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Takahashi T, Kimura R, Shirai T, Sada M, Sugai T, Murakami K, Harada K, Ito K, Matsushima Y, Mizukoshi F, Okayama K, Hayashi Y, Kondo M, Kageyama T, Suzuki Y, Ishii H, Ryo A, Katayama K, Fujita K, Kimura H. Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase ( RdRp) Region and VP1 Gene in Human Norovirus Genotypes GII.P6-GII.6 and GII.P7-GII.6. Viruses 2023; 15:1497. [PMID: 37515184 PMCID: PMC10383674 DOI: 10.3390/v15071497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/24/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
To understand the evolution of GII.P6-GII.6 and GII.P7-GII.6 strains, the prevalent human norovirus genotypes, we analysed both the RdRp region and VP1 gene in globally collected strains using authentic bioinformatics technologies. A common ancestor of the P6- and P7-type RdRp region emerged approximately 50 years ago and a common ancestor of the P6- and P7-type VP1 gene emerged approximately 110 years ago. Subsequently, the RdRp region and VP1 gene evolved. Moreover, the evolutionary rates were significantly faster for the P6-type RdRp region and VP1 gene than for the P7-type RdRp region and VP1 genes. Large genetic divergence was observed in the P7-type RdRp region and VP1 gene compared with the P6-type RdRp region and VP1 gene. The phylodynamics of the RdRp region and VP1 gene fluctuated after the year 2000. Positive selection sites in VP1 proteins were located in the antigenicity-related protruding 2 domain, and these sites overlapped with conformational epitopes. These results suggest that the GII.6 VP1 gene and VP1 proteins evolved uniquely due to recombination between the P6- and P7-type RdRp regions in the HuNoV GII.P6-GII.6 and GII.P7-GII.6 virus strains.
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Affiliation(s)
- Tomoko Takahashi
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi, Gunma 370-0006, Japan
- Iwate Prefectural Research Institute for Environmental Science and Public Health, Morioka-shi, Iwate 020-0857, Japan
| | - Ryusuke Kimura
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, Shibukawa-shi, Gunma 377-0008, Japan
- Department of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi-shi, Gunma 371-8514, Japan
| | - Tatsuya Shirai
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, Shibukawa-shi, Gunma 377-0008, Japan
- Department of Respiratory Medicine, School of Medicine, Kyorin University, Mitaka-shi, Tokyo 181-8611, Japan
| | - Mitsuru Sada
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, Shibukawa-shi, Gunma 377-0008, Japan
- Department of Respiratory Medicine, School of Medicine, Kyorin University, Mitaka-shi, Tokyo 181-8611, Japan
| | - Toshiyuki Sugai
- Department of Nursing Science, Graduate School of Health Science, Hiroshima University, Hiroshima-shi, Hiroshima 734-8551, Japan
| | - Kosuke Murakami
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Kazuhiko Harada
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, Shibukawa-shi, Gunma 377-0008, Japan
| | - Kazuto Ito
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, Shibukawa-shi, Gunma 377-0008, Japan
| | - Yuki Matsushima
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fuminori Mizukoshi
- Department of Microbiology, Tochigi Prefectural Institute of Public Health and Environmental Science, Utsunomiya-shi, Tochigi 329-1196, Japan
| | - Kaori Okayama
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi, Gunma 370-0006, Japan
| | - Yuriko Hayashi
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi, Gunma 370-0006, Japan
| | - Mayumi Kondo
- Department of Clinical Engineering, Faculty of Medical Technology, Gunma Paz University, Takasaki-shi, Gunma 370-0006, Japan
| | - Tsutomu Kageyama
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Yoshiyuki Suzuki
- Division of Biological Science, Department of Information and Basic Science, Graduate School of Natural Sciences, Nagoya City University, Nagoya-shi, Aichi 467-8501, Japan
| | - Haruyuki Ishii
- Department of Respiratory Medicine, School of Medicine, Kyorin University, Mitaka-shi, Tokyo 181-8611, Japan
| | - Akihide Ryo
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection Control, Graduate School of Infection Control Sciences, Ōmura Satoshi Memorial Institute, Kitasato University, Minato-ku, Tokyo 108-8641, Japan
| | - Kiyotaka Fujita
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi, Gunma 370-0006, Japan
| | - Hirokazu Kimura
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi, Gunma 370-0006, Japan
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, Shibukawa-shi, Gunma 377-0008, Japan
- Department of Clinical Engineering, Faculty of Medical Technology, Gunma Paz University, Takasaki-shi, Gunma 370-0006, Japan
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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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Lucero Y, Matson DO, Ashkenazi S, George S, O’Ryan M. Norovirus: Facts and Reflections from Past, Present, and Future. Viruses 2021; 13:v13122399. [PMID: 34960668 PMCID: PMC8707792 DOI: 10.3390/v13122399] [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] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 02/07/2023] Open
Abstract
Human Norovirus is currently the main viral cause of acute gastroenteritis (AGEs) in most countries worldwide. Nearly 50 years after the discovery of the "Norwalk virus" by Kapikian and colleagues, the scientific and medical community continue to generate new knowledge on the full biological and disease spectrum of Norovirus infection. Nevertheless, several areas remain incompletely understood due to the serious constraints to effectively replicate and propagate the virus. Here, we present a narrated historic perspective and summarize our current knowledge, including insights and reflections on current points of interest for a broad medical community, including clinical and molecular epidemiology, viral-host-microbiota interactions, antivirals, and vaccine prototypes. We also include a reflection on the present and future impacts of the COVID-19 pandemic on Norovirus infection and disease.
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Affiliation(s)
- Yalda Lucero
- Microbiology and Mycology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile; (Y.L.); (S.G.)
- Hospital Dr. Roberto del Río Hospital, Department of Pediatrics and Pediatric Surgery (Northern Campus), Faculty of Medicine, Universidad de Chile, Santiago 8380418, Chile
- Clínica Alemana de Santiago, Faculty of Medicine, Universidad del Desarrollo-Clínica Alemana, Santiago 7650568, Chile
| | - David O. Matson
- Eastern Shore Health Department, Virginia Department of Public Health, Accomack County, VA 23301, USA;
| | - Shai Ashkenazi
- Adelson School of Medicine, Ariel University, Ariel 40700, Israel;
- Department of Pediatrics A, Schneider Children’s Medical Center, Petach Tikva 49202, Israel
| | - Sergio George
- Microbiology and Mycology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile; (Y.L.); (S.G.)
| | - Miguel O’Ryan
- Microbiology and Mycology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile; (Y.L.); (S.G.)
- Correspondence:
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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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Symes SJ, Allen JL, Mansell PD, Woodward KL, Bailey KE, Gilkerson JR, Browning GF. First detection of bovine noroviruses and detection of bovine coronavirus in Australian dairy cattle. Aust Vet J 2018; 96:203-208. [PMID: 29878330 PMCID: PMC7159654 DOI: 10.1111/avj.12695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 07/31/2017] [Accepted: 08/22/2017] [Indexed: 01/20/2023]
Abstract
Background and objective Noroviruses have been recognised as a significant cause of neonatal enteritis in calves in many countries, but there has been no investigation of their occurrence in Australian cattle. This study aimed to establish whether bovine noroviruses could be detected in faecal samples from Australian dairy cattle. It also sought to determine whether bovine coronaviruses, also associated with neonatal enteritis in calves, could be detected in the same faecal samples. Methods A selection of faecal samples that were negative for rotaviruses from dairy farms located in three geographically distinct regions of Victoria were pooled and tested by reverse transcription‐PCR for the presence of noroviruses (genogroup III), neboviruses and bovine coronaviruses. Results and conclusion Genetically distinct genogroup III noroviruses were detected in two sample pools from different geographic regions and bovine coronavirus was detected in a third pool of samples. This is the first report of bovine norovirus infection in Australian cattle and suggests that future work is required to determine the significance of these agents as a cause of bovine enteric disease in Australia.
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Affiliation(s)
- S J Symes
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - J L Allen
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - P D Mansell
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Werribee, Victoria, Australia
| | | | - K E Bailey
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - J R Gilkerson
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - G F Browning
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
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Ludwig-Begall LF, Mauroy A, Thiry E. Norovirus recombinants: recurrent in the field, recalcitrant in the lab - a scoping review of recombination and recombinant types of noroviruses. J Gen Virol 2018; 99:970-988. [PMID: 29906257 DOI: 10.1099/jgv.0.001103] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Noroviruses are recognized as the major global cause of sporadic and epidemic non-bacterial gastroenteritis in humans. Molecular mechanisms driving norovirus evolution are the accumulation of point mutations and recombination. Intragenotypic recombination has long been postulated to be a driving force of GII.4 noroviruses, the predominant genotype circulating in humans for over two decades. Increasingly, emergence and re-emergence of different intragenotype recombinants have been reported. The number and types of norovirus recombinants remained undefined until the 2007 Journal of General Virology research article 'Norovirus recombination' reported an assembly of 20 hitherto unclassified intergenotypic norovirus recombinant types. In the intervening decade, a host of novel recombinants has been analysed. New recombination breakpoints have been described, in vitro and in vivo studies supplement in silico analyses, and advances have been made in analysing factors driving norovirus recombination. This work presents a timely overview of these data and focuses on important aspects of norovirus recombination and its role in norovirus molecular evolution. An overview of intergenogroup, intergenotype, intragenotype and 'obligatory' norovirus recombinants as detected via in silico methods in the field is provided, enlarging the scope of intergenotypic recombinant types to 80 in total, and notably including three intergenogroup recombinants. A recap of advances made studying norovirus recombination in the laboratory is given. Putative drivers and constraints of norovirus recombination are discussed and the potential link between recombination and norovirus zoonosis risk is examined.
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Affiliation(s)
- Louisa F Ludwig-Begall
- 1Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, B43b, Quartier Vallée 2, Avenue de Cureghem, 10, B-4000 Liège, Belgium
| | - Axel Mauroy
- 2Staff direction for risk assessment, Control Policy, Federal Agency for the Safety of the Food Chain, Blv du Jardin Botanique 55, 1000 Brussels, Belgium
| | - Etienne Thiry
- 1Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, B43b, Quartier Vallée 2, Avenue de Cureghem, 10, B-4000 Liège, Belgium
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Tsimpidis M, Bachoumis G, Mimouli K, Kyriakopoulou Z, Robertson DL, Markoulatos P, Amoutzias GD. T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes. BMC Bioinformatics 2017; 18:13. [PMID: 28056784 PMCID: PMC5216575 DOI: 10.1186/s12859-016-1420-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/10/2016] [Indexed: 12/22/2022] Open
Abstract
Background Many computational tools that detect recombination in viruses are not adapted for the ongoing genomic revolution. A computational tool is needed, that will rapidly scan hundreds/thousands of genomes or sequence fragments and detect candidate recombination events that may later be further analyzed with more sensitive and specialized methods. Results T-RECs, a Windows based graphical tool, employs pairwise alignment of sliding windows and can perform (i) genotyping, (ii) clustering of new genomes, (iii) detect recent recombination events among different evolutionary lineages, (iv) manual inspection of detected recombination events by similarity plots and (v) annotation of genomic regions. Conclusions T-RECs is very effective, as demonstrated by an analysis of 555 Norovirus complete genomes and 2500 sequence fragments, where a recombination hotspot was identified at the ORF1-ORF2 junction.
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Affiliation(s)
- Michail Tsimpidis
- Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece
| | - Georgios Bachoumis
- Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece
| | - Kalliopi Mimouli
- Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece
| | - Zaharoula Kyriakopoulou
- Department of Biochemistry and Biotechnology, Molecular Virology Laboratory, University of Thessaly, Larisa, Greece
| | | | - Panayotis Markoulatos
- Department of Biochemistry and Biotechnology, Molecular Virology Laboratory, University of Thessaly, Larisa, Greece
| | - Grigoris D Amoutzias
- Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece.
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Phumpholsup T, Chieochansin T, Vongpunsawad S, Vuthitanachot V, Payungporn S, Poovorawan Y. Human norovirus genogroup II recombinants in Thailand, 2009-2014. Arch Virol 2015. [PMID: 26215446 DOI: 10.1007/s00705-015-2545-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Norovirus (NoV) is a major cause of nonbacterial acute gastroenteritis worldwide. New strains emerge partly due to viral recombination. In Thailand, there is a lack of data on NoV recombinants among clinical isolates. We screened stool samples from pediatric diarrheal patients for norovirus by RT-PCR and found GII.4 to be the most prevalent genotype. Phylogenetic and SimPlot analyses detected seven intra-genogroup recombinant strains: three GII.21/GII.3, two GII.12/GII.3, and two GII.12/GII.1 recombinants. Maximum chi-square analysis indicated that all had similar breakpoints near the ORF1/ORF2 junction (p < 0.001), either slightly upstream within the C-terminus of RdRp or downstream within the N-terminal domain of VP1.
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Affiliation(s)
- Tikumporn Phumpholsup
- Department of Pediatrics, Faculty of Medicine, Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thaweesak Chieochansin
- Department of Pediatrics, Faculty of Medicine, Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, 10330, Thailand.,Division of Molecular Medicine, Department of Research and Development, Faculty of Medicine, Mahidol University, Bangkok, Thailand
| | - Sompong Vongpunsawad
- Department of Pediatrics, Faculty of Medicine, Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, 10330, Thailand
| | | | - Sunchai Payungporn
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Department of Pediatrics, Faculty of Medicine, Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, 10330, Thailand.
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Takano T, Kusuhara H, Kuroishi A, Takashina M, Doki T, Nishinaka T, Hohdatsu T. Molecular characterization and pathogenicity of a genogroup GVI feline norovirus. Vet Microbiol 2015; 178:201-7. [PMID: 26026731 PMCID: PMC7125706 DOI: 10.1016/j.vetmic.2015.05.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 05/18/2015] [Accepted: 05/21/2015] [Indexed: 02/01/2023]
Abstract
We identified novel feline norovirus (FNoV) M49-1 strain. Based on the analysis of VP1, FNoV M49-1 strain was classified into genogroup GVI. FNoV M49-1 strain seems to be produced by recombination between GIV and GVI NoV. Cats inoculated with FNoV gene-positive-fecal samples showed clinical symptoms.
Norovirus (NoV) has been classified into 6 genogroups, GI-GVI. In the present study, we identified novel feline NoV (FNoV) M49-1 strain. The C-terminal of RNA-dependent RNA polymerase of the FNoV M49-1 strain was highly homologous with GIV FNoV and GIV lion norovirus, whereas VP1 was highly homologous with GVI canine NoV (CNoV). Based on the results of the Simplot analysis, the FNoV M49-1 strain may have been produced by recombination between GIV.2 FNoV and GVI.1 CNoV. In addition, specific pathogen-free cats inoculated with FNoV gene-positive-fecal samples developed diarrhea symptoms, and the viral gene was detected in their feces and blood.
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Affiliation(s)
- Tomomi Takano
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - Hajime Kusuhara
- Health and Environment Research Institute, Yokkaichi, Mie, Japan
| | - Akira Kuroishi
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - Midori Takashina
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - Tomoyoshi Doki
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | | | - Tsutomu Hohdatsu
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan.
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Symes SJ, Job N, Ficorilli N, Hartley CA, Browning GF, Gilkerson JR. Novel assay to quantify recombination in a calicivirus. Vet Microbiol 2015; 177:25-31. [PMID: 25801938 DOI: 10.1016/j.vetmic.2015.02.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 02/16/2015] [Accepted: 02/18/2015] [Indexed: 10/23/2022]
Abstract
Recombination is an important contributor to genomic evolution in many viral families, including the Caliciviridae. While it is known that genomic recombination in caliciviruses contributes to their rapid evolution, the precise molecular mechanisms are poorly understood. The majority of reported recombination events in feline calicivirus (FCV) occur at a "hot spot" between the non-structural protein coding region (open reading frame 1) and structural protein coding region (open reading frame 2). To gain a better understanding of the rate of recombination at this point, we developed a quantitative reverse transcription-polymerase chain reaction (RT-qPCR) assay to quantify the rate of recombination between two divergent strains of FCV during co-infection in cell culture. The assay utilised virus-specific primers upstream and downstream of the recombinational "hot spot" that hybridise with only one of the strains in the co-infection. Recombinant progeny that shared ORF1 sequence identity with one parental virus and ORF2 sequence identity with the other parental virus, and the site of recombination, was confirmed by sequencing the amplicon generated by the assay. Recombinants were detected in co-infected cells using this assay, but not in cells infected with single strains that were mixed together following infection, thus confirming its specificity. Recombination between two FCVs in co-infected cell cultures was estimated to occur at a rate of at least 6.8×10(-6) single direction recombinant genomes per parental virus genome. Further application of this assay will enable factors influencing recombination in caliciviruses to be explored in greater detail, both in vitro and in vivo.
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Affiliation(s)
- Sally J Symes
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Natalie Job
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Nino Ficorilli
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Carol A Hartley
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Glenn F Browning
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - James R Gilkerson
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Truong TC, Than VT, Kim W. Evolutionary phylodynamics of Korean noroviruses reveals a novel GII.2/GII.10 recombination event. PLoS One 2014; 9:e113966. [PMID: 25500567 PMCID: PMC4264735 DOI: 10.1371/journal.pone.0113966] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 10/27/2014] [Indexed: 11/20/2022] Open
Abstract
Viral gastroenteritis is the most common causal agent of public health problems worldwide. Noroviruses cause nonbacterial acute gastroenteritis in humans of all ages. In this study, we investigated the occurrence of norovirus infection in children with acute gastroenteritis admitted to university hospitals in South Korea. We also analyzed the genetic diversity of the viruses and identified novel recombination events among the identified viral strains. Of 502 children with acute gastroenteritis admitted to our three hospitals between January 2011 and March 2012, genotyping of human noroviruses was performed in 171 (34%) norovirus-positive samples. Of these samples, 170 (99.5%) were in genogroup II (GII), while only one (0.5%) was in genogroup I (GI). The most common GII strain was the GII.4-2006b variant (n = 96, 56.5%), followed by GII.6 (n = 23, 13.5%), GII.12 (n = 22, 12.9%), GII.3 (n = 20, 11.8%), GII.2 (n = 6, 3.5%), GII.b (n = 2, 1.2%), and GII.10 (n = 1, 0.6%). Potential recombination events (polymerase/capsid) were detected in 39 GII strains (22.9%), and the most frequent genotypes were GII.4/GII.12 (n = 12, 30.8%), GII.4/GII.6 (n = 12, 30.8%), GII.4/GII.3 (n = 8, 20.5%), GII.b/GII.3 (n = 3, 7.7%), GII.16/GII.2 (n = 2, 5.1%), GII.4/GII.2 (n = 1, 2.6%), and GII.2/GII.10 (n = 1, 2.6%). For the first time, a novel GII.2/GII.10 recombination was detected; we also identified the GII.16/GII.2 strain for the first time in South Korea. Our data provided important insights into new recombination events, which may prove valuable for predicting the emergence of circulating norovirus strains with global epidemic potential.
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Affiliation(s)
- Thoi Cong Truong
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Van Thai Than
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
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13
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Fajardo Á, Tort FL, Victoria M, Fumian TM, Miagostovich MP, Leite JPG, Cristina J, Colina R. Phylogenetic analyses of Norovirus strains detected in Uruguay reveal the circulation of the novel GII.P7/GII.6 recombinant variant. INFECTION GENETICS AND EVOLUTION 2014; 28:328-32. [PMID: 25445648 DOI: 10.1016/j.meegid.2014.10.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/22/2014] [Accepted: 10/27/2014] [Indexed: 11/29/2022]
Abstract
Noroviruses (NoV) are one of the major etiological agent of acute gastroenteritis (AGE) outbreaks worldwide. Distinct NoV genotypes have been associated with different transmission patterns and disease severity in humans. Therefore, it is important to identify genetically different NoV genotypes circulating in a particular region. However, genotyping has become a challenge due to recombination events occurring mainly nearby ORF1/ORF2 junction of NoV genome, leading to distinct genotypes with polymerase and capsid regions derived from parenteral strains. Taking this into account, ORF1/ORF2 sequences were obtained from NoV strains collected from patients with AGE in Uruguay. This study reveals in silico evidences of recombination events taking place in four out of six strains analyzed for which its polymerase gene and its capsid region correspond to GII.P7 and to GII.6 genotype, respectively. These results also reveal the circulation of a GII.P7/GII.6 recombinant variant in the natural populations of NoV strains in the northwestern region of Uruguay. As far as we know this is the first report about the circulation of a NoV GII.P7/GII.6 recombinant variant in the Americas.
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Affiliation(s)
- Álvaro Fajardo
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay
| | - Fernando López Tort
- Laboratorio de Virología Molecular, Regional Norte, Universidad de la Republica, Gral. Rivera 1350, 50000 Salto, Uruguay
| | - Matías Victoria
- Laboratorio de Virología Molecular, Regional Norte, Universidad de la Republica, Gral. Rivera 1350, 50000 Salto, Uruguay
| | - Tulio M Fumian
- Laboratorio de Virología Comparada e Ambiental, Instituto Oswaldo Cruz, Ministerio da Saude, Avenida Brasil, 4365 - Pav. Helio & Peggy Pereira, 21040-360 Manguinhos, Rio de Janeiro, Brazil
| | - Marize P Miagostovich
- Laboratorio de Virología Comparada e Ambiental, Instituto Oswaldo Cruz, Ministerio da Saude, Avenida Brasil, 4365 - Pav. Helio & Peggy Pereira, 21040-360 Manguinhos, Rio de Janeiro, Brazil
| | - José Paulo G Leite
- Laboratorio de Virología Comparada e Ambiental, Instituto Oswaldo Cruz, Ministerio da Saude, Avenida Brasil, 4365 - Pav. Helio & Peggy Pereira, 21040-360 Manguinhos, Rio de Janeiro, Brazil
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay
| | - Rodney Colina
- Laboratorio de Virología Molecular, Regional Norte, Universidad de la Republica, Gral. Rivera 1350, 50000 Salto, Uruguay.
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Genetic diversity and distribution of human norovirus in China (1999-2011). BIOMED RESEARCH INTERNATIONAL 2014; 2014:196169. [PMID: 24672783 PMCID: PMC3918700 DOI: 10.1155/2014/196169] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 10/25/2013] [Accepted: 11/02/2013] [Indexed: 01/23/2023]
Abstract
Noroviruses (NoVs) are a leading cause of epidemic and sporadic acute gastroenteritis worldwide. However, the genetic diversity and geographical distribution of NoV isolates from China have not been well described thus far. In this study, all NoV sequences obtained in China from 1999 to 2011 (n = 983), both partial and complete genomes, were downloaded from GenBank. Genotyping and phylogenetic and recombination analyses were performed in order to gain a better understanding of the distribution and genetic diversity of NoVs in China. The results indicated that approximately 90% of NoV sequences were obtained from the coastal regions of China, and most of the NoV sequences from distinct geographical regions appeared to be closely related. GII.4 was the most prevalent genotype, accounting for 64.4% of all genotypes, followed by GII.12 (13.9%) and GII.3 (7.0%). Over the last decade, the GII.4 variants were dominated by successive circulation of GII.4/2002, GII.4/2004, GII.4/2006b, and GII.4/2008, with GII.4/2006b continuing to date. A relatively high frequency of NoV intergenotype recombinants was identified. The most common ORF1/ORF2 intergenotype recombinant was GII.12/GII.4 (n = 11), and the relative frequency was up to 30% among all the recombinant strains (n = 36). These findings may aid in the evaluation and implementation of appropriate measures for monitoring NoV infectious diseases in China.
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Seto Y, Iritani N, Kubo H, Kaida A, Murakami T, Haruki K, Nishio O, Ayata M, Ogura H. Genotyping ofNorovirusStrains Detected in Outbreaks between April 2002 and March 2003 in Osaka City, Japan. Microbiol Immunol 2013; 49:275-83. [PMID: 15782001 DOI: 10.1111/j.1348-0421.2005.tb03718.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Noroviruses (NVs) are the major cause of food- and waterborne nonbacterial gastroenteritis in Japan. Between April 2002 and March 2003, a total of 111 fecal specimens from 40 outbreaks of acute nonbacterial gastroenteritis in Osaka City, Japan were subject to NV detection. Seventy-two samples (64.9%) from 31 outbreaks (77.5%) were NV positive by a real time reverse transcription (RT)-PCR assay. To further determine the genotype of individual NV strains, we sequenced the capsid N-terminal/shell (N/S) domain of some representative strains from each outbreak. The 51 NV strains detected in this study were segregated into 15 genotypes (6 in genogroup I and 9 in genogroup II), and GII/5 genotype NV was a dominant outbreak genotype.
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Affiliation(s)
- Yoshiyuki Seto
- Department of Virology, Osaka City University Medical School, Osaka, Japan.
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16
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Genetic characterization of feline calicivirus strains associated with varying disease manifestations during an outbreak season in Missouri (1995–1996). Virus Genes 2013; 48:96-110. [DOI: 10.1007/s11262-013-1005-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/24/2013] [Indexed: 11/26/2022]
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17
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Nahar S, Afrad MH, Matthijnssens J, Rahman MZ, Momtaz Z, Yasmin R, Jubair M, Faruque ASG, Choudhuri MSK, Azim T, Rahman M. Novel intergenotype human norovirus recombinant GII.16/GII.3 in Bangladesh. INFECTION GENETICS AND EVOLUTION 2013; 20:325-9. [PMID: 24080167 DOI: 10.1016/j.meegid.2013.09.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 09/16/2013] [Accepted: 09/18/2013] [Indexed: 11/15/2022]
Abstract
Noroviruses (NoVs) are one of the major etiological agents of acute gastroenteritis in all age groups. In this study, we identified an intergenotype NoV recombinant strain in the fecal specimens of two male infants with acute diarrhea in Bangladesh. Phylogenetic analysis showed that the identified strains were recombinant NoV strains with a GII.3 capsid and a GII.16 polymerase gene. The recombination breakpoint was located in the ORF1/ORF2 overlap region. To the best of our knowledge this is the first report of a NoV recombinant GII.16/GII.3 strain worldwide.
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Affiliation(s)
- Shamsun Nahar
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh.
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Tra My PV, Lam HM, Thompson CN, Phuc HL, Tuyet PTN, Vinh H, Hoang NVM, Minh P, Vinh NT, Thuy CT, Nga TTT, Hau NTT, Chinh NT, Thuong TC, Tuan HM, Campbell JI, Clements AC, Farrar J, Boni MF, Baker S. The dynamics of GII.4 Norovirus in Ho Chi Minh City, Vietnam. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2013; 18:335-43. [PMID: 23612321 PMCID: PMC4047827 DOI: 10.1016/j.meegid.2013.04.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 04/05/2013] [Accepted: 04/06/2013] [Indexed: 11/01/2022]
Abstract
Norovirus (NoV) is a major cause of epidemic gastroenteritis in industrialized countries, yet the epidemiological significance of NoV in industrializing countries remains poorly understood. The spatiotemporal distribution of NoV genotypes identified in 2054 enrolled children was investigated between May 2009 and December 2010, in Ho Chi Minh City (HCMC), Vietnam. A total of 315 NoV extracted from stool samples were genotyped and GPS mapped to their source. Genogroup II NoV, particularly GII.4, were predominant, and the GII.4 strains could be subgrouped into GII.4-2006b (Minerva) and GII.4-2010 (New Orleans) variants. There was no spatiotemporal structure among the endemic GII strains; yet a significant spatiotemporal signal corresponding with the novel introduction of GII.4-2010 variant was detected. These data show that NoV GII.4 variants are highly endemic in HCMC and describe a scenario of rapid NoV strain replacement occurring in HCMC in early 2010.
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Affiliation(s)
- Phan Vu Tra My
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Wellington Square, Oxford OX1 2JD, United Kingdom
| | - Ha Minh Lam
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam
| | - Corinne N. Thompson
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Wellington Square, Oxford OX1 2JD, United Kingdom
| | - Hoang Le Phuc
- Children’s Hospital 1, 341 Su Van Hanh, District 5, Ho Chi Minh City, Viet Nam
| | - Pham Thi Ngoc Tuyet
- Children’s Hospital 2, 14 Ly Tu Trong, District 1, Ho Chi Minh City, Viet Nam
| | - Ha Vinh
- Hospital for Tropical Diseases, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam
| | - Nguyen Van Minh Hoang
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam
| | - PhamVan Minh
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam
| | - Nguyen Thanh Vinh
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam
| | - Cao Thu Thuy
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam
| | - Tran Thi Thu Nga
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam
| | - Nguyen Thi Thu Hau
- Children’s Hospital 2, 14 Ly Tu Trong, District 1, Ho Chi Minh City, Viet Nam
| | - Nguyen Tran Chinh
- Hospital for Tropical Diseases, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam
| | - Tang Chi Thuong
- Children’s Hospital 1, 341 Su Van Hanh, District 5, Ho Chi Minh City, Viet Nam
| | - Ha Manh Tuan
- Children’s Hospital 2, 14 Ly Tu Trong, District 1, Ho Chi Minh City, Viet Nam
| | - James I. Campbell
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Wellington Square, Oxford OX1 2JD, United Kingdom
| | - Archie C.A. Clements
- University of Queensland, School of Population Health, Brisbane St Lucia, QLD 4072, Australia
| | - Jeremy Farrar
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Wellington Square, Oxford OX1 2JD, United Kingdom
| | - Maciej F. Boni
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Wellington Square, Oxford OX1 2JD, United Kingdom
| | - Stephen Baker
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Wellington Square, Oxford OX1 2JD, United Kingdom
- The London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
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Siqueira JAM, Linhares ADC, de Carvalho TCN, Aragão GC, Oliveira DDS, Dos Santos MC, de Sousa MS, Justino MCA, Mascarenhas JDP, Gabbay YB. Norovirus infection in children admitted to hospital for acute gastroenteritis in Belém, Pará, Northern Brazil. J Med Virol 2013; 85:737-44. [PMID: 23359323 DOI: 10.1002/jmv.23506] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2012] [Indexed: 11/05/2022]
Abstract
Noroviruses are the leading cause of epidemic, non-bacterial outbreaks of acute gastroenteritis, and are also a major cause of sporadic acute gastroenteritis in infants. The aim of the present study was to identify norovirus infections in children not infected by rotavirus admitted to hospital for acute gastroenteritis in Belém. A total of 348 fecal specimens were obtained from children with diarrhea aged less than 5 years, all of whom had tested negative for rotavirus, between May 2008 and April 2010. Fecal samples were screened for norovirus antigen using enzyme-immunoassay (EIA). Specimens were subjected to reverse-transcription polymerase chain reaction (RT-PCR) using the primers Mon432/434-Mon431/433 for detection of the GI and GII norovirus strains, respectively. Based on both methods, the overall norovirus positivity rate was 36.5% (127/348). Of the 169 samples collected in the first year, 44.4% (n = 75) tested positive for norovirus using both methods, 35.5% (n = 60) by EIA and 40.8% (n = 69) by RT-PCR. Using RT-PCR as a reference standard, a sensitivity of 78.3%, specificity of 94%, and agreement of 87.6% were recorded. Genome sequencing was obtained for 22 (31.9%) of the 69 positive samples, of which 90.9% (20/22) were genotype GII.4d and 9.1% (2/22) were genotype GII.b. Norovirus infection was most frequent in children under 2 years of age (41.5%-115/277). The peak incidence (62.1%) of norovirus-related acute gastroenteritis in these patients (not infected by rotavirus) was observed in February 2010. These findings emphasize the importance of norovirus as a cause of severe acute gastroenteritis among children in Belém, Pará, Northern Brazil.
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Hoa Tran TN, Trainor E, Nakagomi T, Cunliffe NA, Nakagomi O. Molecular epidemiology of noroviruses associated with acute sporadic gastroenteritis in children: global distribution of genogroups, genotypes and GII.4 variants. J Clin Virol 2012; 56:185-93. [PMID: 23218993 DOI: 10.1016/j.jcv.2012.11.011] [Citation(s) in RCA: 208] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 11/07/2012] [Accepted: 11/13/2012] [Indexed: 12/22/2022]
Abstract
Noroviruses are a leading cause of epidemic and sporadic acute gastroenteritis worldwide. The development of sensitive molecular diagnostic techniques has revolutionized our understanding of norovirus epidemiology over the past two decades, but norovirus strain types associated with sporadic gastroenteritis remain poorly described. Therefore, we conducted a systematic review of studies performed after 2000 to clarify the genotypic distribution of noroviruses in children (≤18 years of age) with sporadic acute gastroenteritis. Genogroup GII norovirus was the most prevalent, accounting for 96% of all sporadic infections. GII.4 was the most prevalent genotype, accounting for 70% of the capsid genotypes and 60% of the polymerase genotypes, followed by the capsid genotype GII.3 (16%) and the polymerase genotype GII.b (14%). The most common ORF1/ORF2 inter-genotype recombinants were GII.b, GII.12, and GII.4 polymerase genotypes combined with the capsid genotype GII.3, accounting for 19% of all genotyped strains. The distribution of GII.4 variants over the last decade was dominated by successive circulation of GII.4/2002, GII.4/2004, GII.4/2006b, and GII.4/2008 with GII.4/2006b continuing to date. Genotypes GII.4 and GII.3 have predominated in children during the past decade; this is most notable in the global emergence of GII.4 variant noroviruses. As the burden of rotavirus disease decreases following the introduction of childhood immunization programs, the relative importance of norovirus in the etiology of acute childhood gastroenteritis will likely increase. In order for a successful norovirus vaccine to be developed, it should provide immunity against strains with capsid genotypes GII.4 and GII.3.
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Affiliation(s)
- T N Hoa Tran
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, The Global Center of Excellence, Nagasaki University, Nagasaki, Japan
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21
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Genomic sequences of two novel levivirus single-stranded RNA coliphages (family Leviviridae): evidence for recombinationin environmental strains. Viruses 2012; 4:1548-68. [PMID: 23170172 PMCID: PMC3499819 DOI: 10.3390/v4091548] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 08/30/2012] [Accepted: 09/03/2012] [Indexed: 12/03/2022] Open
Abstract
Bacteriophages are likely the most abundant entities in the aquatic environment, yet knowledge of their ecology is limited. During a fecal source-tracking study, two genetically novel Leviviridae strains were discovered. Although the novel strains were isolated from coastal waters 1130 km apart (North Carolina and Rhode Island, USA), these strains shared 97% nucleotide similarity and 97–100% amino acid similarity. When the novel strains were compared to nine Levivirus genogroup I strains, they shared 95–100% similarity among the maturation, capsid and lysis proteins, but only 84–85% in the RNA-dependent RNA polymerase gene. Further bioinformatic analyses suggested a recombination event occurred. To the best of our knowledge, this is the first description of viral recombinants in environmental Leviviridae ssRNA bacteriophages.
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Shen Q, Zhang W, Yang S, Yang Z, Chen Y, Cui L, Zhu J, Hua X. Recombinant porcine norovirus identified from piglet with diarrhea. BMC Vet Res 2012; 8:155. [PMID: 22938017 PMCID: PMC3514297 DOI: 10.1186/1746-6148-8-155] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 08/22/2012] [Indexed: 11/17/2022] Open
Abstract
Background Noroviruses (NoVs) are members of the family Caliciviridae and are emerging enteric pathogens of humans and animals. Some porcine NoVs are genetically similar to human strains and are classified into GII, like most epidemic human NoVs. So far, PoNoV have been exclusively detected in fecal samples of adult pig without clinical signs. Results Result showed that 2 of the 12 evaluated fecal samples were positive for PoNoVs, one of which was positive for PoNoV alone, and the other was coinfected with porcine circovirus and PoNoV. Phylogenetic and recombination analysis showed that the PoNoV positive alone strain was a recombinant new genotype strain. Experimental infection of miniature pigs with fecal suspensions confirmed that this strain can cause gastroenteritis in piglets. Conclusion This is the first report that recombinant new genotype PoNoV exised in pig herd of China, which cause diarrhea in pigs in nature condition. This find raised questions about the putative epidemiologic role of PoNoV.
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Affiliation(s)
- Quan Shen
- Key laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai JiaoTong University, 800 Dongchuan Road, Shanghai, People's Republic of China
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23
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Ferreira RG, Borges AMT, Fiaccadori FS, Souza MBDLDE, Santos RAT, Cardoso DDDDP. Gastroenteric virus detection in fecal samples from women in Goiânia, State of Goiás, Brazil. Rev Soc Bras Med Trop 2011; 43:240-3. [PMID: 20563488 DOI: 10.1590/s0037-86822010000300005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 03/25/2010] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION This was a prospective study that included women seen in the obstetrics and gynecology sector of Hospital das Clínicas, Federal University of Goiás, in Goiânia, State of Goiás, with the aim of detecting rotaviruses, adenoviruses, caliciviruses and astroviruses. Eighty-four women participated in the study and from these, 314 fecal samples were collected. Out of all of the women, 29 were seropositive for HIV and 55 were seronegative, and 45 and 39 were pregnant and non-pregnant, respectively. METHODS Fecal samples were collected from each woman once every two months over the period from July 2006 to June 2007, and they were screened for rotaviruses by means of polyacrylamide gel electrophoresis and immunoenzymatic assays, for caliciviruses and astroviruses by means of RT-PCR and for adenovirus by means of immunoenzymatic assays. The astroviruses were genotyped using nested PCR. RESULTS Among the 84 patients, 19 (22.6%) were positive for either calicivirus (14/19) or astrovirus (6/19), while one women was positive for both viruses in fecal samples collected on different occasions. Most of the positive samples were collected during the months of July and August (astrovirus) and September and October (calicivirus). None of the samples analyzed was positive for rotavirus or adenovirus. Gastroenteric viruses were detected in 13/19 (68.4%) of the pregnant women, whether HIV-seropositive or not. CONCLUSIONS The results from the present study showed that neither pregnancy nor HIV-seropositive status among the women increased the risk of infection by any of the gastroenteric viruses studied. This study presents data on gastroenteric virus detection among pregnant and/or HIV-positive women.
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Affiliation(s)
- Rui Gilberto Ferreira
- Departamento de Ginecologia e Obstetrícia, Faculdade de Medicina, Universidade Federal de Goiás, Goiânia, GO, Brazil.
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24
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[Survival strategies of human norovirus]. Uirusu 2010; 60:21-32. [PMID: 20848862 DOI: 10.2222/jsv.60.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Human norovirus is a mutatable non-enveloped RNA virus capable of causing acute gastroenteritis in humans. Thus far, no experimental systems can propagate this virus in large amounts. Recent progresses in viral genomics and bioinformatics have led to a better understanding of molecular evolution of this virus in human populations. In addition, progresses in studies of the related noroviruses, those are replicable in laboratory systems, have led to a rapid accumulation of information on structural biology of norovirus. Furthermore, progresses in public health and water environment researches have led to a better understanding of viral ecology. In this review, I will first summarize fundamental characteristics of norovirus and its molecules. Then, I will summarize structure and molecular evolution of norovirus GII/4 subtype, which is now responsible for majorities of norovirus outbreaks in the world. Finally I will discuss survival strategies of human norovirus in nature by integrating the information.
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25
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Mathijs E, Muylkens B, Mauroy A, Ziant D, Delwiche T, Thiry E. Experimental evidence of recombination in murine noroviruses. J Gen Virol 2010; 91:2723-33. [PMID: 20702654 DOI: 10.1099/vir.0.024109-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Based on sequencing data, norovirus (NoV) recombinants have been described, but no experimental evidence of recombination in NoVs has been documented. Using the murine norovirus (MNV) model, we investigated the occurrence of genetic recombination between two co-infecting wild-type MNV isolates in RAW cells. The design of a PCR-based genotyping tool allowed accurate discrimination between the parental genomes and the detection of a viable recombinant MNV (Rec MNV) in the progeny viruses. Genetic analysis of Rec MNV identified a homologous-recombination event located at the ORF1-ORF2 overlap. Rec MNV exhibited distinct growth curves and produced smaller plaques than the wild-type MNV in RAW cells. Here, we demonstrate experimentally that MNV undergoes homologous recombination at the previously described recombination hot spot for NoVs, suggesting that the MNV model might be suitable for in vitro studies of NoV recombination. Moreover, the results show that exchange of genetic material between NoVs can generate viruses with distinct biological properties from the parental viruses.
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Affiliation(s)
- Elisabeth Mathijs
- Department of Infectious and Parasitic Diseases, Virology and Viral Diseases, Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
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Yun SI, Kim JK, Song BH, Jeong AY, Jee YM, Lee CH, Paik SY, Koo Y, Jeon I, Byun SJ, Lee YM. Complete genome sequence and phylogenetic analysis of a recombinant Korean norovirus, CBNU1, recovered from a 2006 outbreak. Virus Res 2010; 152:137-52. [PMID: 20599576 DOI: 10.1016/j.virusres.2010.06.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 06/17/2010] [Accepted: 06/18/2010] [Indexed: 11/19/2022]
Abstract
We have determined the complete nucleotide and deduced amino acid sequences of the RNA genome of CBNU1, a human norovirus (NoV) recovered from a 2006 outbreak in South Korea. The genome of 7547 nucleotides, excluding a 3'-poly(A) tail of 11-105 nucleotides, encodes three overlapping open reading frames (ORFs): ORF1 (nucleotides 5-5104), ORF2 (nucleotides 5085-6731), and ORF3 (nucleotides 6731-7495). In a comparison to 108 other currently available completely sequenced NoVs representing all five genogroups (GI-GV) except GIV, the CBNU1 strain was highly similar to GII.3 NoVs. Multiple sequence alignments of the completely sequenced NoV genomes revealed five hypervariable regions throughout their genomes: two in ORF1, one in ORF2, and two in ORF3. At both the nucleotide and amino acid levels, genome-based phylogenetic analyses invariably showed that the CBNU1 strain was most closely related to three GII.3 NoVs: the American Texas/TCH04-577 and the two Japanese Saitama U18 and Saitama U201 strains; furthermore, these genome-based phylogenetic topologies corresponded most closely to those based on the ORF2 genes, as compared to those based on the ORF1 and ORF3 genes. Subsequent ORF2-based phylogenetic analyses of a selection of 126 other NoVs representing all 19 GII genotypes, in combination with genome-based Simplot analyses, showed that the CBNU1 strain was a recombinant GII.3 NoV with a breakpoint at the ORF1/ORF2 junction between two putative parent-like strains, Guangzhou/NVgz01 and Texas/TCH04-577. Overall, the CBNU1 strain represents the first Korean human NoV whose genome has been completely sequenced and for which its relationship with a large panel of genetically diverse NoVs has been extensively characterized.
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Affiliation(s)
- Sang-Im Yun
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, 12 Gaeshin-Dong, Heungduk-Ku, Cheongju, Chungbuk, South Korea
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Divergent evolution of norovirus GII/4 by genome recombination from May 2006 to February 2009 in Japan. J Virol 2010; 84:8085-97. [PMID: 20534859 DOI: 10.1128/jvi.02125-09] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Norovirus GII/4 is a leading cause of acute viral gastroenteritis in humans. We examined here how the GII/4 virus evolves to generate and sustain new epidemics in humans, using 199 near-full-length GII/4 genome sequences and 11 genome segment clones from human stool specimens collected at 19 sites in Japan between May 2006 and February 2009. Phylogenetic studies demonstrated outbreaks of 7 monophyletic GII/4 subtypes, among which a single subtype, termed 2006b, had continually predominated. Phylogenetic-tree, bootscanning-plot, and informative-site analyses revealed that 4 of the 7 GII/4 subtypes were mosaics of recently prevalent GII/4 subtypes and 1 was made up of the GII/4 and GII/12 genotypes. Notably, single putative recombination breakpoints with the highest statistical significance were constantly located around the border of open reading frame 1 (ORF1) and ORF2 (P <or= 0.000001), suggesting outgrowth of specific recombinant viruses in the outbreaks. The GII/4 subtypes had many unique amino acids at the time of their outbreaks, especially in the N-term, 3A-like, and capsid proteins. Unique amino acids in the capsids were preferentially positioned on the outer surface loops of the protruding P2 domain and more abundant in the dominant subtypes. These findings suggest that intersubtype genome recombination at the ORF1/2 boundary region is a common mechanism that realizes independent and concurrent changes on the virion surface and in viral replication proteins for the persistence of norovirus GII/4 in human populations.
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Rohayem J, Bergmann M, Gebhardt J, Gould E, Tucker P, Mattevi A, Unge T, Hilgenfeld R, Neyts J. Antiviral strategies to control calicivirus infections. Antiviral Res 2010; 87:162-78. [PMID: 20471996 PMCID: PMC7114105 DOI: 10.1016/j.antiviral.2010.05.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 05/01/2010] [Accepted: 05/04/2010] [Indexed: 11/29/2022]
Abstract
Caliciviridae are human or non-human pathogenic viruses with a high diversity. Some members of the Caliciviridae, i.e. human pathogenic norovirus or rabbit hemorrhagic disease virus (RHDV), are worldwide emerging pathogens. The norovirus is the major cause of viral gastroenteritis worldwide, accounting for about 85% of the outbreaks in Europe between 1995 and 2000. In the United States, 25 million cases of infection are reported each year. Since its emergence in 1984 as an agent of fatal hemorrhagic diseases in rabbits, RHDV has killed millions of rabbits and has been dispersed to all of the inhabitable continents. In view of their successful and apparently increasing emergence, the development of antiviral strategies to control infections due to these viral pathogens has now become an important issue in medicine and veterinary medicine. Antiviral strategies have to be based on an understanding of the epidemiology, transmission, clinical symptoms, viral replication and immunity to infection resulting from infection by these viruses. Here, we provide an overview of the mechanisms underlying calicivirus infection, focusing on the molecular aspects of replication in the host cell. Recent experimental data generated through an international collaboration on structural biology, virology and drug design within the European consortium VIZIER is also presented. Based on this analysis, we propose antiviral strategies that may significantly impact on the epidemiological characteristics of these highly successful viral pathogens.
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Affiliation(s)
- Jacques Rohayem
- The Calicilab, Institute of Virology, Dresden University of Technology, Dresden, Germany.
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29
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Abstract
An outbreak of norovirus (NoV) infection was identified in a kennel. Sequence analysis of a short fragment in the polymerase complex indicated the clonal origin of the strains, which were similar to the prototype canine NoV strain GIV.2/Bari/170/07-4/ITA (94.7% nucleotide identity). The findings demonstrate that canine NoV circulates in dogs in Greece and that it can spread easily across a group of animals.
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30
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Abente EJ, Sosnovtsev SV, Bok K, Green KY. Visualization of feline calicivirus replication in real-time with recombinant viruses engineered to express fluorescent reporter proteins. Virology 2010; 400:18-31. [PMID: 20137802 PMCID: PMC2855553 DOI: 10.1016/j.virol.2009.12.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 12/15/2009] [Accepted: 12/31/2009] [Indexed: 11/30/2022]
Abstract
Caliciviruses are non-enveloped, icosahedral viruses with a single-stranded, positive sense RNA genome. Transposon-mediated insertional mutagenesis was used to insert a transprimer sequence into random sites of an infectious full-length cDNA clone of the feline calicivirus (FCV) genome. A site in the LC gene (encoding the capsid leader protein) of the FCV genome was identified that could tolerate foreign insertions, and two viable recombinant FCV variants expressing LC fused either to AcGFP, or DsRedFP were recovered. The effects of the insertions on LC processing, RNA replication, and stability of the viral genome were analyzed, and the progression of a calicivirus single infection and co-infection were captured by real-time imaging fluorescent microscopy. The ability to engineer viable recombinant caliciviruses expressing foreign markers enables new approaches to investigate virus and host cell interactions, as well as studies of viral recombination, one of the driving forces of calicivirus evolution.
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Affiliation(s)
- Eugenio J. Abente
- Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD 20892
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | | | - Karin Bok
- Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD 20892
| | - Kim Y. Green
- Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD 20892
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
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de Rougemont A, Ambert-Balay K, Belliot G, Pothier P. [Norovirus infections: an overview]. Med Sci (Paris) 2010; 26:73-8. [PMID: 20132778 DOI: 10.1051/medsci/201026173] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Noroviruses belong to the Caliciviridae family. They are a major cause of sporadic cases and outbreaks of gastroenteritis in all age groups, and are responsible for a considerable disease burden in industrialized countries. Noroviruses are single-stranded RNA viruses, and show great genetic diversity making their detection difficult. Noroviruses can be divided into 5 genogroups, which themselves are subdivided into genotypes. Besides chance mutations that occur during viral replication, the great heterogeneity observed among noroviruses is also due to intra and inter-genotypic recombination events between strains. Some of these new variants or new recombinants are frequently associated with new epidemic waves of gastroenteritis. Finally, it is worth pointing out that the discovery of mechanisms involved in NoV infections through blood antigen-related receptors and cultivation of the first norovirus, a murine norovirus, are milestones in research on this virus. These advances open new promising avenues of research that will help to the understanding of the -pathogenicity of this important pathogen.
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Affiliation(s)
- Alexis de Rougemont
- Centre National de Référence des virus entériques, Laboratoire de virologie, Plateau technique de Biologie, Centre Hospitalier Universitaire de Dijon, 2, rue Angélique Ducoudray, BP 37013, F-21070 Dijon Cedex, France
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32
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Ziemer CJ, Bonner JM, Cole D, Vinjé J, Constantini V, Goyal S, Gramer M, Mackie R, Meng XJ, Myers G, Saif LJ. Fate and transport of zoonotic, bacterial, viral, and parasitic pathogens during swine manure treatment, storage, and land application. J Anim Sci 2010; 88:E84-94. [PMID: 20348375 DOI: 10.2527/jas.2009-2331] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Members of the public are always somewhat aware of foodborne and other zoonotic pathogens; however, recent illnesses traced to produce and the emergence of pandemic H1N1 influenza virus have increased the scrutiny on all areas of food production. The Council for Agricultural Science and Technology has recently published a comprehensive review of the fate and transport of zoonotic pathogens that can be associated with swine manure. The majority of microbes in swine manure are not zoonotic, but several bacterial, viral, and parasitic pathogens have been detected. Awareness of the potential zoonotic pathogens in swine manure and how treatment, storage, and handling affect their survival and their potential to persist in the environment is critical to ensure that producers and consumers are not at risk. This review discusses the primary zoonotic pathogens associated with swine manure, including bacteria, viruses, and parasites, as well as their fate and transport. Because the ecology of microbes in swine waste is still poorly described, several recommendations for future research are made to better understand and reduce human health risks. These recommendations include examination of environmental and ecological conditions that contribute to off-farm transport and development of quantitative risk assessments.
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Affiliation(s)
- C J Ziemer
- National Laboratory for Agriculture and the Environment, USDA-ARS, Ames, IA 50011, USA.
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Huang P, Morrow AL, Jiang X. The carbohydrate moiety and high molecular weight carrier of histo-blood group antigens are both required for norovirus-receptor recognition. Glycoconj J 2010; 26:1085-96. [PMID: 19238539 DOI: 10.1007/s10719-009-9229-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Revised: 01/10/2009] [Accepted: 01/15/2009] [Indexed: 12/18/2022]
Abstract
Histo-blood group antigens (HBGAs) on human intestinal epithelium serve as receptors for noroviruses (NVs). These antigens also are expressed in milk and may act as decoy receptors to protect breast-fed infants and others against NV disease. In this study we demonstrated that human milk is highly variable in synthesis of HBGAs, which differs from that of saliva; a large quantity of small, soluble HBGAs are found in milk, but much less in saliva and are recognized by MAbs, but not by NVs. There is another group of HBGAs, of high MW, found in both milk and saliva, and recognized by both NVs and MAbs. These results suggest that the specificity of NVs and MAbs to HBGAs are different and the backbones in addition to the carbohydrate moiety are required for NV recognition. Further studies to define the structure and genetics of the high MW milk glycans are necessary.
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Affiliation(s)
- Pengwei Huang
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
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34
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Bank-Wolf BR, König M, Thiel HJ. Zoonotic aspects of infections with noroviruses and sapoviruses. Vet Microbiol 2010; 140:204-12. [DOI: 10.1016/j.vetmic.2009.08.021] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Revised: 07/03/2009] [Accepted: 08/21/2009] [Indexed: 10/20/2022]
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Chhabra P, Walimbe AM, Chitambar SD. Molecular characterization of three novel intergenotype norovirus GII recombinant strains from western India. Virus Res 2009; 147:242-6. [PMID: 19941918 DOI: 10.1016/j.virusres.2009.11.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2009] [Revised: 11/16/2009] [Accepted: 11/17/2009] [Indexed: 01/31/2023]
Abstract
The phenomenon of recombination has been widely described among noroviruses (NoVs) in the past few years. In a NoV surveillance study conducted in western India, 3 novel and 3 known combinations of RNA-dependent RNA polymerase (RdRp) and capsid genes were identified in genogroup (G) II NoV strains. The present study pertains to the characterization of three novel intergenotype NoV GII recombinant strains. RT-PCRs were carried out for the amplification of nearly complete RdRp and complete capsid genes spanning ORF1/2 overlap of three strains followed by sequencing of the amplicons. The recombination event was confirmed by phylogenetic analysis using Bayesian MCMC approach, SimPlot analysis and Maximum chi(2) method. Three novel intergenotype (GII) recombinations of GII.b/GII.18, GII.1/GII.12 and GII.3/GII.13 specificities were identified respectively in the strains PC03, PC24 and PC25 for the first time. The breakpoint in the novel recombinants was placed in the vicinity of the 20 bp ORF1/2 overlap, a common hotspot known to exist in NoV recombinants. The capsid genes of all of the 3 recombinants were closely related to their counter parts in reference strains however, a high degree of variation emerged in the polymerase genes especially of PC24 and PC25 in comparison to the reference strains.
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Affiliation(s)
- Preeti Chhabra
- Enteric Viruses Department, National Institute of Virology, Pune, India
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36
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Altindis M, Bányai K, Kalayci R, Gulamber C, Koken R, Yoldas Y, Aykurt P, Martella V. Frequency of norovirus in stool samples from hospitalized children due to acute gastroenteritis in Anatolia, Turkey, 2006–2007. ACTA ACUST UNITED AC 2009; 41:685-8. [DOI: 10.1080/00365540903071342] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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37
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Abstract
Alphatronlike (genogroup IV [GIV]) noroviruses (NoVs) have been recently identified in carnivores. By screening a collection of 183 fecal samples collected during 2007 from dogs with enteric signs, the overall NoV prevalence was found to be 2.2% (4/183). A unique strain, Bari/91/07/ITA, resembled GIV.2 NoVs in its ORF1 (polymerase complex), while it was genetically unrelated in its full-length ORF2 (capsid gene) to GIV animal and human NoVs (54.0 to 54.4% amino acid identity) and to any other NoV genogroup (<54.7% amino acid identity). It displayed the highest identity (58.1% amino acid identity) to unclassified human strain Chiba/040502/04/Jp. Interestingly, the very 5' end of ORF2 of the canine virus matched short noroviral sequences (88.9% nucleotide identity and 98.9% amino acid identity) identified from oysters in Japan, indicating that similar viruses may be common environmental contaminants.
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38
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A new variant of Norovirus GII.4/2007 and inter-genotype recombinant strains of NVGII causing acute watery diarrhoea among children in Kolkata, India. J Clin Virol 2009; 45:223-9. [DOI: 10.1016/j.jcv.2009.04.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 04/18/2009] [Accepted: 04/26/2009] [Indexed: 01/19/2023]
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39
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Genetic diversity among food-borne and waterborne norovirus strains causing outbreaks in Sweden. J Clin Microbiol 2009; 47:2411-8. [PMID: 19494060 DOI: 10.1128/jcm.02168-08] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A total of 101 food-borne and waterborne outbreaks that were caused by norovirus and that resulted in more than 4,100 cases of illness were reported to the Swedish Institute for Infectious Disease Control from January 2002 to December 2006. Sequence and epidemiological data for isolates from 73 outbreaks were analyzed. In contrast to health care-related outbreaks, no clear seasonality could be observed. Sequence analysis showed a high degree of genetic variation among the noroviruses detected. Genogroup II (GII) viruses were detected in 70% of the outbreaks, and of those strains, strains of GII.4 were the most prevalent and were detected in 25% of all outbreaks. The GII.4 variants detected in global outbreaks in health care settings during 2002, 2004, and 2006 were also found in the food-borne outbreaks. GI strains totally dominated as the cause of water-related (drinking and recreational water) outbreaks and were found in 12 of 13 outbreaks. In 14 outbreaks, there were discrepancies among the polymerase and capsid genotype results. In four outbreaks, the polymerase of the recombinant GII.b virus occurred together with the GII.1 or GII.3 capsids, while the GII.7 polymerase occurred together with the GII.6 and GII.7 capsids. Mixed infections were observed in six outbreaks; four of these were due to contaminated water, and two were due to imported frozen berries. Contaminated food and water serve as important reservoirs for noroviruses. The high degree of genetic diversity found among norovirus strains causing food-borne and waterborne infections stresses the importance of the use of broad reaction detection methods when such outbreaks are investigated.
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40
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Xavier M, Oliveira S, Ferreira M, Victoria M, Miranda V, Silva M, Strina A, Barreto M, Miagostovicht M, Leite J. Detection of caliciviruses associated with acute infantile gastroenteritis in Salvador, an urban center in Northeast Brazil. Braz J Med Biol Res 2009; 42:438-44. [DOI: 10.1590/s0100-879x2009000500007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Accepted: 02/26/2009] [Indexed: 11/22/2022] Open
Affiliation(s)
| | | | | | | | | | | | - A. Strina
- Universidade Federal da Bahia, Brasil
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41
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Jeong YJ, Park SI, Hosmillo M, Shin DJ, Chun YH, Kim HJ, Kwon HJ, Kang SY, Woo SK, Park SJ, Kim GY, Kang MI, Cho KO. Detection and molecular characterization of porcine group C rotaviruses in South Korea. Vet Microbiol 2009; 138:217-24. [PMID: 19362434 PMCID: PMC7117287 DOI: 10.1016/j.vetmic.2009.03.024] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Revised: 03/05/2009] [Accepted: 03/11/2009] [Indexed: 11/28/2022]
Abstract
Group C rotaviruses (GCRVs) cause acute diarrhea in humans and animals worldwide and the evidence for a possible zoonotic role of GCRVs has been recently provided. However, there is little evidence of porcine GCRV infections or of their genetic diversity in South Korea. We examined 137 diarrheic fecal specimens from 55 farms collected from six provinces. RT-PCR utilizing primer pairs specific for the GCRV VP6 gene detected GCRV-positive reactions in 36 (26.2%) diarrheic fecal samples. Of these, 17 samples (12.4%) tested positive for porcine GCRVs alone and 19 samples (13.8%) were also positive for other pathogens. Other enteric pathogens except for GCRV were detected in 64 feces samples (46.7%) and no enteric pathogens were evident in 37 feces samples (27.0%). Phylogenetic and sequence homology analyses of GCRV partial VP6 gene between 23 Korean and other known porcine GCRVs demonstrated that Korean strains belonged to the porcine lineage. Furthermore, one Korean porcine strain shared the highest nucleotide (89.7–89.0%) and deduced amino acid sequence (92.9–93.9%) identities with bovine GCRV strains and was placed in the bovine GCRV lineage indicative of bovine origin. In conclusion, porcine GCRV infections are widespread in piglets with diarrhea in South Korea. The infecting porcine GCRVs mostly belong to the porcine lineage with the exception of one bovine-like GCRV, which possibly originated from bovine GCRV due to interspecies transmission.
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Affiliation(s)
- Young-Ju Jeong
- Biotherapy Human Resources Center, Chonnam National University, Gwangju, South Korea
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42
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Abstract
Environmental virology started with the detection of poliovirus in water. Since then other enteric viruses responsible for gastroenteritis and hepatitis have replaced enteroviruses as the main target for detection. Most shellfish-borne viral outbreaks are restricted to norovirus and hepatitis A virus, making them the main targets for bivalve virological analysis. The inclusion of virus analysis in regulatory standards for viruses in molluscan bivalve samples must overcome several shortcomings such as the technical difficulties and high costs of virus monitoring, the lack of harmonised and standardised assays and the challenge posed by the ever-changing nature of viruses. Nowadays methods are available to detect, quantify and characterise viral pathogens in molluscan shellfish to reduce the risks of shellfish-borne virus diseases.
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Rodríguez-Díaz J, Querales L, Caraballo L, Vizzi E, Liprandi F, Takiff H, Betancourt WQ. Detection and characterization of waterborne gastroenteritis viruses in urban sewage and sewage-polluted river waters in Caracas, Venezuela. Appl Environ Microbiol 2009; 75:387-94. [PMID: 19028907 PMCID: PMC2620703 DOI: 10.1128/aem.02045-08] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 11/14/2008] [Indexed: 11/20/2022] Open
Abstract
The detection and molecular characterization of pathogenic human viruses in urban sewage have been used extensively to derive information on circulating viruses in given populations throughout the world. In this study, a similar approach was applied to provide an overview of the epidemiology of waterborne gastroenteritis viruses circulating in urban areas of Caracas, the capital city of Venezuela in South America. Dry season sampling was conducted in sewers and in a major river severely polluted with urban sewage discharges. Nested PCR was used for detection of human adenoviruses (HAds), while reverse transcription plus nested or seminested PCR was used for detection of enteroviruses (HuEVs), rotaviruses (HRVs), noroviruses (HuNoVs), and astroviruses (HAstVs). HRVs were fully characterized with genotype-specific primers for VP4 (genotype P), VP7 (genotype G), and the rotavirus nonstructural protein 4 (NSP4). HuNoVs and HAstVs were characterized by sequencing and phylogenetic analysis. The detection rates of all viruses were >or=50%, and all sampling events were positive for at least one of the pathogenic viruses studied. The predominant HRV types found were G1, P[8], P[4], and NSP4A and -B. Genogroup II of HuNoVs and HAstV type 8 were frequently detected in sewage and sewage-polluted river waters. This study reveals relevant epidemiological data on the distribution and persistence of human pathogenic viruses in sewage-polluted waters and addresses the potential health risks associated with transmission of these viruses through water-related environmental routes.
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Affiliation(s)
- J Rodríguez-Díaz
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
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44
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Andreasi MSA, Cardoso DDDDP, Fernandes SM, Tozetti IA, Borges AMT, Fiaccadori FS, Santos RAT, Souza M. Adenovirus, calicivirus and astrovirus detection in fecal samples of hospitalized children with acute gastroenteritis from Campo Grande, MS, Brazil. Mem Inst Oswaldo Cruz 2008; 103:741-4. [DOI: 10.1590/s0074-02762008000700020] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 09/16/2008] [Indexed: 11/22/2022] Open
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45
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Murine norovirus, a recently discovered and highly prevalent viral agent of mice. Lab Anim (NY) 2008; 37:314-20. [PMID: 18568010 DOI: 10.1038/laban0708-314] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Accepted: 01/30/2008] [Indexed: 11/08/2022]
Abstract
Murine norovirus (MNV), a recently discovered viral agent of laboratory mice, is closely related to human norovirus, a contagious pathogen known to cause gastroenteritis. The prototype strain of MNV (MNV-1) was first isolated and characterized in 2003 as a sporadic, lethal pathogen in certain strains of immunocompromised knockout mice. Serological surveillance data from mouse colonies throughout the US and Canada have since shown that MNV is highly prevalent. Because MNV is unique among norovirus strains in its ability to replicate in cell culture, it serves as the most accessible model to elucidate the mechanisms of infection and replication of human norovirus. The author discusses the genetic diversity of MNV, its prevalence, pathology and potential research implications, as well as techniques for detection and eradication of this virus.
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47
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Pesavento PA, Chang KO, Parker JSL. Molecular virology of feline calicivirus. Vet Clin North Am Small Anim Pract 2008; 38:775-86, vii. [PMID: 18501277 DOI: 10.1016/j.cvsm.2008.03.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Caliciviridae are small, nonenveloped, positive-stranded RNA viruses. Much of our understanding of the molecular biology of the caliciviruses has come from the study of the naturally occurring animal caliciviruses. In particular, many studies have focused on the molecular virology of feline calicivirus (FCV), which reflects its importance as a natural pathogen of cats. FCVs demonstrate a remarkable capacity for high genetic, antigenic, and clinical diversity; "outbreak" vaccine resistant strains occur frequently. This article updates the reader on the current status of clinical behavior and pathogenesis of FCV.
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Affiliation(s)
- Patricia A Pesavento
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, 4206 VM3A, Davis, CA 95616-5270, USA.
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Nayak MK, Balasubramanian G, Sahoo GC, Bhattacharya R, Vinje J, Kobayashi N, Sarkar MC, Bhattacharya MK, Krishnan T. Detection of a novel intergenogroup recombinant Norovirus from Kolkata, India. Virology 2008; 377:117-23. [PMID: 18555887 DOI: 10.1016/j.virol.2008.04.027] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2008] [Revised: 04/12/2008] [Accepted: 04/19/2008] [Indexed: 10/21/2022]
Abstract
Mutation and recombination are recognized as important driving forces of evolution among RNA viruses. An intergenogroup recombinant norovirus strain [Hu/Kol/NLV/L8775/AB290150/2006/India] was detected in the faecal specimen of a 17 year old male, who had suffered from acute watery diarrhea and severe dehydration. Sequence analysis confirmed that this novel recombinant strain had a polymerase gene fragment that closely resembled a Norovirus (NoV) genogroup-I genotype-3 virus (HuCV/NLV/GI.3/VA98115/AY038598/1998/USA) and a capsid gene resembling NoV genogroup-II genotype-4 virus (NoV/Hu/GII.4/Terneuzen70/EF126964/2006/NL). The crossing over and recombination was observed at nucleotide (nt) 790 of NoV GI VA98115 strain and nt808 of NoV GII Terneuzen70 strain. In both parent strains conserved nucleotide sequence and hairpin structure (DNA secondary structure) were reported at the junction point of ORF1 and ORF2, exhibiting the mechanism of recombination in these viruses. Thus this novel recombinant NoV is another step in evolution among NoVs, indicating that constant surveillance is important to successfully monitor emergence of these strains.
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Affiliation(s)
- Mukti K Nayak
- Molecular Virology Laboratory, Diarrhoeal Disease Research and Control Centre, Division of Virology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, 700010, India
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Ishida S, Yoshizumi S, Ikeda T, Miyoshi M, Okano M, Okui T. Sensitive and rapid detection of norovirus using duplex TaqMan reverse transcription-polymerase chain reaction. J Med Virol 2008; 80:913-20. [PMID: 18360905 DOI: 10.1002/jmv.21142] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Conventional reverse transcription-polymerase chain reaction (RT-PCR) to detect norovirus (NV) is a complex of multi-step procedure that requires gel electrophoresis as well as hybridization or sequencing to confirm the final diagnosis. A duplex TaqMan RT-PCR was developed to detect and classify genogroup (G) I and GII of NV. The primers and TaqMan probes for this assay were selected from the region of open reading frame (ORF) 1-ORF2 junction. A total of 796 stool specimens from 103 outbreaks of gastroenteritis, and a series of 46 stool specimens containing most NV genotypes was used for this study. For these specimens from 103 outbreaks, NV was detected and classified by the duplex TaqMan RT-PCR in 536 of the 541 specimens tested previously to be positive using the conventional RT-PCR. Two hundred fifty-one of the 255 specimens that were negative by the conventional RT-PCR were also negative by the TaqMan RT-PCR. No false positive result was observed for other enteric RNA viruses such as rotavirus and sapovirus. This is the first report on the development of a duplex TaqMan RT-PCR end-point assay for detection and differentiation of GI and GII of NV strains simultaneously followed by genotyping. These results suggest the practical application of this duplex TaqMan RT-PCR is useful for the detection of NV in clinical specimens.
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Affiliation(s)
- Setsuko Ishida
- Division of Enteric Virology, Department of Microbiology, Hokkaido Institute of Public Health, Sapporo, Japan.
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Fukuda S, Sasaki Y, Takao S, Seno M. Recombinant norovirus implicated in gastroenteritis outbreaks in Hiroshima Prefecture, Japan. J Med Virol 2008; 80:921-8. [PMID: 18360906 DOI: 10.1002/jmv.21151] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Norovirus (NoV) is a major etiological agent of acute gastroenteritis outbreaks worldwide. A total of 314 fecal specimens collected from patients of 39 NoV gastroenteritis outbreaks in Hiroshima Prefecture, Japan, between December 2001 and April 2006 were tested for the occurrence of recombinant NoVs. Sixteen genotypes (GI/1, GI/2, GI/4, GI/7, GI/8, GI/11, GI/14, GII/2, GII/3, GII/4, GII/5, GII/6, GII/8, GII/12, GII/14, and GII/untypeable) were detected in the 39 outbreaks based on capsid sequences and GII/4 was predominant recently. Twelve strains detected in 11 (28.2%) of the 39 outbreaks were suspected to be recombinants by using Simplot and Recco analyses and five recombinant genotypes, GII/4-GII/12 (five strains), GIIb-GII/3 (four strains), GII/4-GII/2 (one strain), GII/4-GII/14 (one strain), and GI/2-GI/8 (one strain), were identified based on RNA-dependent RNA polymerase and capsid sequences. None of the strains genotyped as GII/4 based on the capsid sequence was identified as a recombinant. The putative recombination points in the recombinant strains were placed either upstream or downstream of the open reading frame (ORF) 1 and ORF2 overlap. The present study indicates the following: (a) recombination among ORFs is common in nature, (b) the involvement of recombinant NoVs in gastroenteritis outbreaks is extensive even in a local area such as Hiroshima Prefecture, Japan, and (c) the conserved region (ORF1 and ORF2 overlap) has a meaningful function against the recombination event.
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Affiliation(s)
- Shinji Fukuda
- Center for Public Health and Environment, Hiroshima Prefectural Technology Research Institute, Hiroshima, Japan.
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