI (RHDV and RCV) in rabbits and GII (EBHSV and HaCV) in hares. To be emphasized is that genomes of lagoviruses, like other caliciviruses, are highly conserved at RdRp-VP60 junctions, favoring intergenotypic recombination events at this point. The recombination between an RCV (genotype GI.3), donor of non-structural (NS) genes, and an unknown virus, donor of structural (S) genes, likely led to the emergence of a new lagovirus in the European rabbit, called RHDV type 2 (GI.2), identified in Europe in 2010. New RHDV2 intergenotypic recombinants isolated in rabbits in Europe and Australia originated from similar events between RHDV2 (GI.2) and RHDV (GI.1) or RCV (GI.3,4). RHDV2 (GI.2) rapidly spread worldwide, replacing RHDV and showing several lagomorph species as secondary hosts. The recombination events in RHDV2 viruses have led to a number of viruses with very different combinations of NS and S genes. Recombinant RHDV2 with NS genes from hare lineage (GII) was recently identified in the European hare. This study investigated the first RHDV2 (GI.2) identified in Italy in European hare (RHDV2_Bg12), demonstrating that it was a new virus that originated from the recombination between RHDV2, as an S-gene donor and a hare lagovirus, not yet identified but presumably nonpathogenic, as an NS gene donor. When rabbits were inoculated with RHDV2_Bg12, neither deaths nor seroconversions were recorded, demonstrating that RHDV2_Bg12 cannot infect the rabbit. Furthermore, despite intensive and continuous field surveillance, RHDV2_Bg12 has never again been identified in either hares or rabbits in Italy or elsewhere. This result showed that the host specificity of lagoviruses can depend not only on S genes, as expected until today, but potentially also on some species-specific NS gene sequences. Therefore, because RHDV2 (GI.2) infects several lagomorphs, which in turn probably harbor several specific nonpathogenic lagoviruses, the possibility of new speciation, especially in those other than rabbits, is real. RHDV2 Bg_12 demonstrated this, although the attempt apparently failed.
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Affiliation(s)
- Patrizia Cavadini
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna Via Bianchi 9, 25124 Brescia, Italy
| | - Tiziana Trogu
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna Via Bianchi 9, 25124 Brescia, Italy
| | - Roser Velarde
- Wildlife Ecology & Health group (WEH) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Antonio Lavazza
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna Via Bianchi 9, 25124 Brescia, Italy.
| | - Lorenzo Capucci
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna Via Bianchi 9, 25124 Brescia, Italy
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Phongroop K, Rattanasrisomporn J, Tangtrongsup S, Rungsipipat A, Piewbang C, Techangamsuwan S. High-resolution melting analysis for simultaneous detection and discrimination between wild-type and vaccine strains of feline calicivirus. Vet Q 2023; 43:1-12. [PMID: 37851857 PMCID: PMC11003490 DOI: 10.1080/01652176.2023.2272188] [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: 04/10/2023] [Accepted: 10/13/2023] [Indexed: 10/20/2023] Open
Abstract
High-resolution melting (HRM) analysis, a post-polymerase chain reaction (PCR) application in a single closed tube, is the straightforward method for simultaneous detection, genotyping, and mutation scanning, enabling more significant dynamic detection and sequencing-free turnaround time. This study aimed to establish a combined reverse-transcription quantitative PCR and HRM (RT-qPCR-HRM) assay for diagnosing and genotyping feline calicivirus (FCV). This developed method was validated with constructed FCV plasmids, clinical swab samples from living cats, fresh-frozen lung tissues from necropsied cats, and four available FCV vaccines. We performed RT-qPCR to amplify a 99-base pair sequence, targeting a segment between open reading frame (ORF) 1 and ORF2. Subsequently, the HRM assay was promptly applied using Rotor-Gene Q® Software. The results significantly revealed simultaneous detection and genetic discrimination between commercially available FCV vaccine strains, wild-type Thai FCV strains, and VS-FCV strains within a single PCR reaction. There was no cross-reactivity with other feline common viruses, including feline herpesvirus-1, feline coronavirus, feline leukemia virus, feline immunodeficiency virus, and feline morbillivirus. The detection limit of the assay was 6.18 × 101 copies/µl. This study, therefore, is the first demonstration of the uses and benefits of the RT-qPCR-HRM assay for FCV detection and strain differentiation in naturally infected cats.
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Affiliation(s)
- Kannika Phongroop
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Department of Companion Animal and Wildlife Clinic, Faculty of Veterinary Medicine, Chiang Mai University, Thailand
| | - Jatuporn Rattanasrisomporn
- Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Sahatchai Tangtrongsup
- Department of Companion Animal and Wildlife Clinic, Faculty of Veterinary Medicine, Chiang Mai University, Thailand
- Research Center of Producing and Development of Products and Innovations for Animal Health and Production, Chiang Mai University, Thailand
| | - Anudep Rungsipipat
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Chutchai Piewbang
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Somporn Techangamsuwan
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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8
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Pham NTK, Khamrin P, Shimizu-Onda Y, Hoque SA, Trinh QD, Komine-Aizawa S, Okitsu S, Maneekarn N, Hayakawa S, Yoshimune K, Ushijima H. Genetic diversity and declining norovirus prevalence in infants and children during Japan's COVID-19 pandemic: a three-year molecular surveillance. Arch Virol 2023; 168:231. [PMID: 37584776 DOI: 10.1007/s00705-023-05856-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/18/2023] [Indexed: 08/17/2023]
Abstract
Noroviruses (NoVs) are a global concern, causing widespread outbreaks and sporadic acute gastroenteritis (AGE) cases across all age groups. Recent research has shed light on the emergence of novel recombinant strains of NoV in various countries. To delve deeper into this phenomenon, we extensively analyzed 1,175 stool samples collected from Japanese infants and children with AGE from six different prefectures in Japan over three years, from July 2018 to June 2021. Our investigation aimed to determine the prevalence and genetic characteristics of NoV associated with sporadic AGE while exploring the possibility of detecting NoV recombination events. Among the analyzed samples, we identified 355 cases positive for NoV, 11 cases attributed to GI genotypes, and 344 associated with GII genotypes. Notably, we discovered four distinct GI genotypes (GI.2, GI.3, GI.4, and GI.6) and seven diverse GII genotypes (GII.2, GII.3, GII.4, GII.6, GII.7, GII.14, and GII.17). The predominant genotypes were GII.4 (56.4%; 194 out of 344), followed by GII.2 and GII.3. Through dual genotyping based on sequencing of the ORF1/ORF2 junction region, we identified a total of 14 different RdRp/capsid genotypes. Of particular interest were the prevalent recombinant genotypes GII.4[P31] and GII.2[P16]. Notably, our study revealed a decrease in the number of children infected with NoV during and after the COVID-19 pandemic. These findings underscore the importance of continuous NoV surveillance efforts.
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Affiliation(s)
- Ngan Thi Kim Pham
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Ohyaguchi Kamicho, Itabashi-ku, Tokyo, 173-8610, Japan
- Department of Applied Molecular Chemistry, College of Industrial Technology, Nihon University, Chiba, Japan
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Yuko Shimizu-Onda
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Ohyaguchi Kamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Sheikh Ariful Hoque
- Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Quang Duy Trinh
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Ohyaguchi Kamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Shihoko Komine-Aizawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Ohyaguchi Kamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Ohyaguchi Kamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Ohyaguchi Kamicho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Kazuaki Yoshimune
- Department of Applied Molecular Chemistry, College of Industrial Technology, Nihon University, Chiba, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Ohyaguchi Kamicho, Itabashi-ku, Tokyo, 173-8610, Japan.
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9
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Zhang P, Xu D, Liu T, Chen L, Ji L. Genetic characterization of rarely reported GII.3[P25] norovirus strain detected in patients with acute gastroenteritis in Huzhou, China, 2021. Virol Sin 2023; 38:646-649. [PMID: 37390869 PMCID: PMC10436046 DOI: 10.1016/j.virs.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 06/25/2023] [Indexed: 07/02/2023] Open
Abstract
•The first genome of GII.3 [P25] strain isolated in China was determined by NGS. •About 19 unique amino acid substitutions were identified in the VP1 region of GII.3 [P25]. •Antigenic variation may have contributed to the re-emerge of GII.3 [P25] strains.
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Affiliation(s)
- Peng Zhang
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China
| | - Deshun Xu
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China
| | - Teng Liu
- Wuxing District Center for Disease Control and Prevention of Huzhou, Huzhou, 313000, China
| | - Liping Chen
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China
| | - Lei Ji
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China.
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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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11
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Lin SC, Bai GH, Lin PC, Chen CY, Hsu YH, Lee YC, Chen SY. Molecular and Genetics-Based Systems for Tracing the Evolution and Exploring the Mechanisms of Human Norovirus Infections. Int J Mol Sci 2023; 24:ijms24109093. [PMID: 37240438 DOI: 10.3390/ijms24109093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/09/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Human noroviruses (HuNoV) are major causes of acute gastroenteritis around the world. The high mutation rate and recombination potential of noroviruses are significant challenges in studying the genetic diversity and evolution pattern of novel strains. In this review, we describe recent advances in the development of technologies for not only the detection but also the analysis of complete genome sequences of noroviruses and the future prospects of detection methods for tracing the evolution and genetic diversity of human noroviruses. The mechanisms of HuNoV infection and the development of antiviral drugs have been hampered by failure to develop the infectious virus in a cell model. However, recent studies have demonstrated the potential of reverse genetics for the recovery and generation of infectious viral particles, suggesting the utility of this genetics-based system as an alternative for studying the mechanisms of viral infection, such as cell entry and replication.
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Affiliation(s)
- Sheng-Chieh Lin
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei City 11031, Taiwan
- Division of Allergy, Asthma, and Immunology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Geng-Hao Bai
- Department of Internal Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei City 10002, Taiwan
| | - Pei-Chun Lin
- Division of Pediatric Gastroenterology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Chung-Yung Chen
- Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan City 32023, Taiwan
- Center for Nanotechnology, Institute of Biomedical Technology, Chung Yuan Christian University, Taoyuan City 32023, Taiwan
| | - Yi-Hsiang Hsu
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yuan-Chang Lee
- Department of Infectious Diseases, School of Medicine, College of Medicine, Taipei Medical University, Taipei City 11031, Taiwan
- Department of Infectious Diseases, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Shih-Yen Chen
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei City 11031, Taiwan
- Division of Pediatric Gastroenterology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
- TMU Research Center for Digestive Medicine, Taipei Medical University, Taipei City 11031, Taiwan
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12
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Kumazaki M, Usuku S. Influence of herd immunity on norovirus: a long-term field study of repeated viral gastroenteritis outbreaks at the same facilities. BMC Infect Dis 2023; 23:265. [PMID: 37101126 PMCID: PMC10132420 DOI: 10.1186/s12879-023-08251-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 04/13/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Viral acute gastroenteritis (AG) is detected worldwide annually. Outbreaks caused by viruses associated with gastroenteritis have been reported repeatedly at the same facilities in Yokohama, Japan over several years. We investigated the statuses of these repeated outbreaks to consider herd immunity at the facility level. METHODS Between September 2007 and August 2017, 1459 AG outbreaks were reported at 1099 facilities. Stool samples were collected for virological testing, and the norovirus gene was amplified and sequenced to determine the genotype using the N-terminal region of the capsid. RESULTS The outbreaks were caused by norovirus, sapovirus, rotavirus A, and rotavirus C. Norovirus was consistently predominant over the 10-year period. Of 1099 facilities, 227 reported multiple outbreaks, of which norovirus-only combinations accounted for 76.2%. More outbreaks were due to different genotype combinations than the same genotype combinations. For facilities that experienced two norovirus outbreaks, the average interval between outbreaks was longer for groups with the same combinations than for groups with different genogroup or genotype combinations, although no statistically significant differences were observed. At 44 facilities, outbreaks occurred repeatedly during the same AG season, and most exhibited combinations of different norovirus genotypes or viruses. Among 49 combinations with the same norovirus genotype at the same facilities over 10 years, the most prevalent genotypes were combinations of genogroup II genotype 4 (GII.4), followed by GII.2, GII.6, GII.3, GII.14, and GI.3. The mean interval between outbreaks was 31.2 ± 26.8 months for all combinations, and the mean intervals were longer for non-GII.4 genotype cases than for GII.4 cases, and statistically significant differences were observed (t-test, P < 0.05). Additionally, these average intervals were longer for kindergarten/nursery schools and primary schools than for nursing homes for older adults (t-test, P < 0.05). CONCLUSIONS Repeated AG outbreaks at the same facilities in Yokohama during the 10-year study period included mainly norovirus combinations. Herd immunity at the facility level was maintained for at least the same AG season. Norovirus genotype-specific herd immunity was maintained for an average of 31.2 months during the study period, and these intervals differed depending on genotype.
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Affiliation(s)
- Makoto Kumazaki
- Microbiological Testing and Research Division, Yokohama City Institute of Public Health, 2-7-1 Tomiokahigashi, Kanazawa-Ku, Yokohama, Kanagawa, 236-0051, Japan.
| | - Shuzo Usuku
- Microbiological Testing and Research Division, Yokohama City Institute of Public Health, 2-7-1 Tomiokahigashi, Kanazawa-Ku, Yokohama, Kanagawa, 236-0051, Japan
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13
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Chen LN, Wang SJ, Wang SM, Fu XL, Zheng WJ, Hao ZY, Zhou HS, Zhang XJ, Zhao YL, Qiu C, von Seidlein L, Qiu TY, Wang XY. Molecular epidemiology analysis of symptomatic and asymptomatic norovirus infections in Chinese infants. Virol J 2023; 20:60. [PMID: 37016444 PMCID: PMC10074819 DOI: 10.1186/s12985-023-02024-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/28/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Norovirus is a leading cause of acute gastroenteritis among children. Previous studies based on symptomatic infections indicated that mutations, rather than recombination drove the evolution of the norovirus ORF2. These characteristics were found in hospital-based symptomatic infections, whereas, asymptomatic infections are frequent and contribute significantly to transmission. METHODS We conducted the first norovirus molecular epidemiology analysis covering both symptomatic and asymptomatic infections derived from a birth cohort study in the northern China. RESULTS During the study, 14 symptomatic and 20 asymptomatic norovirus infections were detected in 32 infants. Out of the 14 strains that caused symptomatic infections, 12 strains were identified as GII.3[P12], and others were GII.4[P31]. Conversely, 17 asymptomatic infections were caused by GII.4[P31], two by GII.2[P16], and one by GII.4[P16]. Regardless of symptomatic and asymptomatic infections, the mutations were detected frequently in the ORF2 region, and almost all recombination were identified in the RdRp-ORF2 region. The majority of the mutations were located around the predefined epitope regions of P2 subdomain indicating a potential for immune evasion. CONCLUSION The role of symptomatic as well as asymptomatic infections in the evolution of norovirus needs to be evaluated continuously.
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Affiliation(s)
- Li-Na Chen
- Key Laboratory of Medical Molecular Virology of MoE & MoH and Institutes of Biomedical Sciences, Fudan University, 138 Yi Xue Yuan Rd., Shanghai, 200032, People's Republic of China
| | - Si-Jie Wang
- Key Laboratory of Medical Molecular Virology of MoE & MoH and Institutes of Biomedical Sciences, Fudan University, 138 Yi Xue Yuan Rd., Shanghai, 200032, People's Republic of China
| | - Song-Mei Wang
- Laboratory of Molecular Biology, Training Center of Medical Experiments, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, People's Republic of China
| | - Xiao-Li Fu
- Key Laboratory of Medical Molecular Virology of MoE & MoH and Institutes of Biomedical Sciences, Fudan University, 138 Yi Xue Yuan Rd., Shanghai, 200032, People's Republic of China
| | - Wen-Jing Zheng
- Key Laboratory of Medical Molecular Virology of MoE & MoH and Institutes of Biomedical Sciences, Fudan University, 138 Yi Xue Yuan Rd., Shanghai, 200032, People's Republic of China
| | - Zhi-Yong Hao
- Zhengding County Center for Disease Control and Prevention, Zhengding, 050800, People's Republic of China
| | - Hai-Song Zhou
- Zhengding County Center for Disease Control and Prevention, Zhengding, 050800, People's Republic of China
| | - Xin-Jiang Zhang
- Zhengding County Center for Disease Control and Prevention, Zhengding, 050800, People's Republic of China
| | - Yu-Liang Zhao
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, 050021, People's Republic of China
| | - Chao Qiu
- Key Laboratory of Medical Molecular Virology of MoE & MoH and Institutes of Biomedical Sciences, Fudan University, 138 Yi Xue Yuan Rd., Shanghai, 200032, People's Republic of China
| | - Lorenz von Seidlein
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 73170, Thailand
| | - Tian-Yi Qiu
- Institute of Clinical Science, ZhongShan Hospital, Fudan University, 180 Feng Ling Road, Shanghai, People's Republic of China.
| | - Xuan-Yi Wang
- Key Laboratory of Medical Molecular Virology of MoE & MoH and Institutes of Biomedical Sciences, Fudan University, 138 Yi Xue Yuan Rd., Shanghai, 200032, People's Republic of China.
- Shanghai Institute of Infectious Disease and Biosecurity, Shanghai, 200032, People's Republic of China.
- Children's Hospital, Fudan University, Shanghai, 200032, People's Republic of China.
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14
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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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15
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Alarcón-Linares ME, Moreno-Docón A, Pérez-Serna L, Camacho J, Rodriguez DS, Gutiérrez-Martín ML, Broncano-Lavado A, Echevarria JE, Cabrerizo M, Fernández-García MD. Rare Recombinant GI.5[P4] Norovirus That Caused a Large Foodborne Outbreak of Gastroenteritis in a Hotel in Spain in 2021. Microbiol Spectr 2023; 11:e0485722. [PMID: 36809021 PMCID: PMC10100975 DOI: 10.1128/spectrum.04857-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 01/25/2023] [Indexed: 02/23/2023] Open
Abstract
Noroviruses are among the most important causes of acute gastroenteritis (AGE). In summer 2021, a large outbreak of norovirus infections affecting 163 patients, including 15 norovirus-confirmed food handlers, occurred in a hotel in Murcia in southeast Spain. A rare GI.5[P4] norovirus strain was identified as the cause of the outbreak. The epidemiological investigation determined that norovirus transmission might have been initiated through an infected food handler. The food safety inspection found that some symptomatic food handlers continued working during illness. Molecular investigation with whole-genome and ORF1 sequencing provided enhanced genetic discrimination over ORF2 sequencing alone and enabled differentiation of the GI.5[P4] strains into separate subclusters, suggesting different chains of transmission. These recombinant viruses have been identified circulating globally over the last 5 years, warranting further global surveillance. IMPORTANCE Due to the large genetic diversity of noroviruses, it is important to enhance the discriminatory power of typing techniques to differentiate strains when investigating outbreaks and elucidating transmission chains. This study highlights the importance of (i) using whole-genome sequencing to ensure genetic differentiation of GI noroviruses to track chains of transmission during outbreak investigations and (ii) the adherence of symptomatic food handlers to work exclusion rules and strict hand hygiene practices. To our knowledge, this study provides the first full-length genome sequences of GI.5[P4] strains apart from the prototype strain.
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Affiliation(s)
| | - Antonio Moreno-Docón
- Hospital Universitario Virgen de la Arrixaca, Murcia, Spain
- IMIB—Arrixaca, Universidad de Murcia, Murcia, Spain
| | | | - Juan Camacho
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | | | | | - Antonio Broncano-Lavado
- Instituto de Investigación Sanitaria—Fundación Jiménez Díaz Hospital Universitario, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Juan-Emilio Echevarria
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - María Cabrerizo
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - María D. Fernández-García
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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16
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Patterns and Temporal Dynamics of Natural Recombination in Noroviruses. Viruses 2023; 15:v15020372. [PMID: 36851586 PMCID: PMC9961210 DOI: 10.3390/v15020372] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/16/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
Noroviruses infect a wide range of mammals and are the major cause of gastroenteritis in humans. Recombination at the junction of ORF1 encoding nonstructural proteins and ORF2 encoding major capsid protein VP1 is a well-known feature of noroviruses. Using all available complete norovirus sequences, we systematically analyzed patterns of natural recombination in the genus Norovirus both throughout the genome and across the genogroups. Recombination events between nonstructural (ORF1) and structural genomic regions (ORF2 and ORF3) were found in all analyzed genogroups of noroviruses, although recombination was most prominent between members of GII, the most common genogroup that infects humans. The half-life times of recombinant forms (clades without evidence of recombination) of human GI and GII noroviruses were 10.4 and 8.4-11.3 years, respectively. There was evidence of many recent recombination events, and most noroviruses that differed by more than 18% of nucleotide sequence were recombinant relative to each other. However, there were no distinct recombination events between viruses that differed by over 42% in ORF2/3, consistent with the absence of systematic recombination between different genogroups. The few inter-genogroup recombination events most likely occurred between ancient viruses before they diverged into contemporary genogroups. The recombination events within ORF1 or between ORF2/3 were generally rare. Thus, noroviruses routinely exchange full structural and nonstructural blocks of the genome, providing a modular evolution.
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17
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Koh EY, Ong J, Wang Y, Toh X, Fernandez CJ, Huangfu T, Hall RN, Toh S, Lim K, Sng W, Lim HP, Ho K, Chang SF, Yap HH. Rabbit haemorrhagic disease virus 2 from Singapore 2020 outbreak revealed an Australian recombinant variant. Virus Evol 2023; 9:vead029. [PMID: 37207001 PMCID: PMC10190043 DOI: 10.1093/ve/vead029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 03/25/2023] [Accepted: 04/27/2023] [Indexed: 05/21/2023] Open
Abstract
Rabbit haemorrhagic disease (RHD) is a significant and debilitating viral disease affecting lagomorphs. In September 2020, Singapore reported its first cases of RHD virus (RHDV) infection in domesticated rabbits. The initial findings reported that the outbreak strain belonged to genotype GI.2 (RHDV2/RHDVb), and epidemiological investigations could not identify the definitive source of the virus origin. Further recombination detection and phylogenetic analyses of the Singapore outbreak strain revealed that the RHDV was a GI.2 structural (S)/GI.4 non-structural (NS) recombinant variant. Sequence analyses on the National Centre for Biotechnology Information (NCBI) database showed high homology to recently emerged Australian variants, which were prevalent in local Australian lagomorph populations since 2017. Time-structured and phylogeographic analyses for the S and NS genes revealed a close genetic relationship between the Singapore RHDV strain and the Australian RHDV variants. More thorough epidemiological inquiries are necessary to ascertain how an Australian RHDV was introduced into the Singapore rabbit population, and opportune development of RHDV diagnostics and vaccines will be important to safeguard lagomorphs from future RHDV infection and disease management.
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Affiliation(s)
| | - Jasmine Ong
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Yifan Wang
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Xinyu Toh
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Charlene Judith Fernandez
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Taoqi Huangfu
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | | | - Steffie Toh
- Centre for Animal & Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Kelvin Lim
- Veterinary Health Management, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Wendy Sng
- Veterinary Health Management, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Hwee Ping Lim
- Veterinary Health Management, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Kelvin Ho
- Veterinary Health Management, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Siow Foong Chang
- Professional and Scientific Services, Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
| | - Him Hoo Yap
- Animal and Veterinary Service, National Parks Board (NParks), 1 Cluny Road, Singapore Botanic Gardens 259569, Singapore
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18
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Winder N, Gohar S, Muthana M. Norovirus: An Overview of Virology and Preventative Measures. Viruses 2022; 14:v14122811. [PMID: 36560815 PMCID: PMC9781483 DOI: 10.3390/v14122811] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Norovirus (NoV) is an enteric non-enveloped virus which is the leading cause of gastroenteritis across all age groups. It is responsible for around 200,000 deaths annually and outbreaks are common in small communities such as educational and care facilities. 40% of all NoV outbreaks occur in long-term and acute-care facilities, forming the majority of outbreaks. Nosocomial settings set ideal environments for ease of transmission, especially due to the presence of immunocompromised groups. It is estimated to cost global economies around £48 billion a year, making it a global issue. NoV is transmitted via the faecal-oral route and infection with it results in asymptomatic cases or gastrointestinal disease. It has high mutational rates and this allows for new variants to emerge and be more resistant. The classification system available divides NoV into 10 genogroups and 49 genotypes based on whole amino acid sequencing of VP1 capsid protein and partial sequencing of RdRp, respectively. The most predominant genotypes which cause gastroenteritis in humans include GI.1 and GII.4, where GII.4 is responsible for more extreme clinical implications such as hospitalisation. In addition, GII.4 has been responsible for 6 pandemic strains, the last of which is the GII.4 Sydney (2012) variant. In recent years, the successful cultivation of HuNoV was reported in stem cell-derived human intestinal enteroids (HIEs), which promises to assist in giving a deeper understanding of its underlying mechanisms of infection and the development of more personalized control measures. There are no specific control measures against NoV, therefore common practices are used against it such as hand washing. No vaccine is available, but the HIL-214 candidate passed clinical phase 2b and shows promise.
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19
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Navarro-Lleó N, Santiso-Bellón C, Vila-Vicent S, Carmona-Vicente N, Gozalbo-Rovira R, Cárcamo-Calvo R, Rodríguez-Díaz J, Buesa J. Recombinant Noroviruses Circulating in Spain from 2016 to 2020 and Proposal of Two Novel Genotypes within Genogroup I. Microbiol Spectr 2022; 10:e0250521. [PMID: 35862999 PMCID: PMC9430863 DOI: 10.1128/spectrum.02505-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 06/25/2022] [Indexed: 11/20/2022] Open
Abstract
Noroviruses are the leading cause of sporadic cases and outbreaks of viral gastroenteritis. For more than 20 years, most norovirus infections have been caused by the pandemic genotype GII.4, yet recent studies have reported the emergence of recombinant strains in many countries. In the present study, 4,950 stool samples collected between January 2016 and April 2020 in Valencia, Spain, from patients with acute gastroenteritis were analyzed to investigate the etiological agent. Norovirus was the most frequently detected enteric virus, with a positivity rate of 9.5% (471/4,950). Among 224 norovirus strains characterized, 175 belonged to genogroup II (GII) and 49 belonged to GI. Using dual genotyping based on sequencing of the open reading frame 1 (ORF1)/ORF2 junction region, we detected 25 different capsid-polymerase-type associations. The most common GII capsid genotype was GII.4 Sydney 2012, followed by GII.2, GII.3, GII.6, and GII.17. A high prevalence of recombinant strains (90.4%) was observed among GII infections between 2018 and 2020. GII.4 Sydney[P16] was the predominant genotype from 2019 to 2020. In addition, GII.P16 polymerase was found harbored within six different capsid genes. GI.4 and GI.3 were the predominant genotypes in genogroup I, in which recombinant strains were also found, such as GI.3[P10], GI.3[P13], and GI.5[P4]. Interestingly, applying the criterion of 2 times the standard deviation, we found that 12 sequences initially classified as GI.3 may represent two new tentative genotypes in genogroup I, designated GI.10 and GI.11. This study shows the extensive diversity of recombinant noroviruses circulating in Spain and highlights the role of recombination events in the spread of noroviruses. IMPORTANCE Human noroviruses are the most common cause of viral diarrhea. There are no approved vaccines to prevent their infections yet, which would be very useful to protect infants, small children, and the elderly in residential institutions. These viruses are extremely contagious and can be transmitted by contaminated food and water as well as directly from person to person. Molecular surveillance and epidemiology of norovirus infections allow the identification of the most common viral strains in different geographical areas over time. Noroviruses show wide genetic variability due to a high rate of mutations but also due to genomic recombinations, as we demonstrate in this study. We have detected 25 different viral capsid-polymerase gene associations among 224 norovirus strains characterized in Spain between January 2016 and April 2020, including two tentative new capsid genotypes in genogroup I.
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Affiliation(s)
- Noemi Navarro-Lleó
- Department of Microbiology, School of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Cristina Santiso-Bellón
- Department of Microbiology, School of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Susana Vila-Vicent
- Department of Microbiology, School of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Noelia Carmona-Vicente
- Department of Microbiology, School of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Roberto Gozalbo-Rovira
- Department of Microbiology, School of Medicine and Dentistry, University of Valencia, Valencia, Spain
- INCLIVA, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Roberto Cárcamo-Calvo
- Department of Microbiology, School of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Jesús Rodríguez-Díaz
- Department of Microbiology, School of Medicine and Dentistry, University of Valencia, Valencia, Spain
- INCLIVA, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Javier Buesa
- Department of Microbiology, School of Medicine and Dentistry, University of Valencia, Valencia, Spain
- INCLIVA, Hospital Clínico Universitario de Valencia, Valencia, Spain
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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: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/16/2022] [Accepted: 04/01/2022] [Indexed: 12/25/2022]
Abstract
Human noroviruses are the leading global cause of viral gastroenteritis. Attempts at developing effective vaccines and treatments against norovirus disease have been stymied by the extreme genetic diversity and rapid geographic distribution of these viruses. The emergence and replacement of predominantly circulating norovirus genotypes has primarily been attributed to mutations on the VP1 capsid protein leading to genetic drift, and more recently to recombination events between the ORF1/ORF2 junction. However, large‐scale research into the historical and geographic distribution of recombinant norovirus strains has been limited in the literature. We performed a comprehensive historical analysis on 30,810 human norovirus sequences submitted to public databases between the years 1995 and 2019. During this time, 37 capsid genotypes and 56 polymerase types were detected across 90 different countries, and 97 unique recombinant genomes were also identified. GII.4, both capsid and polymerase, was the predominately circulating type worldwide for the majority of this time span, save for a brief swell of GII.17 and GII.2 capsid genotypes and a near‐total eclipse by GII.P16, GII.P21 and GII.P31 beginning in 2013. Interestingly, an analysis of 4067 recombinants found that 50.2% (N = 2039) of all recorded sequences belonged to three recently emerged recombinant strains: GII.2[P16], GII.4[P31], and GII.4[P16]. This analysis should provide an important historical foundation for future studies that evaluate the emergence and distribution of noroviruses, as well as the design of cross‐protective vaccines.
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Affiliation(s)
- Joseph A Kendra
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, USA
| | - Kentaro Tohma
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, USA
| | - Gabriel I Parra
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, USA
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21
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Davidson I, Stamelou E, Giantsis IA, Papageorgiou KV, Petridou E, Kritas SK. The Complexity of Swine Caliciviruses. A Mini Review on Genomic Diversity, Infection Diagnostics, World Prevalence and Pathogenicity. Pathogens 2022; 11:pathogens11040413. [PMID: 35456088 PMCID: PMC9030053 DOI: 10.3390/pathogens11040413] [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: 02/23/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 02/01/2023] Open
Abstract
Caliciviruses are single stranded RNA viruses, non-enveloped structurally, that are implicated in the non-bacterial gastroenteritis in various mammal species. Particularly in swine, viral gastroenteritis represents a major problem worldwide, responsible for significant economic losses for the pig industry. Among the wide range of viruses that are the proven or suspected etiological agents of gastroenteritis, the pathogenicity of the members of Caliciviridae family is among the less well understood. In this context, the present review presents and discusses the current knowledge of two genera belonging to this family, namely the Norovirus and the Sapovirus, in relation to swine. Aspects such as pathogenicity, clinical evidence, symptoms, epidemiology and worldwide prevalence, genomic diversity, identification tools as well as interchanging hosts are not only reviewed but also critically evaluated. Generally, although often asymptomatic in pigs, the prevalence of those microbes in pig farms exhibits a worldwide substantial increasing trend. It should be mentioned, however, that the factors influencing the symptomatology of these viruses are still far from well established. Interestingly, both these viruses are also characterized by high genetic diversity. These high levels of molecular diversity in Caliciviridae family are more likely a result of recombination rather than evolutionary or selective adaptation via mutational steps. Thus, molecular markers for their detection are mostly based on conserved regions such as the RdRp region. Finally, it should be emphasized that Norovirus and the Sapovirus may also infect other domestic, farm and wild animals, including humans, and therefore their surveillance and clarification role in diseases such as diarrhea is a matter of public health importance as well.
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Affiliation(s)
- Irit Davidson
- Division of Avian Diseases, Kimron Veterinary Institute, Bet Dagan 50250, Israel;
| | - Efthymia Stamelou
- Department of Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, School of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (E.S.); (K.V.P.); (E.P.); (S.K.K.)
| | - Ioannis A. Giantsis
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece
- Correspondence:
| | - Konstantinos V. Papageorgiou
- Department of Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, School of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (E.S.); (K.V.P.); (E.P.); (S.K.K.)
| | - Evanthia Petridou
- Department of Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, School of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (E.S.); (K.V.P.); (E.P.); (S.K.K.)
| | - Spyridon K. Kritas
- Department of Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, School of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (E.S.); (K.V.P.); (E.P.); (S.K.K.)
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22
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Wang J, Li L, Xu Y, Mao T, Ma Y, Sun X, Liu X, Wang Y, Duan Z. Identification of a novel norovirus species in fox. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 98:105214. [PMID: 35051652 DOI: 10.1016/j.meegid.2022.105214] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/04/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
A novel Norovirus (NoV) was identified by viral metagenomic analysis in fox fecal samples from the Xinjiang Uygur Autonomous Region of China. The virus exhibited typical genomic characteristics of NoVs. It was closely related to the canine NoV GVII strains with 86.0-86.2% and 91.9% amino acid identities in the capsid protein VP1 and RNA-dependent RNA polymerase (RdRp), respectively. The fox NoV clustered phylogenetically with the two canine NoV GVII strains, and it was distant from other NoVs. According to the new classification criteria of NoVs, the new fox NoV belongs to the same genotype as GVII, similar to canine GVII NoVs. Moreover, key amino acid residues in the Histo-blood group antigen (HBGA) binding sites and the HBGA binding pattern of the fox NoV differed significantly from those of human and canine GVII NoVs. This study identified a new GVII norovirus from wild foxes in China. These findings enrich our understanding of the diversity of NoVs and provide further evidence regarding the genetic heterogeneity of NoVs in carnivores.
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Affiliation(s)
- Jindong Wang
- National Institute for Viral Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Lili Li
- National Institute for Viral Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yalong Xu
- Shaanxi Provincial Centre for Disease Control and Prevention, Xi'an 710054, China
| | - Tongyao Mao
- National Institute for Viral Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yalin Ma
- National Institute for Viral Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiaoman Sun
- National Institute for Viral Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiafei Liu
- National Institute for Viral Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yuanzhi Wang
- School of Medicine, Shihezi University, Shihezi 832000, China.
| | - Zhaojun Duan
- National Institute for Viral Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
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23
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Cui Y, Chen X, Yue H, Tang C. First Detection and Genomic Characterization of Bovine Norovirus from Yak. Pathogens 2022; 11:pathogens11020192. [PMID: 35215135 PMCID: PMC8874446 DOI: 10.3390/pathogens11020192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/27/2022] [Accepted: 01/27/2022] [Indexed: 11/16/2022] Open
Abstract
Yak are a unique free-grazing bovine species in high-altitude areas. The objective of this study was to investigate the presence and molecular characteristics of BNoV in yak. A total of 205 diarrheal samples of yak (aged ≤ 3 months) were collected from 10 farms in Sichuan Province, China, from May 2018 to October 2020, and four samples were detected as BNoV-positive with RT-PCR. Moreover, a nearly full-length genome of SMU-YAK-J1 containing three complete ORFs was successfully sequenced. Sequence analysis with only nine genome sequences of the GIII genogroup showed that SMU-YAK-J1 was most closely related with GIII.P2 GIII.4, sharing 90.9% gnomic nucleotide identity, but only shared 71.6–85.9% with other genotypes, which confirmed that SMU-YAK-J1 belongs to genotype GIII.P2 GIII.4. However, compared with the sole genome of GIII.4 in GenBank, the BNoV in this study also exhibited many unique amino acid changes among all the three ORFs, which may represent the unique genetic evolution of BNoV in yak. This study first determined the presence of BNoV in yak, contributing to a better understanding of the prevalence and genetic evolution of BNoV.
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Affiliation(s)
| | | | - Hua Yue
- Correspondence: (H.Y.); (C.T.)
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24
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Tohma K, Saito M, Pajuelo MJ, Mayta H, Zimic M, Lepore CJ, Ford-Siltz LA, Gilman RH, Parra GI. Viral intra-host evolution in immunocompetent children contributes to human norovirus diversification at the global scale. Emerg Microbes Infect 2021; 10:1717-1730. [PMID: 34376124 PMCID: PMC8425682 DOI: 10.1080/22221751.2021.1967706] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/30/2021] [Accepted: 08/08/2021] [Indexed: 11/03/2022]
Abstract
Norovirus is a major cause of acute gastroenteritis. Human noroviruses present >30 different genotypes, with a single genotype (GII.4) predominating worldwide. Concurrent outbreaks of norovirus are often associated with the emergence of new viruses. While different hypotheses have been presented, the source of new mutations in noroviruses is still unknown. In this study, we applied high-resolution sequencing to determine the intra-host viral diversity presented by noroviruses during the acute and shedding phase of infection in children. Profiling viral intra-host diversification at nearly full genome level indicated that GII.4 viruses presented dynamic intra-host variation, while non-GII.4 viruses presented minimal variation throughout the infection. Notably, the intra-host genetic variation during the shedding phase recapitulates the genetic diversity observed at the global level, particularly those mapping at the VP1 antigenic sites. Thus the intra-host evolution in healthy children explains the source of norovirus mutations that results in diversification at the global scale.
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Affiliation(s)
- Kentaro Tohma
- Division of Viral Products, CBER, FDA, Silver Spring, MD, USA
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Monica J. Pajuelo
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Holger Mayta
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirko Zimic
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Cara J Lepore
- Division of Viral Products, CBER, FDA, Silver Spring, MD, USA
| | | | - Robert H. Gilman
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
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25
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Mahar JE, Jenckel M, Huang N, Smertina E, Holmes EC, Strive T, Hall RN. Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses. Virus Evol 2021; 7:veab080. [PMID: 34754513 PMCID: PMC8570162 DOI: 10.1093/ve/veab080] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/14/2021] [Accepted: 09/15/2021] [Indexed: 12/21/2022] Open
Abstract
The diversity of lagoviruses (Caliciviridae) in Australia has increased considerably in recent years. By the end of 2017, five variants from three viral genotypes were present in populations of Australian rabbits, while prior to 2014 only two variants were known. To understand the evolutionary interactions among these lagovirus variants, we monitored their geographical distribution and relative incidence over time in a continental-scale competition study. Within 3 years of the incursion of rabbit haemorrhagic disease virus 2 (RHDV2, denoted genotype GI.1bP-GI.2 [polymerase genotype]P-[capsid genotype]) into Australia, two novel recombinant lagovirus variants emerged: RHDV2-4e (genotype GI.4eP-GI.2) in New South Wales and RHDV2-4c (genotype GI.4cP-GI.2) in Victoria. Although both novel recombinants contain non-structural genes related to those from benign, rabbit-specific, enterotropic viruses, these variants were recovered from the livers of both rabbits and hares that had died acutely. This suggests that the determinants of host and tissue tropism for lagoviruses are associated with the structural genes, and that tropism is intricately connected with pathogenicity. Phylogenetic analyses demonstrated that the RHDV2-4c recombinant emerged independently on multiple occasions, with five distinct lineages observed. Both the new RHDV2-4e and -4c recombinant variants replaced the previous dominant parental RHDV2 (genotype GI.1bP-GI.2) in their respective geographical areas, despite sharing an identical or near-identical (i.e. single amino acid change) VP60 major capsid protein with the parental virus. This suggests that the observed replacement by these recombinants was not driven by antigenic variation in VP60, implicating the non-structural genes as key drivers of epidemiological fitness. Molecular clock estimates place the RHDV2-4e recombination event in early to mid-2015, while the five RHDV2-4c recombination events occurred from late 2015 through to early 2017. The emergence of at least six viable recombinant variants within a 2-year period highlights the high frequency of these events, detectable only through intensive surveillance, and demonstrates the importance of recombination in lagovirus evolution.
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Affiliation(s)
- Jackie E Mahar
- Marie Bashir Institute for Infectious Disease and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Maria Jenckel
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, ACT 2601, Australia
| | - Nina Huang
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, ACT 2601, Australia
| | - Elena Smertina
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, ACT 2601, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Disease and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Tanja Strive
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, ACT 2601, Australia
| | - Robyn N Hall
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, ACT 2601, Australia
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26
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Wang J, Jin M, Zhang H, Zhu Y, Yang H, Yao X, Chen L, Meng J, Hu G, He Y, Duan Z. Norovirus GII.2[P16] strain in Shenzhen, China: a retrospective study. BMC Infect Dis 2021; 21:1122. [PMID: 34717565 PMCID: PMC8556823 DOI: 10.1186/s12879-021-06746-9] [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: 05/25/2020] [Accepted: 09/29/2021] [Indexed: 11/11/2022] Open
Abstract
Background Norovirus (NoV) is the main cause of non-bacterial acute gastroenteritis (AGE) outbreaks worldwide. From September 2015 through August 2018, 203 NoV outbreaks involving 2500 cases were reported to the Shenzhen Center for Disease Control and Prevention. Methods Faecal specimens for 203 outbreaks were collected and epidemiological data were obtained through the AGE outbreak surveillance system in Shenzhen. Genotypes were determined by sequencing analysis. To gain a better understanding of the evolutionary characteristics of NoV in Shenzhen, molecular evolution and mutations were evaluated based on time-scale evolutionary phylogeny and amino acid mutations. Results A total of nine districts reported NoV outbreaks and the reported NoV outbreaks peaked from November to March. Among the 203 NoV outbreaks, 150 were sequenced successfully. Most of these outbreaks were associated with the NoV GII.2[P16] strain (45.3%, 92/203) and occurred in school settings (91.6%, 186/203). The evolutionary rates of the RdRp region and the VP1 sequence were 2.1 × 10–3 (95% HPD interval, 1.7 × 10–3–2.5 × 10–3) substitutions/site/year and 2.7 × 10–3 (95% HPD interval, 2.4 × 10–3–3.1 × 10–3) substitutions/site/year, respectively. The common ancestors of the GII.2[P16] strain from Shenzhen and GII.4 Sydney 2012[P16] diverged from 2011 to 2012. The common ancestors of the GII.2[P16] strain from Shenzhen and previous GII.2[P16] (2010–2012) diverged from 2003 to 2004. The results of amino acid mutations showed 6 amino acid substitutions (*77E, R750K, P845Q, H1310Y, K1546Q, T1549A) were found only in GII.4 Sydney 2012[P16] and the GII.2[P16] recombinant strain. Conclusions This study illustrates the molecular epidemiological patterns in Shenzhen, China, from September 2015 to August 2018 and provides evidence that the epidemic trend of GII.2[P16] recombinant strain had weakened and the non-structural proteins of the recombinant strain might have played a more significant role than VP1. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06746-9.
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Affiliation(s)
- Jing Wang
- Wuhan Wuchang Hospital, Wuchang Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, 430063, China.,Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Miao Jin
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center Control and Prevention, Beijing, 102206, China
| | - Hailong Zhang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Yanan Zhu
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Hong Yang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Xiangjie Yao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Long Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Jun Meng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Guifang Hu
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yaqing He
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China.
| | - Zhaojun Duan
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center Control and Prevention, Beijing, 102206, China
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27
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Zhao B, Hu L, Song Y, Patil K, Ramani S, Atmar RL, Estes MK, Prasad BVV. Norovirus Protease Structure and Antivirals Development. Viruses 2021; 13:v13102069. [PMID: 34696498 PMCID: PMC8537771 DOI: 10.3390/v13102069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/06/2021] [Accepted: 10/09/2021] [Indexed: 11/30/2022] Open
Abstract
Human norovirus (HuNoV) infection is a global health and economic burden. Currently, there are no licensed HuNoV vaccines or antiviral drugs available. The protease encoded by the HuNoV genome plays a critical role in virus replication by cleaving the polyprotein and is an excellent target for developing small-molecule inhibitors. The current strategy for developing HuNoV protease inhibitors is by targeting the enzyme’s active site and designing inhibitors that bind to the substrate-binding pockets located near the active site. However, subtle differential conformational flexibility in response to the different substrates in the polyprotein and structural differences in the active site and substrate-binding pockets across different genogroups, hamper the development of effective broad-spectrum inhibitors. A comparative analysis of the available HuNoV protease structures may provide valuable insight for identifying novel strategies for the design and development of such inhibitors. The goal of this review is to provide such analysis together with an overview of the current status of the design and development of HuNoV protease inhibitors.
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Affiliation(s)
- Boyang Zhao
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (B.Z.); (K.P.); (S.R.); (R.L.A.); (M.K.E.)
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Ketki Patil
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (B.Z.); (K.P.); (S.R.); (R.L.A.); (M.K.E.)
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (B.Z.); (K.P.); (S.R.); (R.L.A.); (M.K.E.)
| | - Robert L. Atmar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (B.Z.); (K.P.); (S.R.); (R.L.A.); (M.K.E.)
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mary K. Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (B.Z.); (K.P.); (S.R.); (R.L.A.); (M.K.E.)
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - B. V. Venkataram Prasad
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (B.Z.); (K.P.); (S.R.); (R.L.A.); (M.K.E.)
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA;
- Correspondence: ; Tel.: +1-713-798-5686
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28
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Glud HA, George S, Skovgaard K, Larsen LE. Zoonotic and reverse zoonotic transmission of viruses between humans and pigs. APMIS 2021; 129:675-693. [PMID: 34586648 PMCID: PMC9297979 DOI: 10.1111/apm.13178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/28/2021] [Indexed: 12/30/2022]
Abstract
Humans and pigs share a close contact relationship, similar biological traits, and one of the highest estimated number of viruses compared to other mammalian species. The contribution and directionality of viral exchange between humans and pigs remain unclear for some of these viruses, but their transmission routes are important to characterize in order to prevent outbreaks of disease in both host species. This review collects and assesses the evidence to determine the likely transmission route of 27 viruses between humans and pigs.
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Affiliation(s)
- Helena Aagaard Glud
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sophie George
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lars Erik Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
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29
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Wei N, Ge J, Tan C, Song Y, Wang S, Bao M, Li J. Epidemiology and evolution of Norovirus in China. Hum Vaccin Immunother 2021; 17:4553-4566. [PMID: 34495811 DOI: 10.1080/21645515.2021.1961465] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Norovirus (NoV) has been recognized as a leading cause of gastroenteritis worldwide. This review estimates the prevalence and genotype distribution of NoV in China to provide a sound reference for vaccine development. Studies were searched up to October 2020 from CNKI database and inclusion criteria were study duration of at least one calendar year and population size of >100. The mean overall NoV prevalence in individuals with sporadic diarrhea/gastroenteritis was 16.68% (20796/124649, 95% CI 16.63-16.72), and the detection rate of NoV was the highest among children. Non-GII.4 strains have replaced GII.4 as the predominant caused multiple outbreaks since 2014. Especially the recombinant GII.P16-GII.2 increased sharply, and virologic data show that the polymerase GII.P16 rather than VP1 triggers pandemic. Due to genetic diversity and rapid evolution, predominant genotypes might change unexpectedly, which has become major obstacle for the development of effective NoV vaccines.
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Affiliation(s)
- Na Wei
- Vaccine R&D, Grand Theravac Life Science (Nanjing) Co., Ltd, Nanjing, China
| | - Jun Ge
- Vaccine R&D, Grand Theravac Life Science (Nanjing) Co., Ltd, Nanjing, China
| | - Changyao Tan
- Vaccine R&D, Grand Theravac Life Science (Nanjing) Co., Ltd, Nanjing, China
| | - Yunlong Song
- Vaccine R&D, Grand Theravac Life Science (Nanjing) Co., Ltd, Nanjing, China
| | - Shiwei Wang
- Vaccine R&D, Grand Theravac Life Science (Nanjing) Co., Ltd, Nanjing, China
| | - Mengru Bao
- Vaccine R&D, Grand Theravac Life Science (Nanjing) Co., Ltd, Nanjing, China
| | - Jianqiang Li
- Vaccine R&D, Grand Theravac Life Science (Nanjing) Co., Ltd, Nanjing, China
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Noroviruses-The State of the Art, Nearly Fifty Years after Their Initial Discovery. Viruses 2021; 13:v13081541. [PMID: 34452406 PMCID: PMC8402810 DOI: 10.3390/v13081541] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/06/2021] [Accepted: 07/31/2021] [Indexed: 12/11/2022] Open
Abstract
Human noroviruses are recognised as the major global cause of viral gastroenteritis. Here, we provide an overview of notable advances in norovirus research and provide a short recap of the novel model systems to which much of the recent progress is owed. Significant advances include an updated classification system, the description of alternative virus-like protein morphologies and capsid dynamics, and the further elucidation of the functions and roles of various viral proteins. Important milestones include new insights into cell tropism, host and microbial attachment factors and receptors, interactions with the cellular translational apparatus, and viral egress from cells. Noroviruses have been detected in previously unrecognised hosts and detection itself is facilitated by improved analytical techniques. New potential transmission routes and/or viral reservoirs have been proposed. Recent in vivo and in vitro findings have added to the understanding of host immunity in response to norovirus infection, and vaccine development has progressed to preclinical and even clinical trial testing. Ongoing development of therapeutics includes promising direct-acting small molecules and host-factor drugs.
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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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Ludwig-Begall LF, Di Felice E, Toffoli B, Ceci C, Di Martino B, Marsilio F, Mauroy A, Thiry E. Analysis of Synchronous and Asynchronous In Vitro Infections with Homologous Murine Norovirus Strains Reveals Time-Dependent Viral Interference Effects. Viruses 2021; 13:823. [PMID: 34063220 PMCID: PMC8147416 DOI: 10.3390/v13050823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 11/16/2022] Open
Abstract
Viral recombination is a key mechanism in the evolution and diversity of noroviruses. In vivo, synchronous single-cell coinfection by multiple viruses, the ultimate prerequisite to viral recombination, is likely to be a rare event and delayed secondary infections are a more probable occurrence. Here, we determine the effect of a temporal separation of in vitro infections with the two homologous murine norovirus strains MNV-1 WU20 and CW1 on the composition of nascent viral populations. WU20 and CW1 were either synchronously inoculated onto murine macrophage cell monolayers (coinfection) or asynchronously applied (superinfection with varying titres of CW1 at half-hour to 24-h delays). Then, 24 h after initial co-or superinfection, quantification of genomic copy numbers and discriminative screening of plaque picked infectious progeny viruses demonstrated a time-dependent predominance of primary infecting WU20 in the majority of viral progenies. Our results indicate that a time interval from one to two hours onwards between two consecutive norovirus infections allows for the establishment of a barrier that reduces or prevents superinfection.
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Affiliation(s)
- Louisa F. Ludwig-Begall
- FARAH Research Centre, Faculty of Veterinary Medicine, Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, Liège University, 4000 Liège, Belgium; (L.F.L.-B.); (B.T.); (A.M.)
| | - Elisabetta Di Felice
- Department of Diagnosis and Surveillance of Exotic Disease, IZS Istituto Zooprofilattico Sperimentale A&M G. Caporale, 64100 Teramo, Italy;
| | - Barbara Toffoli
- FARAH Research Centre, Faculty of Veterinary Medicine, Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, Liège University, 4000 Liège, Belgium; (L.F.L.-B.); (B.T.); (A.M.)
| | - Chiara Ceci
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, Italy; (C.C.); (B.D.M.); (F.M.)
| | - Barbara Di Martino
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, Italy; (C.C.); (B.D.M.); (F.M.)
| | - Fulvio Marsilio
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, Italy; (C.C.); (B.D.M.); (F.M.)
| | - Axel Mauroy
- FARAH Research Centre, Faculty of Veterinary Medicine, Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, Liège University, 4000 Liège, Belgium; (L.F.L.-B.); (B.T.); (A.M.)
- Staff Direction for Risk Assessment, Control Policy, FASFC, 1000 Brussels, Belgium
| | - Etienne Thiry
- FARAH Research Centre, Faculty of Veterinary Medicine, Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, Liège University, 4000 Liège, Belgium; (L.F.L.-B.); (B.T.); (A.M.)
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Cheng HY, Lee CC, Chang YC, Tsai CN, Chao HC, Tsai YT, Hsieh CH, Su SS, Chen SY. Viral shedding in gastroenteritis in children caused by variants and novel recombinant norovirus infections. Medicine (Baltimore) 2021; 100:e25123. [PMID: 33761678 PMCID: PMC9282056 DOI: 10.1097/md.0000000000025123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 02/17/2021] [Indexed: 01/05/2023] Open
Abstract
Human norovirus (NoV) is the leading cause of acute gastroenteritis and the rapid transmission of NoV renders infection control problematic. Our study aimed to investigate viral shedding in gastroenteritis in children caused by variants of emerging norovirus strains infections.We used RNA-dependent RNA polymerase (RdRp) sequencing to measure NoV genome copies in stool to understand the relationship between the clinical manifestations and viral shedding in hospitalized patients. The near full-length NoV genome sequence was amplified via reverse transcription-polymerase chain reaction (RT-PCR) and NoV recombination was analyzed using the Recombination Analysis Tool (RAT).From January 2015 to March 2018, 77 fecal specimens were collected from hospitalized pediatric patients with confirmed NoV gastroenteritis. The NoV genotypes were GII.4 (n = 22), non-GII.4 (n = 14), GII.4 Sydney (n = 21), and GII.P16-GII.2 (n = 20). Viral load increased from days 2 to 9 from the illness onset, resulting in an irregular plateau without peaks. After day 9, the viral load declined gradually and most viral shedding in feces ceased by day 15. The average viral load was highest in GII.4 Sydney followed by GII.P16-GII.2 infections and lowest in non-GII.4 infections. GII.4 unclassified infections showed the longest viral shedding time, followed by GII.4 Sydney infections, GII.P16-GII.2 recombinant infection resulted in the shortest duration. NoVs evolved to form a group of GII.P16-GII.2 variants during the 2017 to 2018 period.The viral load and shedding period and was different in variants of NoV infections in children. High mutation rate of emerging and re-emerging variants was observed to an enhanced epidemic risk rendering continuous surveillance.
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Affiliation(s)
- Hung-Yen Cheng
- Division of Pediatric Gastroenterology, Department of Pediatrics, Taipei Medical University-Shuang Ho Hospital, Taipei
| | - Chung-Chan Lee
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan
| | | | - Chi-Neu Tsai
- Graduate Institute of Clinical Medical Sciences, Chang Gung University College of Medicine, Department of Pediatrics, Chang Gung Memorial Hospital
| | - Hsun-Ching Chao
- Division of Pediatric Gastroenterology, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan
| | - Yin-Tai Tsai
- Department of Medicine Laboratory, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Chia-Hsin Hsieh
- Department of Medicine Laboratory, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Sin-Sheng Su
- Department of Medicine Laboratory, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Shih-Yen Chen
- Division of Pediatric Gastroenterology, Department of Pediatrics, Taipei Medical University-Shuang Ho Hospital, Taipei
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Pairing of Parental Noroviruses with Unequal Competitiveness Provides a Clear Advantage for Emergence of Progeny Recombinants. Appl Environ Microbiol 2021; 87:AEM.02015-20. [PMID: 33187997 PMCID: PMC7848925 DOI: 10.1128/aem.02015-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/02/2020] [Indexed: 11/20/2022] Open
Abstract
Genetic recombination plays a pivotal role in the appearance of human norovirus recombinants that cause global epidemics. However, the factors responsible for the appearance of these recombinants remains largely unknown. In this study, we revealed a selective pressure that restricts parental combinations leading to the emergence of norovirus recombinants. To investigate traces of emerging novel recombinants and their parents in the human population, we isolated mass nucleotide sequence clones of human norovirus genogroups I and II in sewage-affected waters over a 4-year sampling period. Fourteen different phylogenetic combinations of recombinants and their parents were defined from the dozens of phylogenetic lineages circulating in the human population. To evaluate the probability of these combinations, parental lineages of each recombinant were categorized into two groups as HP (relatively higher-competitiveness parents) and LP (relatively lower-competitiveness parents), according to their relative detection frequency. Strong categorization of HP and LP was confirmed by tests with modified data and additional variables. An algorithm that was developed in this study to visualize the chance of mixed infection between parents revealed that HP lineages have a higher chance of mixed infection than LP lineages in the human population. Three parental pairing types in recombinants were defined: HP-HP, HP-LP, and LP-LP. Among these, most recombinants were identified as HP-LP, despite the prediction of dominant emergence of HP-HP-type recombinants. These results suggest that nature favors recombinants of human norovirus that originate from parental pairing of heterogeneous competitiveness.IMPORTANCE Novel recombinants, generated from inter- and intraspecies recombination of norovirus lineages, often emerge and pose a threat to public health. However, the factors determining emergence of these particular recombinants from all possible combinations of parental lineages remain largely unknown. Therefore, current investigations on these recombinants are inevitably limited to postepidemic analyses, which merely identify genetic or phenotypic changes in the newly emerged recombinants compared to their parents. Here, we provide a new theoretical concept that emergence of novel recombinants could be explained by a combination of parental noroviruses thriving in the human population and those circulating at lower levels. This study could provide an additional and important rationale for the proactive environmental monitoring of potential future epidemics due to viral recombinants.
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Ji L, Hu G, Xu D, Wu X, Fu Y, Chen L. Molecular epidemiology and changes in genotype diversity of norovirus infections in acute gastroenteritis patients in Huzhou, China, 2018. J Med Virol 2020; 92:3173-3178. [PMID: 32603477 PMCID: PMC7692952 DOI: 10.1002/jmv.26247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 06/24/2020] [Indexed: 11/09/2022]
Abstract
Norovirus is an important causative agent of acute gastroenteritis worldwide, affecting people of all ages. Stool samples collected from patients with clinical symptoms of acute gastroenteritis in all age groups at the diarrhea outpatient department of the First People's Hospital in Huzhou were analyzed to gain insight into the prevalence and genetic characteristics of norovirus. From January to December 2018, a total of 551 specimens were screened for norovirus by real-time reverse transcription-polymerase chain reaction (RT-PCR). RT-PCR was used for genomic amplification and sequencing of the RNA-dependent RNA polymerase and capsid gene of the positive samples. Genotypes of norovirus were assigned using the norovirus Noronet typing tool and phylogenetic analysis. About 100 (18.1%) specimens were identified as norovirus positive. GII genogroup was the main genogroup identified (83.0%; 83/100). About 42 (42.0%) samples were successfully sequenced and genotyped by RT-PCR. Since one of the samples was dual infection, so we got 43 virus finally. Nine norovirus GII genotypes and four norovirus GI genotypes were detected in Huzhou during our research period. The main two norovirus GII genotypes were GII.2[P16] (54.8%; 23/43) and GII.17[P17] (11.9%; 5/43). We characterized the molecular epidemiology of norovirus infection in acute gastroenteritis patients during 2018. GII genogroup was the main genogroup identified. The dominance norovirus genotype circulating in the population of Huzhou was GII.2[P16] in 2018.
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Affiliation(s)
- Lei Ji
- Microbiological LaboratoryHuzhou Center for Disease Control and PreventionHuzhouChina
| | - Gang Hu
- Obstetrics and GynecologyHuzhou Maternity and Child Health Care HospitalHuzhouChina
| | - Deshun Xu
- Microbiological LaboratoryHuzhou Center for Disease Control and PreventionHuzhouChina
| | - Xiaofang Wu
- Microbiological LaboratoryHuzhou Center for Disease Control and PreventionHuzhouChina
| | - Yun Fu
- Microbiological LaboratoryHuzhou Center for Disease Control and PreventionHuzhouChina
| | - Liping Chen
- Microbiological LaboratoryHuzhou Center for Disease Control and PreventionHuzhouChina
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Na Z, Bo J, Yifei Y, Fuyuan C, Bin H, Yanshu Z, Huan J, Jingliang S, Shuang L. Isolation and Identification of a Murine Norovirus Persistent Infection Strain in China. Front Vet Sci 2020; 7:571730. [PMID: 33335918 PMCID: PMC7736604 DOI: 10.3389/fvets.2020.571730] [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: 06/11/2020] [Accepted: 11/02/2020] [Indexed: 11/13/2022] Open
Abstract
Murine Norovirus (MNV) is one of the most known viruses among viruses in mice. Because of the high prevalence of MNV in frequently used laboratory animals in biomedical researches, there is a significant impact of MNV. There may be different prevalence degrees and molecular characteristics of MNV in different regions around the world. Here, we reported an MNV strain "designated HBTS-1806" isolation from commercial mice's feces that caused a detectable cytopathic effect (CPE) in RAW264.7 cells. According to electron microscopy, the virus was 50-70 nm in diameter. The complete genome of HBTS-1806 is 7383 nucleotides with a structure similar to that of MNV reference strains. According to phylogenetic analysis on the basis of the whole genome, HBTS-1806 shared nucleotide sequence identities of 90.2-95.4% with other Chinese isolates reported. Analysis of amino acid sequence on the basis of ORF1 and ORF2 suggested that the isolated strain may be derived from recombination. Although no gross lesions or histopathological changes were found from mice infected with 5 × 105 TCLD50 of MNV by oral gavage inoculation, the intestinal virus loads lasted 12 weeks, suggesting a persistent infection strain of MNV isolate in China.
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Affiliation(s)
- Zhao Na
- The Experiment Animal Center, North China University of Science and Technology, Tangshan, China
| | - Jiang Bo
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Yang Yifei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Cao Fuyuan
- The Experiment Animal Center, North China University of Science and Technology, Tangshan, China
| | - He Bin
- The Experiment Animal Center, North China University of Science and Technology, Tangshan, China
| | - Zhang Yanshu
- The Experiment Animal Center, North China University of Science and Technology, Tangshan, China
| | - Jin Huan
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Su Jingliang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Li Shuang
- The Experiment Animal Center, North China University of Science and Technology, Tangshan, China
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Chhabra P, Browne H, Huynh T, Diez-Valcarce M, Barclay L, Kosek MN, Ahmed T, Lopez MR, Pan CY, Vinjé J. Single-step RT-PCR assay for dual genotyping of GI and GII norovirus strains. J Clin Virol 2020; 134:104689. [PMID: 33260046 PMCID: PMC7816162 DOI: 10.1016/j.jcv.2020.104689] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/21/2020] [Accepted: 11/06/2020] [Indexed: 01/21/2023]
Abstract
BACKGROUND Noroviruses are the major cause of acute gastroenteritis (AGE) in people of all ages globally. Standardized genotyping is key for outbreak investigations and surveillance networks. OBJECTIVE Here we describe the validation of a one-step conventional RT-PCR assay for sequence-based dual typing of GI and GII noroviruses. This polymerase (P) and capsid (C) dual typing assay uses a combination of previously published oligonucleotide primers amplifying a genomic region spanning the 3'-end of ORF1 and 5'end of ORF2 resulting in a 579 bp product for GI and 570 bp product for GII viruses. RESULTS The limit of detection of the assay ranged from 5 to 50 copies of viral RNA per reaction for GI and GII. To validate the assay, we tested 2,663 noroviruspositive stool samples from outbreaks and sporadic cases of AGE in Bangladesh, Guatemala, Peru, and USA collected between 2010-2019, of which 2,392 (90 %) were genotyped successfully. Most of the known genotypes infecting humans (GI (n = 9) and GII (n = 23)) and P types (GI (n = 15), GII, (n = 20)) could be detected. The remaining 270 samples had low viral load (Ct > 30) by real-time RT-PCR. A panel of 166 samples positive for other enteric viruses (rotavirus, astrovirus, sapovirus, adenovirus type 40/41) tested negative. CONCLUSION The use of broadly reactive genotyping assays greatly strengthens exchange of standardized genotype data globally to monitor trends in genotype diversity which is important for both the development of vaccines and to measure their impact.
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Affiliation(s)
- Preeti Chhabra
- Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Hannah Browne
- National Foundation for the Centers for Disease Control and Prevention Inc., Atlanta, GA, USA
| | - Thalia Huynh
- California Department of Public Health, Richmond, CA, USA
| | | | - Leslie Barclay
- Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Margaret N Kosek
- University of Virginia Division of Infectious Diseases and International Health, Charlottesville, VA, USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | - Chao-Yang Pan
- California Department of Public Health, Richmond, CA, USA
| | - Jan Vinjé
- Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Norovirus compared to other relevant etiologies of acute gastroenteritis among families from a semirural county in Chile. Int J Infect Dis 2020; 101:353-360. [PMID: 33059093 DOI: 10.1016/j.ijid.2020.10.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 01/13/2023] Open
Abstract
OBJECTIVE To determine the dynamics of norovirus disease, a major cause of acute gastroenteritis (AGE), compared to other relevant etiologies, among families living in a lower middle income area. STUDY DESIGN Families with three or more members and with one or more healthy children <24 months of age were followed for 1-2 years to detect any AGE. Stool samples were tested for viral and bacterial pathogens and a questionnaire was completed for those with norovirus or rotavirus AGE. RESULTS Between April and June 2016, 110 families were enrolled, with 103 of them completing ≥12 months of follow-up. A total of 159 family AGE episodes were detected, mostly affecting one individual (92%). At least one pathogen was detected in 56% (94/169) of samples, of which 75/94 (80%) were sole infections. Norovirus was most common (n=26), followed closely by enteropathogenic Escherichia coli (EPEC) (n=25), rotavirus (n=24), and astrovirus (n=23). The annual incidence of family AGE was 0.77, and 0.12 for norovirus. Most norovirus AGE occurred in children <4 years old (96%). Only 13/159 (8%) index AGE cases resulted in a secondary case, of which four were associated with norovirus. The majority of norovirus strains were GII (85%), with a mild predominance of GII.4 (9/26; 35%); most norovirus isolates (69%) were recombinants. CONCLUSIONS The family incidence of AGE in this lower middle income community was nearly one episode per year, mostly caused by viruses, specifically norovirus closely followed by rotavirus and astrovirus. Norovirus infections primarily affected children <4 years old and secondary cases were uncommon.
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Recombination at the emergence of the pathogenic rabbit haemorrhagic disease virus Lagovirus europaeus/GI.2. Sci Rep 2020; 10:14502. [PMID: 32879332 PMCID: PMC7468141 DOI: 10.1038/s41598-020-71303-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 08/10/2020] [Indexed: 12/20/2022] Open
Abstract
Rabbit haemorrhagic disease is a viral disease that emerged in the 1980s and causes high mortality and morbidity in the European rabbit (Oryctolagus cuniculus). In 2010, a new genotype of the rabbit haemorrhagic disease virus emerged and replaced the former circulating Lagovirus europaeus/GI.1 strains. Several recombination events have been reported for the new genotype Lagovirus europaeus/GI.2, with pathogenic (variants GI.1a and GI.1b) and benign (genotype GI.4) strains that served as donors for the non-structural part while GI.2 composed the structural part; another recombination event has also been described at the p16/p23 junction involving GI.4 strains. In this study, we analysed new complete coding sequences of four benign GI.3 strains and four GI.2 strains. Phylogenetic and recombination detection analyses revealed that the first GI.2 strains, considered as non-recombinant, resulted from a recombination event between GI.3 and GI.2, with GI.3 as the major donor for the non-structural part and GI.2 for the structural part. Our results indicate that recombination contributed to the emergence, persistence and dissemination of GI.2 as a pathogenic form and that all described GI.2 strains so far are the product of recombination. This highlights the need to study full-genomic sequences of lagoviruses to understand their emergence and evolution.
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Abrantes J, Lopes AM, Lemaitre E, Ahola H, Banihashem F, Droillard C, Marchandeau S, Esteves PJ, Neimanis A, Le Gall-Reculé G. Retrospective Analysis Shows That Most RHDV GI.1 Strains Circulating Since the Late 1990s in France and Sweden Were Recombinant GI.3P-GI.1d Strains. Genes (Basel) 2020; 11:E910. [PMID: 32784857 PMCID: PMC7464634 DOI: 10.3390/genes11080910] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/27/2020] [Accepted: 08/06/2020] [Indexed: 12/27/2022] Open
Abstract
Recombination is one of the major sources of genetic variation in viruses. RNA viruses, such as rabbit hemorrhagic disease virus (RHDV), are among the viruses with the highest recombination rates. Several recombination events have been described for RHDV, mostly as a consequence of their genomic architecture. Here, we undertook phylogenetic and recombination analyses of French and Swedish RHDV strains from 1994 to 2016 and uncovered a new intergenotypic recombination event. This event occurred in the late 1990s/early 2000s and involved nonpathogenic GI.3 strains as donors for the nonstructural part of the genome of these recombinants, while pathogenic GI.1d strains contributed to the structural part. These GI.3P-GI.1d recombinant strains did not entirely replace GI.1d (nonrecombinant) strains, but became the dominant strains in France and Sweden, likely due to a fitness advantage associated with this genomic architecture. GI.3P-GI.1d (P stands for polymerase) strains persisted until 2013 and 2016 in Sweden and France, respectively, and cocirculated with the new genotype GI.2 in France. Since strains from the first GI.2 outbreaks were GI.3P-GI.2, we hypothesize that GI.3P-GI.1d could be the parental strain. Our results confirm the outstanding recombination ability of RHDV and its importance in the evolution of lagoviruses, which was only revealed by studying complete genomic sequences.
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Affiliation(s)
- Joana Abrantes
- CIBIO/InBio-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.M.L.); (P.J.E.)
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Ana M. Lopes
- CIBIO/InBio-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.M.L.); (P.J.E.)
- Instituto de Ciências Biomédicas Abel Salazar/Unidade Multidisciplinar de Investigação Biomédica, Universidade do Porto, 4050-313 Porto, Portugal
| | - Evelyne Lemaitre
- Unité de Virologie, Immunologie, Parasitologie, Aviaires et Cunicoles, Laboratoire de Ploufragan-Plouzané-Niort, Agence nationale de sécurité sanitaire, de l’alimentation, de l’environnement et du travail (Anses), 22440 Ploufragan, France; (E.L.); (C.D.)
| | - Harri Ahola
- Department of Microbiology, National Veterinary Institute (SVA), Ulls väg 2B, SE75189 Uppsala, Sweden; (H.A.); (F.B.)
| | - Fereshteh Banihashem
- Department of Microbiology, National Veterinary Institute (SVA), Ulls väg 2B, SE75189 Uppsala, Sweden; (H.A.); (F.B.)
| | - Clément Droillard
- Unité de Virologie, Immunologie, Parasitologie, Aviaires et Cunicoles, Laboratoire de Ploufragan-Plouzané-Niort, Agence nationale de sécurité sanitaire, de l’alimentation, de l’environnement et du travail (Anses), 22440 Ploufragan, France; (E.L.); (C.D.)
| | - Stéphane Marchandeau
- Unité Petite Faune Sédentaire et Espèces Outre-Mer, Direction de la Recherche et de l’Appui Scientifique, Office Français de la Biodiversité (OFB), 44300 Nantes, France;
| | - Pedro J. Esteves
- CIBIO/InBio-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.M.L.); (P.J.E.)
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Aleksija Neimanis
- Department of Pathology and Wildlife Diseases, National Veterinary Institute (SVA), Ulls väg 2B, SE75189 Uppsala, Sweden
| | - Ghislaine Le Gall-Reculé
- Unité de Virologie, Immunologie, Parasitologie, Aviaires et Cunicoles, Laboratoire de Ploufragan-Plouzané-Niort, Agence nationale de sécurité sanitaire, de l’alimentation, de l’environnement et du travail (Anses), 22440 Ploufragan, France; (E.L.); (C.D.)
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41
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Zhang W, Wang R, Liang J, Zhao N, Li G, Gao Q, Su S. Epidemiology, genetic diversity and evolution of canine astrovirus. Transbound Emerg Dis 2020; 67:2901-2910. [PMID: 32946195 DOI: 10.1111/tbed.13663] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/30/2020] [Accepted: 05/30/2020] [Indexed: 01/19/2023]
Abstract
Astroviruses (AstVs) are major causative agents of gastroenteritis in children and have been reported in many species. Canine astrovirus (CaAstV), as an enteric pathogen, has been widely detected worldwide, but little is known about their genetic diversity and evolution, partly owing to a lack of genomic data. Here, we sequenced 12 nearly full-length CaAstV genomes to address the gap in knowledge. We found 14 (13.2%) and 7 (3.35%) CaAstV-positive samples from pet dogs with and without diarrhoea, respectively. Co-infections were with co-infection with Torque teno canis virus (TTCaV) reported for the first time. Phylogenetic analysis of the ORF2 gene revealed four major lineages. In particular, lineage 4 might have evolved from a recombinant virus from lineage 2 and lineage 3. The strains sequenced here clustered with lineages 2, 3 and 4 in contrast with other Chinese strains identified previously that clustered with lineages 2 and 4. Amino acid sequence alignment within lineage revealed intralineage amino acid diversity and that the type of epidemic strains within lineages changes over time. Three amino acids substitutions located in predicted B-cell epitopes, which might be involved escape of host immunity. Moreover, frequent inter-clade ORF2 gene recombinants were identified. The identification of individual recombination events and a recombinant lineage indicated that recombination plays a crucial role in CaAstV genetic evolution and diversity by generating divergent viruses. Moreover, phylogenetic analysis of ORF1b, the most conserved gene of astrovirus, revealed a close relationship between CaAstV and California sea lion astroviruses. Overall, we report detailed information on the genetic evolution and diversity of CaAstV, which indicates that CaAstV may pose challenges for diagnostics and future control strategies.
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Affiliation(s)
- Wenyan Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering 1. Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Ruyi Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering 1. Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jiawei Liang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering 1. Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Naiyu Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering 1. Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Gairu Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering 1. Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Qi Gao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering 1. Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Shuo Su
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering 1. Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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42
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Campillay-Véliz CP, Carvajal JJ, Avellaneda AM, Escobar D, Covián C, Kalergis AM, Lay MK. Human Norovirus Proteins: Implications in the Replicative Cycle, Pathogenesis, and the Host Immune Response. Front Immunol 2020; 11:961. [PMID: 32612600 PMCID: PMC7308418 DOI: 10.3389/fimmu.2020.00961] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/23/2020] [Indexed: 12/19/2022] Open
Abstract
Human noroviruses (HuNoVs) are the cause of more than 95% of epidemic non-bacterial gastroenteritis worldwide, with some lethal cases. These viral agents affect people of all ages. However, young children and older adults are the highest-risk groups, being affected with the greatest rate of hospitalizations and morbidity cases. HuNoV structural proteins, especially VP1, have been studied extensively. In contrast, the functions of the non-structural proteins of the virus have been undescribed in depth. Studies on HuNoV non-structural proteins have mostly been made by expressing them individually in in vitro cultures, providing insights of their functions and the role that they play in HuNoV replication and pathogenesis. This review examines exhaustively the functions of both HuNoV structural and non-structural proteins and their possible role within the viral replicative cycle and the pathogenesis of the virus. It also highlights recent findings regarding the host's innate and adaptive immune responses against HuNoV, which are of great relevance for diagnostics and vaccine development so as to prevent infections caused by these fastidious viruses.
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Affiliation(s)
- Claudia P Campillay-Véliz
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Jonatan J Carvajal
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Andrea M Avellaneda
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Darling Escobar
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Camila Covián
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad de Chile, Santiago, Chile
| | - Alexis M Kalergis
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad de Chile, Santiago, Chile.,Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Margarita K Lay
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad de Chile, Santiago, Chile
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43
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Infectious Norovirus Is Chronically Shed by Immunocompromised Pediatric Hosts. Viruses 2020; 12:v12060619. [PMID: 32516960 PMCID: PMC7354526 DOI: 10.3390/v12060619] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 12/17/2022] Open
Abstract
Noroviruses are a leading cause of gastroenteritis worldwide. Although infections in healthy individuals are self-resolving, immunocompromised individuals are at risk for chronic disease and severe complications. Chronic norovirus infections in immunocompromised hosts are often characterized by long-term virus shedding, but it is unclear whether this shed virus remains infectious. We investigated the prevalence, genetic heterogeneity, and temporal aspects of norovirus infections in 1140 patients treated during a 6-year period at a pediatric research hospital. Additionally, we identified 20 patients with chronic infections lasting 37 to >418 days. Using a new human norovirus in vitro assay, we confirmed the continuous shedding of infectious virus for the first time. Shedding lasted longer in male patients and those with diarrheal symptoms. Prolonged shedding of infectious norovirus in immunocompromised hosts can potentially increase the likelihood of transmission, highlighting the importance of isolation precautions to prevent nosocomial infections.
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Imai K, Hagi A, Inoue Y, Amarasiri M, Sano D. Virucidal Efficacy of Olanexidine Gluconate as a Hand Antiseptic Against Human Norovirus. FOOD AND ENVIRONMENTAL VIROLOGY 2020; 12:180-190. [PMID: 32124244 PMCID: PMC7225205 DOI: 10.1007/s12560-020-09422-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/24/2020] [Indexed: 05/05/2023]
Abstract
Human noroviruses are the major cause of non-bacterial acute gastroenteritis worldwide. Since no therapeutic agent has been proven to prevent human norovirus infection yet, preventive healthcare interventions to block the infection routes play an important role in infection control. One of the possible infection routes of human noroviruses are through contaminated hands, but no hand antiseptics have been proven effective. Olanexidine gluconate is a new biguanide compound that has already been approved for sale as an antiseptic for the surgical field in Japan. A new hand antiseptic was developed using olanexidine gluconate in this study, and its virucidal efficacy against human noroviruses was evaluated using modified RT-qPCR that can account for genome derived from intact viruses using RNase A and photo-reactive intercalators. We tested the virucidal efficacy of five materials; two olanexidine gluconate antiseptics (hand rub formulation and surgical field formulation), two kinds of ethanol solutions at different pH (approx. 3 or 7), and a base component of olanexidine gluconate hand rub formulation against 11 human norovirus genotypes by culture-independent methods. The infectivity of murine norovirus (MNV), a surrogate for human norovirus, was significantly reduced after use of the antiseptics. The olanexidine gluconate hand rub demonstrated the strongest virucidal efficacy against human norovirus among the five tested materials. This study showed that olanexidine gluconate has the potential to become a strong tool for the prevention of human norovirus infection.
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Affiliation(s)
- Kaoru Imai
- Naruto Research Institute, Research and Development Center, Otsuka Pharmaceutical Factory, Inc., Naruto, Tokushima, 772-8601, Japan
- Department of Frontier Science for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Akifumi Hagi
- Naruto Research Institute, Research and Development Center, Otsuka Pharmaceutical Factory, Inc., Naruto, Tokushima, 772-8601, Japan
| | - Yasuhide Inoue
- Naruto Research Institute, Research and Development Center, Otsuka Pharmaceutical Factory, Inc., Naruto, Tokushima, 772-8601, Japan
| | - Mohan Amarasiri
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Daisuke Sano
- Department of Frontier Science for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan.
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan.
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45
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Genomic Analyses of Human Sapoviruses Detected over a 40-Year Period Reveal Disparate Patterns of Evolution among Genotypes and Genome Regions. Viruses 2020; 12:v12050516. [PMID: 32392864 PMCID: PMC7290424 DOI: 10.3390/v12050516] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/22/2022] Open
Abstract
Human sapovirus is a causative agent of acute gastroenteritis in all age groups. The use of full-length viral genomes has proven beneficial to investigate evolutionary dynamics and transmission chains. In this study, we developed a full-length genome sequencing platform for human sapovirus and sequenced the oldest available strains (collected in the 1970s) to analyse diversification of sapoviruses. Sequence analyses from five major genotypes (GI.1, GI.2, GII.1, GII.3, and GIV.1) showed limited intra-genotypic diversification for over 20–40 years. The accumulation of amino acid mutations in VP1 was detected for GI.2 and GIV.1 viruses, while having a similar rate of nucleotide evolution to the other genotypes. Differences in the phylogenetic clustering were detected between RdRp and VP1 sequences of our archival strains as well as other reported putative recombinants. However, the lack of the parental strains and differences in diversification among genomic regions suggest that discrepancies in the phylogenetic clustering of sapoviruses could be explained, not only by recombination, but also by disparate nucleotide substitution patterns between RdRp and VP1 sequences. Together, this study shows that, contrary to noroviruses, sapoviruses present limited diversification by means of intra-genotype variation and recombination.
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46
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Amarasiri M, Utagawa E, Sano D, Katayama K. Identification of novel norovirus polymerase genotypes from pediatric fecal samples collected between the year 1997 and 2000 in Japan. INFECTION GENETICS AND EVOLUTION 2020; 82:104313. [PMID: 32259662 DOI: 10.1016/j.meegid.2020.104313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/12/2020] [Accepted: 04/01/2020] [Indexed: 11/24/2022]
Abstract
We analyzed 46 pediatric fecal samples collected between the years 1997 and 2000 to retrospectively evaluate the norovirus strains circulating during that era and to identify possible re-emergence patterns. From the tested fecal samples, we detected GII.1, GII.3, GII.4 (95/96-US) and GII.6 strains. Most importantly, two novel polymerase genotypes (GI.PNA4 and GII.PNA7) were detected during the study. Two possible recombinant strains (GII.6[P7] and GII.3[P29]) were identified and SimPlot analysis confirmed that GII.6[P7] is a recombinant strain. The study emphasizes the importance of retrospective evaluation of human fecal samples in obtaining a better understanding of norovirus circulation, re-emergence and evolution.
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Affiliation(s)
- Mohan Amarasiri
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
| | - Etsuko Utagawa
- National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo 208-0011, Japan.
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan; Department of Frontier Science for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Department of Infection Control and Immunology, Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
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47
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Ludwig-Begall LF, Lu J, Hosmillo M, de Oliveira-Filho EF, Mathijs E, Goodfellow I, Mauroy A, Thiry E. Replicative fitness recuperation of a recombinant murine norovirus - in vitro reciprocity of genetic shift and drift. J Gen Virol 2020; 101:510-522. [PMID: 32242791 DOI: 10.1099/jgv.0.001406] [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] [Indexed: 12/24/2022] Open
Abstract
Noroviruses are recognized as the major cause of non-bacterial gastroenteritis in humans. Molecular mechanisms driving norovirus evolution are the accumulation of point mutations and recombination. Recombination can create considerable changes in a viral genome, potentially eliciting a fitness cost, which must be compensated via the adaptive capacity of a recombinant virus. We previously described replicative fitness reduction of the first in vitro generated WU20-CW1 recombinant murine norovirus, RecMNV. In this follow-up study, RecMNV's capability of replicative fitness recuperation and genetic characteristics of RecMNV progenies at early and late stages of an adaptation experiment were evaluated. Replicative fitness regain of the recombinant was demonstrated via growth kinetics and plaque size differences between viral progenies prior to and post serial in vitro passaging. Point mutations at consensus and sub-consensus population levels of early and late viral progenies were characterized via next-generation sequencing and putatively associated to fitness changes. To investigate the effect of genomic changes separately and in combination in the context of a lab-generated inter-MNV infectious virus, mutations were introduced into a recombinant WU20-CW1 cDNA for subsequent DNA-based reverse genetics recovery. We thus associated fitness loss of RecMNV to a C7245T mutation and functional VP2 (ORF3) truncation and demonstrated individual and cumulative compensatory effects of one synonymous OFR2 and two non-synonymous ORF1 consensus-level mutations acquired during successive rounds of in vitro replication. Our data provide evidence of viral adaptation in a controlled environment via genetic drift after genetic shift induced a fitness cost of an infectious recombinant norovirus.
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Affiliation(s)
- Louisa F Ludwig-Begall
- Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, Liège, Belgium
| | - Jia Lu
- Present address: The Babraham Institute, Babraham Hall House, Babraham, Cambridge, UK.,Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Edmilson F de Oliveira-Filho
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, Liège, Belgium
| | - Elisabeth Mathijs
- Infectious diseases in animals, Sciensano, Ukkel, Belgium.,Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, Liège, Belgium
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Axel Mauroy
- Staff direction for risk assessment, Control Policy, FASFC, Brussels, Belgium.,Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, Liège, Belgium
| | - Etienne Thiry
- Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, Liège, Belgium
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48
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Domman D, Ruis C, Dorman MJ, Shakya M, Chain PSG. Novel Insights Into the Spread of Enteric Pathogens Using Genomics. J Infect Dis 2020; 221:S319-S330. [PMID: 31538189 DOI: 10.1093/infdis/jiz220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/19/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Daryl Domman
- Bioscience Division, Los Alamos National Laboratory, New Mexico
| | - Christopher Ruis
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Matthew J Dorman
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Migun Shakya
- Bioscience Division, Los Alamos National Laboratory, New Mexico
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Phylogenetics, Genomic Recombination, and NSP2 Polymorphic Patterns of Porcine Reproductive and Respiratory Syndrome Virus in China and the United States in 2014-2018. J Virol 2020; 94:JVI.01813-19. [PMID: 31896589 DOI: 10.1128/jvi.01813-19] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/16/2019] [Indexed: 01/03/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV), an important pathogen that affects the pig industry, is a highly genetically diverse RNA virus. However, the phylogenetic and genomic recombination properties of this virus have not been completely elucidated. In this study, comparative analyses of all available genomic sequences of North American (NA)-type PRRSVs (n = 355, including 138 PRRSV genomes sequenced in this study) in China and the United States during 2014-2018 revealed a high frequency of interlineage recombination hot spots in nonstructural protein 9 (NSP9) and the GP2 to GP3 regions. Lineage 1 (L1) PRRSV was found to be susceptible to recombination among PRRSVs both in China and the United States. The recombinant major parent between the 1991-2013 data and the 2014-2018 data showed a trend from complex to simple. The major recombination pattern changed from an L8 to L1 backbone during 2014-2018 for Chinese PRRSVs, whereas L1 was always the major backbone for US PRRSVs. Intralineage recombination hot spots were not as concentrated as interlineage recombination hot spots. In the two main clades with differential diversity in L1, NADC30-like PRRSVs are undergoing a decrease in population genetic diversity, NADC34-like PRRSVs have been relatively stable in population genetic diversity for years. Systematic analyses of insertion and deletion (indel) polymorphisms of NSP2 divided PRRSVs into 25 patterns, which could generate novel references for the classification of PRRSVs. The results of this study contribute to a deeper understanding of the recombination of PRRSVs and indicate the need for coordinated epidemiological investigations among countries.IMPORTANCE Porcine reproductive and respiratory syndrome (PRRS) is one of the most significant swine diseases. However, the phylogenetic and genomic recombination properties of the PRRS virus (PRRSV) have not been completely elucidated. In this study, we systematically compared differences in the lineage distribution, recombination, NSP2 polymorphisms, and evolutionary dynamics between North American (NA)-type PRRSVs in China and in the United States. Strikingly, we found high frequency of interlineage recombination hot spots in nonstructural protein 9 (NSP9) and in the GP2 to GP3 region. Also, intralineage recombination hot spots were scattered across the genome between Chinese and US strains. Furthermore, we proposed novel methods based on NSP2 indel patterns for the classification of PRRSVs. Evolutionary dynamics analysis revealed that NADC30-like PRRSVs are undergoing a decrease in population genetic diversity, suggesting that a dominant population may occur and cause an outbreak. Our findings offer important insights into the recombination of PRRSVs and suggest the need for coordinated international epidemiological investigations.
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50
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Molecular Epidemiology of GI.3 Norovirus Outbreaks from Acute Gastroenteritis Surveillance System in Taiwan, 2015-2019. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4707538. [PMID: 32104692 PMCID: PMC7040384 DOI: 10.1155/2020/4707538] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/17/2020] [Indexed: 11/17/2022]
Abstract
Norovirus is the leading cause of food-borne disease outbreaks. We conducted this study to examine the incidence and molecular characteristics of norovirus genogroup I infections from acute gastroenteritis outbreaks in Taiwan. Between January 2015 and June 2019, 2121 acute gastroenteritis clusters were reported to Taiwan CDC, of which 351 (16.5%) clusters were positive for NoV GI, and GI.3 was the most prevalent (36.8%) during the study period. The GI.3 infections were significantly higher than non-GI.3 infections in the age groups of 0-5 and 6-18 years. The phylogenetic analysis of the MCC tree revealed that VP1 genes were divided into 3 groups: the GI.P3-GI.3 strains in Taiwan were genetically close to Japan and the GI.Pd-GI.3 strains were segregated into 2 other groups which were genetically closely related to China. In addition, 7 GI.Pd-GI.3 recombinants were identified circulating in Taiwan between 2018 and 2019, and the prevalence of GI.Pd-GI.3 should be monitored to assess whether this could become the new predominant strains in neighboring Asian countries or other parts of the world. Both GI.P3-GI.3 and GI.Pd-GI.3 strains cocirculate, the recombination among these two lineages occurs frequently, contributing to the genetic diversity and multiple occurrences of different norovirus lineages, and their rapid evolution makes future control more difficult. Continued surveillance and timely interventions are critical to understand the complexity of norovirus gene variation and to monitor the new emerging norovirus strains.
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