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Yang Z, Kulka M, Yang Q, Papafragkou E, Yu C, Wales SQ, Ngo D, Chen H. Whole-Genome Sequencing-Based Confirmatory Methods on RT-qPCR Results for the Detection of Foodborne Viruses in Frozen Berries. FOOD AND ENVIRONMENTAL VIROLOGY 2024; 16:225-240. [PMID: 38687458 PMCID: PMC11186866 DOI: 10.1007/s12560-024-09591-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/13/2024] [Indexed: 05/02/2024]
Abstract
Accurate detection, identification, and subsequent confirmation of pathogens causing foodborne illness are essential for the prevention and investigation of foodborne outbreaks. This is particularly true when the causative agent is an enteric virus that has a very low infectious dose and is likely to be present at or near the limit of detection. In this study, whole-genome sequencing (WGS) was combined with either of two non-targeted pre-amplification methods (SPIA and SISPA) to investigate their utility as a confirmatory method for RT-qPCR positive results of foods contaminated with enteric viruses. Frozen berries (raspberries, strawberries, and blackberries) were chosen as the food matrix of interest due to their association with numerous outbreaks of foodborne illness. The hepatitis A virus (HAV) and human norovirus (HuNoV) were used as the contaminating agents. The non-targeted WGS strategy employed in this study could detect and confirm HuNoV and HAV at genomic copy numbers in the single digit range, and in a few cases, identified viruses present in samples that had been found negative by RT-qPCR analyses. However, some RT-qPCR-positive samples could not be confirmed using the WGS method, and in cases with very high Ct values, only a few viral reads and short sequences were recovered from the samples. WGS techniques show great potential for confirmation and identification of virally contaminated food items. The approaches described here should be further optimized for routine application to confirm the viral contamination in berries.
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Affiliation(s)
- Zhihui Yang
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD, 20708, USA.
| | - Michael Kulka
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD, 20708, USA
| | - Qianru Yang
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD, 20708, USA
| | - Efstathia Papafragkou
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD, 20708, USA
| | - Christine Yu
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD, 20708, USA
| | - Samantha Q Wales
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD, 20708, USA
| | - Diana Ngo
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD, 20708, USA
| | - Haifeng Chen
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD, 20708, USA
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Mecklenburg L, Ducore R, Boyle M, Newell A, Boone L, Luft J, Romeike A, Haverkamp AK, Mansfield K, Penraat KA, Baczenas JJ, Minor N, O'Connor SL, O'Connor DH. A new genotype of hepatitis A virus causing transient liver enzyme elevations in Mauritius-origin laboratory-housed Macaca fascicularis. Vet Pathol 2024; 61:488-496. [PMID: 37953600 DOI: 10.1177/03009858231209691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Hepatitis A virus (HAV) infects humans and nonhuman primates, typically causing an acute self-limited illness. Three HAV genotypes have been described so far for humans, and three genotypes have been described for nonhuman primates. We observed transiently elevated liver enzymes in Mauritius-origin laboratory-housed macaques in Germany and were not able to demonstrate an etiology including HAV by serology and polymerase chain reaction (PCR). HAV is a rare pathogen in cynomolgus macaques, and since all employees were routinely vaccinated against HAV, it was not a part of the routine vaccination and screening program. A deep sequencing approach identified a new HAV genotype (referred to as Simian_HAV_Macaca/Germany/Mue-1/2022) in blood samples from affected animals. This HAV was demonstrated by reverse transcription PCR in blood and liver and by in situ hybridization in liver, gall bladder, and septal ducts. A commercial vaccine was used to protect animals from liver enzyme elevation. The newly identified simian HAV genotype demonstrates 80% nucleotide sequence identity to other simian and human HAV genotypes. There was deeper divergence between Simian_HAV_Macaca/Germany/Mue-1/2022 and other previously described HAVs, including both human and simian viruses. In situ hybridization indicated persistence in the biliary epithelium up to 3 months after liver enzymes were elevated. Vaccination using a commercial vaccine against human HAV prevented reoccurrence of liver enzyme elevations. Because available assays for HAV did not detect this new HAV genotype, knowledge of its existence may ameliorate potential significant epidemiological and research implications in laboratories globally.
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Affiliation(s)
| | - Rebecca Ducore
- Labcorp Early Development Laboratories Inc., Chantilly, VA
| | - Molly Boyle
- Labcorp Early Development Laboratories Inc., Somerset, NJ
| | - Andrew Newell
- Labcorp Early Development Laboratories Ltd., Harrogate, UK
| | - Laura Boone
- Labcorp Early Development Laboratories Inc., Greenfield, IN
| | - Joerg Luft
- Labcorp Early Development Services GmbH, Muenster, Germany
| | | | | | | | | | | | - Nick Minor
- University of Wisconsin-Madison, Madison, WI
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Ohta E. Pathologic characteristics of infectious diseases in macaque monkeys used in biomedical and toxicologic studies. J Toxicol Pathol 2023; 36:95-122. [PMID: 37101957 PMCID: PMC10123295 DOI: 10.1293/tox.2022-0089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/16/2023] [Indexed: 04/28/2023] Open
Abstract
Nonhuman primates (NHPs), which have many advantages in scientific research and are often the only relevant animals to use in assessing the safety profiles and biological or pharmacological effects of drug candidates, including biologics. In scientific or developmental experiments, the immune systems of animals can be spontaneously compromised possibly due to background infection, experimental procedure-associated stress, poor physical condition, or intended or unintended mechanisms of action of test articles. Under these circumstances, background, incidental, or opportunistic infections can seriously can significantly complicate the interpretation of research results and findings and consequently affect experimental conclusions. Pathologists and toxicologists must understand the clinical manifestations and pathologic features of infectious diseases and the effects of these diseases on animal physiology and experimental results in addition to the spectrum of infectious diseases in healthy NHP colonies. This review provides an overview of the clinical and pathologic characteristics of common viral, bacterial, fungal, and parasitic infectious diseases in NHPs, especially macaque monkeys, as well as methods for definitive diagnosis of these diseases. Opportunistic infections that can occur in the laboratory setting have also been addressed in this review with examples of cases of infection disease manifestation that was observed or influenced during safety assessment studies or under experimental conditions.
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Affiliation(s)
- Etsuko Ohta
- Global Drug Safety, Eisai Co., Ltd., 5-1-3 Tokodai,
Tsukuba-shi, Ibaraki 300-2635, Japan
- *Corresponding author: E Ohta (e-mail: )
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Moreira LVL, Malheiros AP, Barbosa KMV, Freitas PEB, Silva AL, Cruz ACR, Nunes HM, Corrêa das Chagas AA, Souza de Souza AJ. The first evidence of Hepatitis A virus subgenotype IIIA in the Eastern Brazilian Amazon, 1982‐1983. J Med Virol 2022; 94:2887-2891. [DOI: 10.1002/jmv.27625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/18/2022] [Accepted: 01/21/2022] [Indexed: 11/09/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | - Alex Junior Souza de Souza
- Universidade Paulista, Instituto de Ciências da SaúdeCampinasSPBrasil
- Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Departamento de PatologiaSão PauloSPBrasil
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Enkirch T, Severi E, Vennema H, Thornton L, Dean J, Borg ML, Ciccaglione AR, Bruni R, Christova I, Ngui SL, Balogun K, Němeček V, Kontio M, Takács M, Hettmann A, Korotinska R, Löve A, Avellón A, Muñoz-Chimeno M, de Sousa R, Janta D, Epštein J, Klamer S, Suin V, Aberle SW, Holzmann H, Mellou K, Ederth JL, Sundqvist L, Roque-Afonso AM, Filipović SK, Poljak M, Vold L, Stene-Johansen K, Midgley S, Fischer TK, Faber M, Wenzel JJ, Takkinen J, Leitmeyer K. Improving preparedness to respond to cross-border hepatitis A outbreaks in the European Union/European Economic Area: towards comparable sequencing of hepatitis A virus. Euro Surveill 2019; 24:1800397. [PMID: 31311618 PMCID: PMC6636214 DOI: 10.2807/1560-7917.es.2019.24.28.1800397] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/18/2019] [Indexed: 12/13/2022] Open
Abstract
IntroductionSequence-based typing of hepatitis A virus (HAV) is important for outbreak detection, investigation and surveillance. In 2013, sequencing was central to resolving a large European Union (EU)-wide outbreak related to frozen berries. However, as the sequenced HAV genome regions were only partly comparable between countries, results were not always conclusive.AimThe objective was to gather information on HAV surveillance and sequencing in EU/European Economic Area (EEA) countries to find ways to harmonise their procedures, for improvement of cross-border outbreak responses.MethodsIn 2014, the European Centre for Disease Prevention and Control (ECDC) conducted a survey on HAV surveillance practices in EU/EEA countries. The survey enquired whether a referral system for confirming primary diagnostics of hepatitis A existed as well as a central collection/storage of hepatitis A cases' samples for typing. Questions on HAV sequencing procedures were also asked. Based on the results, an expert consultation proposed harmonised procedures for cross-border outbreak response, in particular regarding sequencing. In 2016, a follow-up survey assessed uptake of suggested methods.ResultsOf 31 EU/EEA countries, 23 (2014) and 27 (2016) participated. Numbers of countries with central collection and storage of HAV positive samples and of those performing sequencing increased from 12 to 15 and 12 to 14 respectively in 2016, with all countries typing an overlapping fragment of 218 nt. However, variation existed in the sequenced genomic regions and their lengths.ConclusionsWhile HAV sequences in EU/EEA countries are comparable for surveillance, collaboration in sharing and comparing these can be further strengthened.
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Affiliation(s)
- Theresa Enkirch
- Public Health Agency of Sweden, Solna, Sweden
- European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Ettore Severi
- European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
- Karolinska Institutet, Stockholm, Sweden
| | - Harry Vennema
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Lelia Thornton
- HSE - Health Protection Surveillance Centre, Dublin, Ireland
| | - Jonathan Dean
- National Virus Reference Laboratory, Dublin, Ireland
| | | | | | | | - Iva Christova
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Koye Balogun
- Public Health England (PHE), London, United Kingdom
| | | | - Mia Kontio
- National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Mária Takács
- National Public Health Institute, Budapest, Hungary
| | | | | | - Arthur Löve
- Landspitali- National University Hospital, Reykjavik, Iceland
| | - Ana Avellón
- Carlos III Institute of Health, Madrid, Spain
| | | | - Rita de Sousa
- National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - Denisa Janta
- National Institute of Public Health, Bucharest, Romania
| | | | - Sofieke Klamer
- Scientific Institute of Public Health, Brussels, Belgium
| | - Vanessa Suin
- Sciensano, Directorate Infectious diseases in humans, Brussels, Belgium
| | - Stephan W Aberle
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | | | - Kassiani Mellou
- Hellenic Centre for Disease Control and Prevention, Athens, Greece
| | | | | | | | | | - Mario Poljak
- Institute of Microbiology and Immunology, Ljubljana, Slovenia
| | - Line Vold
- Norwegian institute of Public Health, Oslo, Norway
| | | | | | - Thea Kølsen Fischer
- Statens Serum Institut (SSI), Copenhagen, Denmark
- Department of Infectious Diseases and Global Health, University of Southern Denmark, Odense, Denmark
| | - Mirko Faber
- Robert Koch Institute (RKI), Berlin, Germany
| | - Jürgen J Wenzel
- National Reference Laboratory for HAV, Regensburg University Medical Center, Regensburg, Germany
| | - Johanna Takkinen
- European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Katrin Leitmeyer
- European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
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Inter- and Intra-Host Nucleotide Variations in Hepatitis A Virus in Culture and Clinical Samples Detected by Next-Generation Sequencing. Viruses 2018; 10:v10110619. [PMID: 30423964 PMCID: PMC6265925 DOI: 10.3390/v10110619] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/23/2018] [Accepted: 11/05/2018] [Indexed: 11/17/2022] Open
Abstract
The accurate virus detection, strain discrimination, and source attribution of contaminated food items remains a persistent challenge because of the high mutation rates anticipated to occur in foodborne RNA viruses, such as hepatitis A virus (HAV). This has led to predictions of the existence of more than one sequence variant between the hosts (inter-host) or within an individual host (intra-host). However, there have been no reports of intra-host variants from an infected single individual, and little is known about the accuracy of the single nucleotide variations (SNVs) calling with various methods. In this study, the presence and identity of viral SNVs, either between HAV clinical specimens or among a series of samples derived from HAV clone1-infected FRhK4 cells, were determined following analyses of nucleotide sequences generated using next-generation sequencing (NGS) and pyrosequencing methods. The results demonstrate the co-existence of inter- and intra-host variants both in the clinical specimens and the cultured samples. The discovery and confirmation of multi-viral RNAs in an infected individual is dependent on the strain discrimination at the SNV level, and critical for successful outbreak traceback and source attribution investigations. The detection of SNVs in a time series of HAV infected FRhK4 cells improved our understanding on the mutation dynamics determined probably by different selective pressures. Additionally, it demonstrated that NGS could potentially provide a valuable investigative approach toward SNV detection and identification for other RNA viruses.
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7
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Smith DB, Simmonds P. Classification and Genomic Diversity of Enterically Transmitted Hepatitis Viruses. Cold Spring Harb Perspect Med 2018; 8:a031880. [PMID: 29530950 PMCID: PMC6120691 DOI: 10.1101/cshperspect.a031880] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Hepatitis A virus (HAV) and hepatitis E virus (HEV) are significant human pathogens and are responsible for a substantial proportion of cases of severe acute hepatitis worldwide. Genetically, both viruses are heterogeneous and are classified into several genotypes that differ in their geographical distribution and risk group association. There is, however, little evidence that variants of HAV or HEV differ antigenically or in their propensity to cause severe disease. Genetically more divergent but primarily hepatotropic variants of both HAV and HEV have been found in several mammalian species, those of HAV being classified into eight species within the genus Hepatovirus in the virus family Picornaviridae. HEV is classified as a member of the species Orthohepevirus A in the virus family Hepeviridae, a species that additionally contains viruses infecting pigs, rabbits, and a variety of other mammalian species. Other species (Orthohepevirus B-D) infect a wide range of other mammalian species including rodents and bats.
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Affiliation(s)
- Donald B Smith
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, United Kingdom
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8
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Full-length genome characterization and quasispecies distribution of hepatitis A virus isolates in China. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.virep.2015.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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9
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Abstract
Describing the viral diversity of wildlife can provide interesting and useful insights into the natural history of established human pathogens. In this study, we describe a previously unknown picornavirus in harbor seals (tentatively named phopivirus) that is related to human hepatitis A virus (HAV). We show that phopivirus shares several genetic and phenotypic characteristics with HAV, including phylogenetic relatedness across the genome, a specific and seemingly quiescent tropism for hepatocytes, structural conservation in a key functional region of the type III internal ribosomal entry site (IRES), and a codon usage bias consistent with that of HAV. Hepatitis A virus (HAV) is an important viral hepatitis in humans because of the substantial number of cases each year in regions with low socioeconomic status. The origin of HAV is unknown, and no nonprimate HAV-like viruses have been described. Here, we describe the discovery of an HAV-like virus in seals. This finding suggests that the diversity and evolutionary history of these viruses might be far greater than previously thought and may provide insight into the origin and pathogenicity of HAV.
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10
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Lee GC, Kim MJ, Nam S, Lee CH. Incidence and molecular characterization of hepatitis A viruses in Korean surface water between 2007 and 2010. Microbiol Immunol 2014; 58:342-51. [DOI: 10.1111/1348-0421.12151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 04/01/2014] [Accepted: 04/14/2014] [Indexed: 01/30/2023]
Affiliation(s)
- Gyu-Cheol Lee
- Water Analysis and Research Center; K-water, 200 Sintanjin-ro Daedeok-gu Daejeon 306-711 Korea
| | - Min-Jeong Kim
- Water Analysis and Research Center; K-water, 200 Sintanjin-ro Daedeok-gu Daejeon 306-711 Korea
| | - Sehee Nam
- Water Analysis and Research Center; K-water, 200 Sintanjin-ro Daedeok-gu Daejeon 306-711 Korea
| | - Chan Hee Lee
- Department of Microbiology; College of Natural Sciences; Chungbuk National University; 52 Naesudong-ro Heungdeok-gu Cheongju Chungbuk 361-763 Korea
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Setzer AP, Coimbra Gaspar AM, Sidoni M, Galvão Bueno M, Catão-Dias JL. Serosurvey for hepatitis A in neotropical primates in southeast Brazil. J Med Primatol 2014. [DOI: 10.1111/jmp.12106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Ariela Priscila Setzer
- Laboratório de Patologia Comparada de Animais Selvagens - LAPCOM; Faculdade de Medicina Veterinária e Zootecnia; Universidade de São Paulo; São Paulo Brazil
| | | | - Marli Sidoni
- Laboratório de Tecnologia Diagnóstica/LATED; Vice-diretoria de Desenvolvimento Tecnológico/Fundação Oswaldo Cruz (Fiocruz); Rio de Janeiro Brazil
| | - Marina Galvão Bueno
- Laboratório de Patologia Comparada de Animais Selvagens - LAPCOM; Faculdade de Medicina Veterinária e Zootecnia; Universidade de São Paulo; São Paulo Brazil
| | - José Luiz Catão-Dias
- Laboratório de Patologia Comparada de Animais Selvagens - LAPCOM; Faculdade de Medicina Veterinária e Zootecnia; Universidade de São Paulo; São Paulo Brazil
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Hepatitis A virus: host interactions, molecular epidemiology and evolution. INFECTION GENETICS AND EVOLUTION 2013; 21:227-43. [PMID: 24200587 DOI: 10.1016/j.meegid.2013.10.023] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Revised: 10/25/2013] [Accepted: 10/26/2013] [Indexed: 12/16/2022]
Abstract
Infection with hepatitis A virus (HAV) is the commonest viral cause of liver disease and presents an important public health problem worldwide. Several unique HAV properties and molecular mechanisms of its interaction with host were recently discovered and should aid in clarifying the pathogenesis of hepatitis A. Genetic characterization of HAV strains have resulted in the identification of different genotypes and subtypes, which exhibit a characteristic worldwide distribution. Shifts in HAV endemicity occurring in different parts of the world, introduction of genetically diverse strains from geographically distant regions, genotype displacement observed in some countries and population expansion detected in the last decades of the 20th century using phylogenetic analysis are important factors contributing to the complex dynamics of HAV infections worldwide. Strong selection pressures, some of which, like usage of deoptimized codons, are unique to HAV, limit genetic variability of the virus. Analysis of subgenomic regions has been proven useful for outbreak investigations. However, sharing short sequences among epidemiologically unrelated strains indicates that specific identification of HAV strains for molecular surveillance can be achieved only using whole-genome sequences. Here, we present up-to-date information on the HAV molecular epidemiology and evolution, and highlight the most relevant features of the HAV-host interactions.
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Kim JH, Yeon JE, Baik SK, Kim YS, Kim HS, Park SH, Lee MS, Sohn JH, Lee JW, Choi SK, Kwon SY, Choi JY, Kim JH, Kang SY, An H, Seo YS, Yim HJ, Song JW, Um SH, Byun KS. Genotypic shift of the hepatitis A virus and its clinical impact on acute hepatitis A in Korea: a nationwide multicenter study. ACTA ACUST UNITED AC 2013; 45:811-8. [PMID: 23826788 DOI: 10.3109/00365548.2013.805425] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND The genotypic shift of hepatitis A virus (HAV) and its correlation with clinical course has not been evaluated in acute hepatitis A (AHA). METHODS From June 2007 to May 2009, we prospectively enrolled 546 AHA patients. We performed a nested reverse transcriptase polymerase chain reaction (RT-PCR) using the serum samples in addition to phylogenetic analysis, then we compared patient clinical features. RESULTS Among 351 successfully genotyped patients, we found genotype IIIA in 178 patients (51%) and IA in 173 patients (49%). The sequences of genotype IA are identical to previously reported Korean genotype IA, and the new IIIA genotype is closely related to NOR24/Norway. We retrospectively analyzed 41 AHA samples collected from 2000 to 2006 and found that all of them were genotype IA. Patients with genotype IIIA showed significantly higher levels of aspartate aminotransferase, higher levels of alanine aminotransferase, and lower platelet counts than patients with genotype IA when comparing baseline laboratory data or peak/lowest laboratory data during the disease course. However, there were no differences in duration of hospital stay, incidence of cholestatic hepatitis, acute kidney injury, and acute liver failure, or mortality between them. CONCLUSIONS A genotypic shift of the HAV was identified in Korean AHA subjects, and genotype IIIA HAV has become endemic. Although there were significant differences in the biochemical responses of AHA between genotype IA and genotype IIIA patients, we did not detect any differences in clinical outcomes such as complications or mortality.
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Affiliation(s)
- Ji Hoon Kim
- From the Department of Internal Medicine, Korea University College of Medicine , Seoul
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Abstract
The diagnostic gold standard for hepatitis A is the detection of anti-hepatitis A virus (HAV) IgM antibodies and the determination of total anti-HAV by enzyme immunoassay. However, detection of HAV RNA can be useful in the diagnosis of patients without specific antibodies for hepatitis A and for the monitoring of infection. Studies using real-time PCR have demonstrated that HAV RNA can be detected not only in feces, but also in serum and saliva samples earlier than detection of antibodies, and that viremia may be present for a much longer period than the convalescent phase of hepatitis A. Alternative samples have been proposed for diagnosis, epidemiological studies, investigation of outbreaks and selection of persons receptive to vaccination. Understanding the events of clinical course that take place during the hepatitis A infection may lead to more effective diagnosis.
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Affiliation(s)
- Vanessa Salete de Paula
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Desenvolvimento Tecnológico em Virologia – Av. Brasil 4365, 21040–360, Rio de Janeiro, Brazil
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15
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Genetic analysis of hepatitis A virus strains that induced epidemics in Korea during 2007-2009. J Clin Microbiol 2012; 50:1252-7. [PMID: 22238447 DOI: 10.1128/jcm.01114-11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Hepatitis A virus is one of the most prominent causes of fecally transmitted acute hepatitis worldwide. In order to characterize the viral agents causing an outbreak in Korea (comprising North and South Korea) from June 2007 to May 2009, we collected specimens and performed genotyping of the VP1/P2A and VP3/VP1 regions of hepatitis A virus. We then used a multiple-alignment algorithm to compare the nucleotide sequences of the 2 regions with those of reference strains. Hepatitis A virus antibodies were detected in 64 patients from 5 reported outbreaks (North Korea, June 2007 [n = 11]; Jeonnam, April 2008 [n = 15]; Daegu, May 2008 [n = 13]; Seoul, May 2009 [n = 22]; and Incheon, May 2009 [n = 3]). We found 100% homology between strains isolated from the Kaesong Industrial Region and Jeonnam. While those strains were classified as genotype IA strains, strains from Seoul and Incheon were identified as genotype IIIA strains and showed 98.9 to 100% homology. Genotype IIIA was also dominant in Daegu, where strains were 95.7 to 100% homologous. All hepatitis A virus strains isolated from the Kaesong Industrial Region, Jeonnam, Seoul, and Incheon belonged to a single cluster. However, strains from Daegu could be classified into 2 clusters, suggesting that the outbreak had multiple sources. This study indicates that hepatitis A virus strains of 2 different genotypes are currently cocirculating in Korea. Moreover, it documents an increasing prevalence of genotype IIIA strains in the country.
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Arankalle VA, Ramakrishnan J. Simian hepatitis A virus derived from a captive rhesus monkey in India is similar to the strain isolated from wild African green monkeys in Kenya. J Viral Hepat 2009; 16:214-8. [PMID: 19175880 DOI: 10.1111/j.1365-2893.2008.01060.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
A simian hepatitis A virus (HAV) was identified retrospectively in a faecal sample from a rhesus monkey in India, inoculated in 1995 with a faecal suspension from a suspected patient of non-A to E hepatitis. The monkey was in captivity for 2 years in one of the experimental primate facilities in western India before being moved to the National Institute of Virology, Pune for experimentation. Phylogenetic analysis based on a partial sequence of the 5' noncoding region placed this virus in genotype V, the only other member being the AGM-27 strain recovered in 1986 from African green monkeys in Kenya. The source of infection of the monkey remains unclear. The full genome was amplified in nine fragments and sequenced. The genome of the Indian simian HAV (IND-SHAV) is 7425 nucleotides long including the poly-A tail of 14 nucleotides at the 3' end. At the nucleotide and amino acid levels, IND-SHAV was 99.8 and 100% identical with AGM27, respectively.
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Affiliation(s)
- V A Arankalle
- Hepatitis Division, National Institute of Virology, Pashan, Pune, India.
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Lee KO, Jeong SJ, Seong HS, Kim KT, Hwang YS, Kim GY, Lee SH. Genetic Analysis of Hepatitis A Virus Isolated from Korea. ACTA ACUST UNITED AC 2009. [DOI: 10.4167/jbv.2009.39.3.165] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Kyung-Ok Lee
- Genome Research Center, Neodin Medical Institute, Seoul, Korea
| | - Su-Jin Jeong
- Genome Research Center, Neodin Medical Institute, Seoul, Korea
| | - Hye-Soon Seong
- Genome Research Center, Neodin Medical Institute, Seoul, Korea
| | - Kyung-Tae Kim
- Genome Research Center, Neodin Medical Institute, Seoul, Korea
| | - Yoo-Sung Hwang
- Genome Research Center, Neodin Medical Institute, Seoul, Korea
| | - Gee-Young Kim
- Genome Research Center, Neodin Medical Institute, Seoul, Korea
| | - Sun-Hwa Lee
- Genome Research Center, Neodin Medical Institute, Seoul, Korea
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18
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Endo K, Takahashi M, Masuko K, Inoue K, Akahane Y, Okamoto H. Full-length sequences of subgenotype IIIA and IIIB hepatitis A virus isolates: Characterization of genotype III HAV genomes. Virus Res 2007; 126:116-27. [PMID: 17376556 DOI: 10.1016/j.virusres.2007.02.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Revised: 02/03/2007] [Accepted: 02/08/2007] [Indexed: 01/08/2023]
Abstract
To elucidate the extent of genomic heterogeneity of human hepatitis A virus (HAV) strains and to characterize genotype III HAV strains over the entire genome, the full-length sequence of three subgenotype IIIA isolates (HA-JNG04-90F, HA-JNG08-92F, and HAJ95-8F) and one IIIB isolate (HAJ85-1F) was determined. The HA-JNG04-90F, HA-JNG08-92F, and HAJ95-8F genomes which comprised 7463 or 7464 nt excluding the poly(A) tail, were closest to a reported nearly entire sequence of a IIIA isolate (NOR-21) with identities of 94.4-97.8% over the entire ORF sequence, and the HAJ85-1 genome (7462 nt) to HA-JNG06-90F of IIIB with an identity of 98.6%. The phylogenetic trees constructed based on the complete ORF sequence or the 168-nt VP1/2A junction sequence and comparative analysis with reported HAV isolates suggested the presence of three distinct clusters within IIIA represented by HA-JNG04-90F, HA-JNG08-92F, and HAJ95-8F. The extreme 5' end sequences of IIIA and IIIB were well-conserved, beginning with the sequence UUCAAGAGGG. A single base deletion of G at nt 20, which is involved in the formation of a small loop in domain I, was characteristic of both IIIA and IIIB. Conserved and divergent amino acid sequences as well as amino acids unique to genotype III, IIIA or IIIB were recognized.
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Affiliation(s)
- Kazunori Endo
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-Shi, Tochigi-Ken 329-0498, Japan
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19
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Cristina J, Costa-Mattioli M. Genetic variability and molecular evolution of hepatitis A virus. Virus Res 2007; 127:151-7. [PMID: 17328982 DOI: 10.1016/j.virusres.2007.01.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Accepted: 01/08/2007] [Indexed: 02/08/2023]
Abstract
Hepatitis A virus (HAV), the causative agent of type A viral hepatitis, was first identified about three decades ago. Recent findings have shown that HAV possess several characteristics that make it unique among the family Picornaviridae, particularly in terms of its mechanisms of polyprotein processing and virion morphogenesis. HAV circulates in vivo as distributions of closely genetically related variants referred to as quasispecies. HAV exploits all known mechanisms of genetic variation to ensure its survival, including mutation and recombination. Only one serotype and six different genetic groups (three humans and three simian) have been described. HAV mutation rate is significantly lower as compared to other members of the family Picornaviridae. The mode of evolution appears, at least in part, to contribute to the presence of only one known serotype.
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Affiliation(s)
- Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay.
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Nainan OV, Xia G, Vaughan G, Margolis HS. Diagnosis of hepatitis a virus infection: a molecular approach. Clin Microbiol Rev 2006; 19:63-79. [PMID: 16418523 PMCID: PMC1360271 DOI: 10.1128/cmr.19.1.63-79.2006] [Citation(s) in RCA: 207] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Current serologic tests provide the foundation for diagnosis of hepatitis A and hepatitis A virus (HAV) infection. Recent advances in methods to identify and characterize nucleic acid markers of viral infections have provided the foundation for the field of molecular epidemiology and increased our knowledge of the molecular biology and epidemiology of HAV. Although HAV is primarily shed in feces, there is a strong viremic phase during infection which has allowed easy access to virus isolates and the use of molecular markers to determine their genetic relatedness. Molecular epidemiologic studies have provided new information on the types and extent of HAV infection and transmission in the United States. In addition, these new diagnostic methods have provided tools for the rapid detection of food-borne HAV transmission and identification of the potential source of the food contamination.
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Affiliation(s)
- Omana V Nainan
- Centers for Disease Control and Prevention, 1600 Clifton Road, N.E., Mailstop A33, Atlanta, GA 30333, USA.
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21
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Nainan OV, Xia G, Vaughan G, Margolis HS. Diagnosis of hepatitis a virus infection: a molecular approach. Clin Microbiol Rev 2006. [PMID: 16418523 DOI: 10.1128/cmr.19.1.63] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023] Open
Abstract
Current serologic tests provide the foundation for diagnosis of hepatitis A and hepatitis A virus (HAV) infection. Recent advances in methods to identify and characterize nucleic acid markers of viral infections have provided the foundation for the field of molecular epidemiology and increased our knowledge of the molecular biology and epidemiology of HAV. Although HAV is primarily shed in feces, there is a strong viremic phase during infection which has allowed easy access to virus isolates and the use of molecular markers to determine their genetic relatedness. Molecular epidemiologic studies have provided new information on the types and extent of HAV infection and transmission in the United States. In addition, these new diagnostic methods have provided tools for the rapid detection of food-borne HAV transmission and identification of the potential source of the food contamination.
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Affiliation(s)
- Omana V Nainan
- Centers for Disease Control and Prevention, 1600 Clifton Road, N.E., Mailstop A33, Atlanta, GA 30333, USA.
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22
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Stene-Johansen K, Jonassen TØ, Skaug K. Characterization and genetic variability of Hepatitis A virus genotype IIIA. J Gen Virol 2005; 86:2739-2745. [PMID: 16186227 DOI: 10.1099/vir.0.81155-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular epidemiological studies of hepatitis A outbreaks in Norway showed the emergence of Hepatitis A virus (HAV) genotype IIIA in association with parenteral transmission among haemophiliacs and intravenous drug users. The complete genomic sequence of one of these outbreak isolates, NOR-21, was determined. This is the first complete genomic sequence of HAV genotype IIIA. Phylogenetic analysis showed that genotype IIIA/NOR-21 was genetically distinct from the other human and simian genotypes. Phylogenetic analysis of the nucleotide sequences clearly distinguished the different HAV genotypes, regardless of the genomic region used for analysis, whereas the amino acid sequences showed a more vague distinction between human HAV genotypes I and II. In particular, the inferred phylogeny based on the capsid proteins showed that the human HAV strains were related more closely to each other than to the simian strains. The greatest variability and clearest distinction between genotypes were observed for the polymerase gene. The outbreak isolates of HAV genotype IIIA in this study showed greater nucleotide variability than is generally seen in outbreaks of genotype I. This high nucleotide variability, which may be characteristic of this HAV genotype, the mode of transmission in this outbreak or parallel introductions, is discussed.
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Affiliation(s)
- Kathrine Stene-Johansen
- Division of Infectious Disease Control, Norwegian Institute of Public Health, PO Box 4404, Nydalen, NO-0403 Oslo, Norway
| | - Tom Øystein Jonassen
- Division of Infectious Disease Control, Norwegian Institute of Public Health, PO Box 4404, Nydalen, NO-0403 Oslo, Norway
| | - Kjell Skaug
- Division of Infectious Disease Control, Norwegian Institute of Public Health, PO Box 4404, Nydalen, NO-0403 Oslo, Norway
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Wattanasri N, Ruchusatsawat K, Wattanasri S. Phylogenetic analysis of hepatitis A virus in Thailand. J Med Virol 2005; 75:1-7. [PMID: 15543573 DOI: 10.1002/jmv.20234] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human hepatitis A virus (HAV) is a major causative agent of acute hepatitis, and the isolates are categorised into four genotypes: I (GI), II (GII), III (GIII), and VII (GVII). Although viral hepatitis has been detected under a nationwide surveillance system in Thailand, the genetic variation of HAV has not yet been determined. In the present study, serum specimens were collected from acute hepatitis patients in Thailand from 1998-2002. The IgM-class antibody to HAV was detected in 156 out of 394 sera, counting as many as 39.6% of acute viral hepatitis cases. HAV RNA in the serum specimens was amplified by reverse-transcription polymerase chain reaction (RT-PCR), and a phylogenetic analysis of the putative VP1/2A junction of the genome was performed. The isolates were grouped into two genetic groups, GIA and GIB. This is the first report to identify subgenotype IB (GIB) in Thailand. The genetic segregation was closely related to the province where hepatitis A occurred and the serum specimens were collected. In addition, genetically similar strains were identified in both 1998 and 2001-2002 isolates from two close provinces in the southern part of Thailand, suggesting that a strain indigenous to the province or district has been circulating in southern Thailand.
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Affiliation(s)
- Naiyana Wattanasri
- Viral Hepatitis Section, National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand.
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24
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Lu L, Ching KZ, de Paula VS, Nakano T, Siegl G, Weitz M, Robertson BH. Characterization of the complete genomic sequence of genotype II hepatitis A virus (CF53/Berne isolate). J Gen Virol 2004; 85:2943-2952. [PMID: 15448357 DOI: 10.1099/vir.0.80304-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The complete genomic sequence of hepatitis A virus (HAV) CF53/Berne strain was determined. Pairwise comparison with other complete HAV genomic sequences demonstrated that the CF53/Berne isolate is most closely related to the single genotype VII strain, SLF88. This close relationship was confirmed by phylogenetic analyses of different genomic regions, and was most pronounced within the capsid region. These data indicated that CF53/Berne and SLF88 isolates are related more closely to each other than are subtypes IA and IB. A histogram of the genetic differences between HAV strains revealed four separate peaks. The distance values for CF53/Berne and SLF88 isolates fell within the peak that contained strains of the same subtype, showing that they should be subtypes within a single genotype. The complete genomic data indicated that genotypes II and VII should be considered a single genotype, based upon the complete VP1 sequence, and it is proposed that the CF53/Berne isolate be classified as genotype IIA and strain SLF88 as genotype IIB. The CF53/Berne isolate is cell-adapted, and therefore its sequence was compared to that of two other strains adapted to cell culture, HM-175/7 grown in MK-5 and GBM grown in FRhK-4 cells. Mutations found at nucleotides 3889, 4087 and 4222 that were associated with HAV attenuation and cell adaptation in HM175/7 and GMB strains were not present in the CF53/Berne strain. Deletions found in the 5'UTR and P3A regions of the CF53/Berne isolate that are common to cell-adapted HAV isolates were identified, however.
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Affiliation(s)
- Ling Lu
- Laboratory Branch, Division of Viral Hepatitis, National Center for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS C12, Atlanta, GA 30333, USA
| | - Karen Z Ching
- Laboratory Branch, Division of Viral Hepatitis, National Center for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS C12, Atlanta, GA 30333, USA
| | - Vanessa Salete de Paula
- Laboratory Branch, Division of Viral Hepatitis, National Center for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS C12, Atlanta, GA 30333, USA
| | - Tatsunori Nakano
- Laboratory Branch, Division of Viral Hepatitis, National Center for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS C12, Atlanta, GA 30333, USA
| | - Gunter Siegl
- Institut für Klinische Mikrobiologie und Immunologie, St Gallen, Switzerland
| | - Manfred Weitz
- Institut für Klinische Mikrobiologie und Immunologie, St Gallen, Switzerland
| | - Betty H Robertson
- Laboratory Branch, Division of Viral Hepatitis, National Center for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS C12, Atlanta, GA 30333, USA
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25
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Costa-Mattioli M, Napoli AD, Ferré V, Billaudel S, Perez-Bercoff R, Cristina J. Genetic variability of hepatitis A virus. J Gen Virol 2004; 84:3191-3201. [PMID: 14645901 DOI: 10.1099/vir.0.19532-0] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Knowledge of the molecular biology of hepatitis A virus (HAV) has increased exponentially since its identification. HAV exploits all known mechanisms of genetic variation to ensure survival, including mutation and genetic recombination. HAV has been characterized by the emergence of different genotypes, three human antigenic variants and only one major serotype. This paper reviews the genetic variability and molecular epidemiology of HAV. Its evolutionary mechanisms are described with particular emphasis on genetic recombination and HAV mutation rate. Genotypic classification methods are also discussed.
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Affiliation(s)
- Mauro Costa-Mattioli
- Department of Biochemistry, McGill University, McIntyre Medical Building, Montreal, Quebec, Canada H3G 1Y6
| | - Anna Di Napoli
- Laboratoire de Virologie Moléculaire et Structurale, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Virginie Ferré
- Laboratorie de Virologie UPRES-EA1156, Institut de Biologie, Centre Hospitalier Regional Universitaire de Nantes, Rue Quai Moncousu 9, 44093 Nantes, France
| | - Sylviane Billaudel
- Laboratorie de Virologie UPRES-EA1156, Institut de Biologie, Centre Hospitalier Regional Universitaire de Nantes, Rue Quai Moncousu 9, 44093 Nantes, France
| | - Raul Perez-Bercoff
- Laboratoire de Virologie Moléculaire et Structurale, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Juan Cristina
- Departamento de Técnicas Nucleares Aplicadas, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay
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26
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Vaidya SR, Chitambar SD, Arankalle VA. Polymerase chain reaction-based prevalence of hepatitis A, hepatitis E and TT viruses in sewage from an endemic area. J Hepatol 2002; 37:131-6. [PMID: 12076872 DOI: 10.1016/s0168-8278(02)00106-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND/AIMS Hepatitis A and E viruses (HAV, HEV) are transmitted enterically and are highly endemic in India. This study aims to evaluate prevalence of these and TT virus (TTV) in the sewage. METHODS Influent and effluent samples from a sewage treatment plant from Pune, India were collected twice a week for 1 year and subjected to nested polymerase chain reaction (PCR) for the detection of HAV RNA, HEV RNA and TTV DNA. HAV and HEV PCR products were sequenced. Effluent samples were not collected for 5 months as the plant was non-functional. RESULTS The overall prevalence was 24.42% (21/86, HAV), 10.98% (9/82, HEV) and 12.7% (8/63, TTV). Prevalence of HAV was significantly higher than HEV (P=0.023). During summer months, significantly higher HAV RNA positivity was noted (P<0.01). A substantial reduction in HAV RNA positivity (15/48 vs. 2/48, P=0.0008) was recorded for treated sewage samples. However, HEV RNA or TTV DNA positivity did not reduce significantly. Of the 17 HAV and HEV RNA negative sewage samples concentrated using ultracentrifugation, 13 and none were positive for HAV and HEV RNA, respectively. Phylogenetic analyses grouped these viruses in IB and Ia, respectively, the genotypes most prevalent in India. CONCLUSIONS Sewage may play an important role in maintaining hyper-endemicity of these infections. Sustained efforts are obligatory to render sewage less/non-infectious.
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Affiliation(s)
- Sunil R Vaidya
- Hepatitis Division, National Institute of Virology, 20-A Dr Ambedkar Road, 411001 Pune, India
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27
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Pinto MA, Marchevsky RS, Baptista ML, de Lima MA, Pelajo-Machado M, Vitral CL, Kubelka CF, Pissurno JW, Franca MS, Schatzmayr HG, Gaspar AMC. Experimental hepatitis A virus (HAV) infection in Callithrix jacchus: early detection of HAV antigen and viral fate. EXPERIMENTAL AND TOXICOLOGIC PATHOLOGY : OFFICIAL JOURNAL OF THE GESELLSCHAFT FUR TOXIKOLOGISCHE PATHOLOGIE 2002; 53:413-20. [PMID: 11930901 DOI: 10.1078/0940-2993-00212] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Common marmosets (Callithrixjacchus) were orally inoculated with a Brazilian strain (HAF-203) of hepatitis A virus (HAy). Three monkeys were euthanized at postinoculation hours 6, 12 and 24 to investigate the early events of HAV infection. Following others three inoculated and one control marmosets remained throughout the 46 day to evaluation of viral excretion. Different samples were collected to detect sequential presence of HAV RNA by nested reverse transcription-polymerase chain reaction (RT-PCR) in liver, saliva, bile and stools at 6 hours to 461h days postinoculation. Liver tissues were examined by immunofluorescence assay in a confocal laser-scanning microscope for the presence of HAV antigen. HAV RNA was detected in saliva during the course of the study, in bile from 24 hours to 46 days. in stools from 7 to 46 days and liver at 12 hours postinfection. In immunofluorescence of liver stained preparations, viral antigen was present at six hours after inoculation throughout the remainder of the 46-day study. The animals developed histological and biochemical acute hepatitis after second week postinoculation. Spleen, duodenum, and mesenteric lymph nodes specimens were negative for HAV antigens. This study supports the possibility that in Callithrixjacchus orally inoculated with hepatitis A virus the saliva route may be additional way of viral elimination. The viral replication in the liver was responsible for biliary HAV presence and latter HAV detection in fecal samples.
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Affiliation(s)
- M A Pinto
- Department of Virology, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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28
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Arauz-Ruiz P, Sundqvist L, García Z, Taylor L, Visoná K, Norder H, Magnius LO. Presumed common source outbreaks of hepatitis A in an endemic area confirmed by limited sequencing within the VP1 region. J Med Virol 2001. [DOI: 10.1002/jmv.2056] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
Several useful animal models for both hepatitis A and E have been identified, characterized, and refined. At present, all of the best models utilize nonhuman primates: chimpanzees, tamarin species, and owl monkeys for hepatitis A; and macaque species, chimpanzees, and owl monkeys for hepatitis E. Pigs may prove useful for some studies of hepatitis E, and it is hoped that serological evidence of widespread infection of rats with an HEV-like agent may lead to the development of an animal model based on laboratory rats. As has been the case for each of the hepatitis viruses as they have been discovered, the development of useful and reproducible animal model systems has been critical for moving the field forward as expeditiously as possible.
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Affiliation(s)
- R H Purcell
- Hepatitis Viruses and Molecular Hepatitis Sections, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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Robertson BH. Viral hepatitis and primates: historical and molecular analysis of human and nonhuman primate hepatitis A, B, and the GB-related viruses. J Viral Hepat 2001; 8:233-42. [PMID: 11454173 DOI: 10.1046/j.1365-2893.2001.00295.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The hepatitis viruses have long been assumed to be highly host-specific, with infection of other nonhuman primates occurring due to inoculation with, or exposure to, human viruses. This paradigm has slowly changed over the last 10 years, as mounting data has revealed nonhuman primate equivalents of hepatitis A virus, hepatitis B virus, and the hepatitis C-related viruses GBV-C and GBV-A. This review summarizes the historical and molecular information for each of these groups and highlights the impact of these nonhuman primate hepatitis viruses on our understanding of the evolution of each of these viruses.
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Affiliation(s)
- B H Robertson
- Hepatitis Branch, Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta 30333, USA.
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31
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Byun KS, Kim JH, Song KJ, Baek LJ, Song JW, Park SH, Kwon OS, Yeon JE, Kim JS, Bak YT, Lee CH. Molecular epidemiology of hepatitis A virus in Korea. J Gastroenterol Hepatol 2001; 16:519-24. [PMID: 11350547 DOI: 10.1046/j.1440-1746.2001.02481.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
BACKGROUND The prevalence of antibodies for hepatitis A virus (anti-HAV) in adolescents and young adults has decreased remarkably following the economic growth in Korea. As a result, this age group has a high risk for HAV infection paradoxically, and over 1500 cases of clinically overt hepatitis A occurred in 1998. Human isolates of hepatitis A virus (HAV) are categorized within four genotypes (I, II, III, and VII). In some geographic regions, closely related isolates cluster, suggesting endemic spread of the virus, while in other regions multiple genotypes circulate. Virtually no data are available with regard to the genetic relatedness of Korean strains of HAV. METHODS AND RESULTS A 168 base pair segment encompassing the putative VP1/2A junction of the HAV genome was amplified by RT-PCR and sequenced in sera of 18 Korean patients with a sporadic form of acute hepatitis A. Pairwise comparisons of the nucleic acid and amino acid sequences of 18 Korean isolates with one another revealed that the Korean isolates showed > 94.6% and > 96.4% identity, respectively. All of the 18 Korean isolates clustered within genotype IA, irrespective of the geographic locations and the time that hepatitis occurred. Unique amino acid sequence changes that had never been reported in genotype IA were found in nine of the 18 isolates. These changes were Gln-->Ser and Lys-->Arg in 2A-19 and 2A-10 amino acid positions. CONCLUSION The presence of single genotype and unique mutations may be related with the circulation of endemic HAV over a long period of time in Korea.
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Affiliation(s)
- K S Byun
- Department of Gastroenterology and Hepatology, Korea University Guro Hospital, Seoul
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32
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Mattioli S, Imberti L, Stellini R, Primi D. Mimicry of the immunodominant conformation-dependent antigenic site of hepatitis A virus by motifs selected from synthetic peptide libraries. J Virol 1995; 69:5294-9. [PMID: 7543581 PMCID: PMC189366 DOI: 10.1128/jvi.69.9.5294-5299.1995] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Hepatitis A virus (HAV) is a positive-strand RNA virus with a genome length of approximately 7,480 nucleotides. Although HAV morphogenesis is thought to be similar to that of poliovirus, the prototype picornavirus, the complete characterization of the antigenic structure of this virus remains elusive. All the available evidences, however, support the existence, on HAV virions and empty capsids, of an immunodominant neutralization antigenic site which is conformation dependent and whose structure involves residues of both VP1 and VP3 capsid proteins. This particular feature and the difficulty of obtaining high virus yield in tissue cultures make HAV an ideal target for developing synthetic peptides that simulate the structure of its main antigenic determinant. To this end we utilized, in the present work, the divide-couple-recombine approach to generate a random library composed of millions of different hexapeptides. This vast library was screened with a well-characterized anti-HAV monoclonal antibody. By this strategy we identified a peptide that reacted specifically with monoclonal and polyclonal anti-HAV antibodies and, in mice, induced a specific anti-virus immune response. Furthermore, the peptide could also be used in an enzyme-linked immunosorbent assay for revealing a primary immunoglobulin M immune response in sera of acutely infected human patients. Interestingly, no sequence homology was found between the identified peptide and the HAV capsid proteins VP1 and VP3. Collectively, these data represent an additional important paradigm of a mimotope capable of mimicking an antigenic determinant with unknown tertiary structure.
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Affiliation(s)
- S Mattioli
- Consorzio per le Biotecnologie, Spedali Civili, Brescia, Italy
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33
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Argentini C, D'Ugo E, Bruni R, Gluck R, Giuseppetti R, Rapicetta M. Sequence and phylogenetic analysis of the VP1 gene in two cell culture-adapted HAV strains from a unique pathogenic isolate. Virus Genes 1995; 10:37-43. [PMID: 7483287 DOI: 10.1007/bf01724295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The nucleotide sequences of the VP1 coding region of two newly characterized, cell culture-adapted hepatitis A virus (HAV) strains (RG-SB11 and RG-SB16) were analyzed and compared with homologous regions of previously characterized HAV strains of human or monkey origin, and at different levels of tissue-culture adaptation. In particular, HM175wt and its derivative strains and MBB, LCDC1, PA21, and AGM27 isolates were considered. RG-SB11 and RG-SB16 HAV strains were derived from a pathogenic isolate from an acutely infected patient, purified from stool, and subjected to different strategies of adaptation. Several nucleotide differences were observed, but high conservation was found in the predicted VP1 protein sequences, which confirms structural constraints for this region. Furthermore, comparative amino-acid sequence analysis of VP1 from all HAV isolates studied has shown, particularly for those from naturally infected monkeys, that differences are limited to the amino and carboxy-terminal part of the molecule. The results of phylogenetic analysis have confirmed the common origin of the RG-SB11 and RG-SB16 strains. The complete nucleotide sequences of the VP1 coding region of the RG-SB11/16, HM175 derivative strains and of other HAV strains has shown that branch-length evolution can give a measure of the evolution of HAV during adaptation processes.
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Affiliation(s)
- C Argentini
- Laboratory of Virology, Istituto Superiore di Sanità, Rome, Italy
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Abstract
To examine whether Indian monkeys are infected with hepatitis E virus (HEV) in nature, serum samples from wild rhesus (Macaca mullata), bonnet (M. radiata) and langur (Presbytes entellus) monkeys were screened for anti-HEV IgG antibodies in recombinant antigen-based ELISA assays. The positivity rates were 36.7%, 19.1% and 2% respectively. The protection of such antibodies against human HEV was studied in four rhesus monkeys. Of the two rhesus monkeys with anti-HEV titres of 100 and 1000 respectively which were inoculated with the KOL-91 strain of HEV, the former demonstrated a 10-fold rise in anti-HEV titres. Anti-HEV titre in the second rhesus monkey remained unchanged. Neither of the monkeys showed any rise in serum alanine transaminase (ALT) or presence of virus in the faeces, as tested by polymerase chain reaction (PCR). Two other rhesus monkeys with anti-HEV titres of 10,000 and 100 respectively were inoculated with the AKL-90 strain of HEV. Serum ALT levels and anti-HEV titres remained unchanged in the first monkey. Excretion of virus in faeces was not noted (PCR). The second monkey developed a typical HEV infection. HEV infection could be produced in anti-HEV negative control monkeys inoculated with both strains of HEV. These results show that either human or simian HEV, or a closely related agent, is circulating among Indian macaques. Titre-dependent protection of naturally occurring anti-HEV antibodies supports this view.
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35
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Lemon SM. Hepatitis A virus: Current concepts of the molecular virology, immunobiology and approaches to vaccine development. Rev Med Virol 1992. [DOI: 10.1002/rmv.1980020204] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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36
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Aye TT, Uchida T, Ma X, Iida F, Shikata T, Zhuang H, Win KM. Sequence comparison of the capsid region of hepatitis E viruses isolated from Myanmar and China. Microbiol Immunol 1992; 36:615-21. [PMID: 1387921 DOI: 10.1111/j.1348-0421.1992.tb02061.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Hepatitis E viruses (HEVs) were isolated during epidemics, one from Myanmar (formerly called Burma) and one from China and were partially sequenced. Another HEV Myanmar strain from sporadic hepatitis was previously sequenced by us. A cDNA sequence comparison was performed among them in the 3'-terminal region, approximately 750-base long. This region contained at least two immunological epitopes and was considered to correspond to the structural protein. The nucleotide sequence identity was 97.2% between the two Myanmar strains and 93.3 and 92.5% between the two Myanmar and the China strain. The deduced amino acid sequence identity ranged from 98.4 to 100.0% among the three strains. Thus this segment was well conserved on the amino acid level among the different strains isolated from these two Asian countries, although the China strain diverged more from the Myanmar strains on the nucleotide sequence level. This data may provide important information for the development of a vaccine and for identification of the virological link between different geographical locations.
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Affiliation(s)
- T T Aye
- Department of Pathology, Nihon University School of Medicine, Tokyo, Japan
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37
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Khanna B, Spelbring JE, Innis BL, Robertson BH. Characterization of a genetic variant of human hepatitis A virus. J Med Virol 1992; 36:118-24. [PMID: 1316423 DOI: 10.1002/jmv.1890360208] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Human isolates of hepatitis A (HAV) are a single serotype; however, recent genetic surveys using limited nucleotide sequencing have provided evidence that more than one genotype is responsible for HAV infection in different parts of the world (Jansen et al. [1990]: Proc Natl Acad Sci USA 87:2867-2871; Robertson et al. [1991] J Infect Dis 163:286-292). One of these genotypes was originally isolated from Panamanian owl monkeys (strain PA21), but has subsequently been found associated with human cases of HAV from Sweden in 1979 (H-122) and the United States of America in 1976 (GA76). The nucleic acid sequence of the exposed capsid polypeptide region of GA76 differs from other human HAV sequences by approximately 20%, yet differs by only 2.4% when compared with P1 sequence of the PA21 strain. The 20% nucleic acid variability between GA76 and other human HAV results in limited amino acid changes (3%), while a comparison with PA21 revealed only four homologous amino acid substitutions within VP2, VP3, and VP1 polypeptides. HAV infected stool specimens from Nepal and northern India during 1989 and 1990 were found to contain virus whose genetic makeup was related to the PA21 and GA76 isolates. This genotype of HAV appears to be circulating in some parts of the world where HAV is hyperendemic, and is a potential cause of hepatitis A infection within a susceptible population.
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Affiliation(s)
- B Khanna
- Hepatitis Branch, Center for Infectious Disease, Centers for Disease Control, Atlanta, Georgia 30333
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38
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Abstract
The host range for hepatitis A virus (HAV) is limited to man and several species of non-human primates, and involvement of vertebrates other than primates in HAV circulation is unlikely. Spontaneous hepatitis A infection has been reported to occur in captive non-human primates including the great apes (chimpanzee) as well as Old World (cynomolgus, African vervet, stump-tailed) and New World (aotus) monkeys. The presence of anti-HAV antibody in the sera of newly captured monkeys of these species shows that infection may also spread in their natural habitat. HAVs isolated from spontaneously infected monkeys, although antigenically closely related to human HAV, exhibit a significant degree of genomic heterogeneity. There are at least four distinct simian HAVs differing from each other and from all human HAV strains. It is suggested that each virus is native to a given species reflecting evolutionary relationships among HAVs and their hosts in the order of Primates.
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Affiliation(s)
- M S Balayan
- Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
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39
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Lemon SM, Jansen RW, Brown EA. Genetic, antigenic and biological differences between strains of hepatitis A virus. Vaccine 1992; 10 Suppl 1:S40-4. [PMID: 1335657 DOI: 10.1016/0264-410x(92)90540-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recent studies have documented a considerable degree of genetic divergence among wild-type hepatitis A virus (HAV) strains recovered from different geographical locations. Human HAV strains can be grouped into four genotypes (I, II, III and VII) and unique simian strains belong to three additional genotypes (IV, V and VI). Between each of these genotypes, the nucleotide sequence varies at 15-25% of base positions in the P1 region. Despite this, there is good evidence that most, if not all, human strains of HAV are closely related antigenically. In contrast, although simian strains recovered from Old World monkeys are cross-reactive in immunoassays employing polyclonal antibodies, these strains have significant antigenic differences from human HAV strains. Nonetheless, because biological differences in the host range of these strains apparently preclude significant human infection, this is unlikely to pose a problem in controlling HAV infections with active immunization. Inactivated and attenuated vaccines produced from genotype I human strains (HM175 or CR326) are likely to provide protection against all relevant human HAV strains.
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Affiliation(s)
- S M Lemon
- Department of Medicine, University of North Carolina, Chapel Hill 27599-7030
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40
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Brown EA, Day SP, Jansen RW, Lemon SM. The 5' nontranslated region of hepatitis A virus RNA: secondary structure and elements required for translation in vitro. J Virol 1991; 65:5828-38. [PMID: 1656072 PMCID: PMC250245 DOI: 10.1128/jvi.65.11.5828-5838.1991] [Citation(s) in RCA: 163] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Although the lengthy 5' nontranslated regions (5'NTRs) of other picornaviral RNAs form highly ordered structures with important functions in viral translation, little is known about the 5'NTR of hepatitis A virus (HAV). We determined the nearly complete 5'NTR nucleotide sequences of two genetically divergent HAV strains (PA21 and CF53) and included these data in a comparative phylogenetic analysis of the HAV 5'NTR. We identified covariant nucleotide substitutions predictive of conserved secondary structures and used this information to develop a model of the 5'NTR secondary structure, which was further refined by thermodynamic predictions and nuclease digestion experiments. According to this model, the 5'NTR comprises six major structural domains. Domains I and II (bases 1 to 95) contain a 5'-terminal hairpin and two stem-loops followed by a single-stranded and highly variable pyrimidine-rich tract (bases 96 to 154). The remainder of the 5'NTR (domains III to VI, bases 155 to 734) contains several complex stem-loops, one of which may form a pseudoknot, and terminates in a highly conserved region containing an oligopyrimidine tract preceding the putative start codon by 13 bases. To determine which structural elements might function as an internal ribosome entry site, RNA transcripts representing the HAV 5'NTR with progressive 5' deletions were translated in rabbit reticulocyte lysates. The translation product was truncated, unprocessed P1 polyprotein. Removal of the 5'-terminal 354 bases of the 5'NTR had little effect on translation. However, deletion to base 447 slightly decreased translation, while deletion to base 533 almost completely abolished it. These data indicate that sequences 3' of base 355 play an important role in the translation mechanism utilized by genomic-length HAV RNA. Significantly, this region shares several conserved structural features with the internal ribosome entry site element of murine encephalomyocarditis virus.
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Affiliation(s)
- E A Brown
- Department of Medicine, University of North Carolina, Chapel Hill 27599-7030
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41
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Lemon SM, Amphlett E, Sangar D. Protease digestion of hepatitis A virus: disparate effects on capsid proteins, antigenicity, and infectivity. J Virol 1991; 65:5636-40. [PMID: 1654460 PMCID: PMC249085 DOI: 10.1128/jvi.65.10.5636-5640.1991] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
High concentrations of either trypsin or chymotrypsin caused nearly complete cleavage of capsid protein VP2 of hepatitis A virus but did not significantly reduce the infectivity, thermostability, or antigenicity of the virus. Chymotrypsin also had a lesser effect on VP1. These findings indicate the presence of a protease-accessible VP2 surface site which neither contributes significantly to the dominant antigenic site nor plays a role in the attachment of the virus to putative cell receptors.
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Affiliation(s)
- S M Lemon
- Department of Medicine, University of North Carolina, Chapel Hill 27599-7030
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42
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Brown EA, Day SP, Jansen RW, Lemon SM. Genetic variability within the 5' nontranslated region of hepatitis A virus RNA. Implications for secondary structure and function. J Hepatol 1991; 13 Suppl 4:S138-43. [PMID: 1668324 DOI: 10.1016/0168-8278(91)90046-e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The RNA genome of hepatitis A virus (HAV) contains a lengthy and relatively well conserved 5' nontranslated region (5'NTR). In other picornaviruses, the 5'NTR has been shown to have important functions related to the initiation of viral translation and replication of viral RNA, functions which are critically dependent on both primary and secondary RNA structure. We have utilized a phylogenetic approach to construct a model of the secondary structure of the HAV 5'NTR. By comparing the nucleotide sequences of genetically divergent simian and human HAV strains, we identified a series of covariant nucleotide substitutions which are predictive of conserved, double-stranded helical structures within the 5'NTR, and which thus permitted improved thermodynamic modeling of the secondary structure. The model was further refined based on the observed sites of cleavage of synthetic RNA by single- and double-strand specific RNAses. The results of these studies suggest that the 5'NTR of HAV has a general organization similar to that of other picornaviruses, and shares certain structural features and perhaps specific functions with the 5'NTRs of the cardioviruses and aphthoviruses.
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Affiliation(s)
- E A Brown
- Department of Medicine, University of North Carolina, Chapel Hill
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43
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Emerson SU, Tsarev SA, Purcell RH. Biological and molecular comparisons of human (HM-175) and simian (AGM-27) hepatitis A viruses. J Hepatol 1991; 13 Suppl 4:S144-5. [PMID: 1668325 DOI: 10.1016/0168-8278(91)90047-f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Comparisons of HM-175, the prototype human strain of hepatitis A virus, and AGM-27, a simian isolate, indicate that the two HAV viruses differ substantially in sequence and in biological characteristics. The extent of the differences suggests that hepatitis A viruses have a greater potential for diversity than previously assumed.
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Affiliation(s)
- S U Emerson
- Hepatitis Viruses Section, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
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44
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Abstract
Picornaviruses are small naked icosahedral viruses with a single-stranded RNA genome of positive polarity. According to current taxonomy, the family includes four genera: Enterouirus (polioviruses, coxsackieviruses, echoviruses, and other enteroviruses), Rhinovirus, Curdiouirus [encephalomyocarditis virus (EMCV), mengovirus, Theiler's murine encephalomyelitis virus (TMEV)], and Aphthouirus [foot-and-mouth disease viruses (FMDV)]. There are also some, as yet, unclassified picornaviruses [e.g., hepatitis A virus (HAW] that should certainly be assessed as a separate genus. Studies on the molecular biology of picornaviruses might be divided into two periods: those before and after the first sequencing of the poliovirus genome. The 5'-untranslated region (5-UTR) of the viral genome was one of the unexpected problems. This segment proved to be immensely long: about 750 nucleotides or ∼10% of the genome length. There were also other unusual features (e.g., multiple AUG triplets preceding the single open reading frame (ORF) that encodes the viral polyprotein). This chapter shows that the picornaviral 5-UTRs are not only involved in such essential events as the synthesis of viral proteins and RNAs that could be expected to some extent, although some of the underlying mechanisms appeared to be quite a surprise, but also may determine diverse biological phenotypes from the plaque size or thermosensitivity of reproduction to attenuation of neurovirulence. Furthermore, a close inspection of the 5-UTR structure unravels certain hidden facets of the evolution of the picornaviral genome. Finally, the conclusions drawn from the experiments with the picornaviral5-UTRs provide important clues for understanding the functional capabilities of the eukaryotic ribosomes.
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Affiliation(s)
- V I Agol
- Institute of Poliomyelitis and Viral Encephalitides, U.S.S.R. Academy of Medical Sciences, Moscow
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45
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Affiliation(s)
- G Siegl
- Division of Virology, University of Bern, Switzerland
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46
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New nucleotide sequence data on the EMBL File Server. Nucleic Acids Res 1990; 18:5587-605. [PMID: 2216753 PMCID: PMC332285 DOI: 10.1093/nar/18.18.5587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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47
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Jansen RW, Siegl G, Lemon SM. Molecular epidemiology of human hepatitis A virus defined by an antigen-capture polymerase chain reaction method. Proc Natl Acad Sci U S A 1990; 87:2867-71. [PMID: 2158093 PMCID: PMC53794 DOI: 10.1073/pnas.87.8.2867] [Citation(s) in RCA: 168] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We describe an immunoaffinity-linked nucleic acid amplification system (antigen-capture/polymerase chain reaction, or AC/PCR) for detection of viruses in clinical specimens and its application to the study of the molecular epidemiology of a picornavirus, hepatitis A virus (HAV). Immunoaffinity capture of virus, synthesis of viral cDNA, and amplification of cDNA by a polymerase chain reaction (PCR) were carried out sequentially in a single reaction vessel. This approach simplified sample preparation and enhanced the specificity of conventional PCR. AC/PCR detected less than one cell culture infectious unit of virus in 80 microliters of sample. Sequencing of AC/PCR reaction products from 34 virus strains demonstrated remarkable conservation at the nucleotide level among most strains but revealed hitherto unsuspected genetic diversity among human isolates. Epidemiologically related strains were identical or closely related in sequence. Virus strains recovered from epidemics of hepatitis A in the United States and Germany were identical in sequence, providing evidence for a previously unrecognized epidemiologic link between these outbreaks.
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Affiliation(s)
- R W Jansen
- Department of Medicine, University of North Carolina, Chapel Hill 27599-7030
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48
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Crevat D, Crance JM, Chevrinais AM, Passagot J, Biziagos E, Somme G, Deloince R. Monoclonal antibodies against an immunodominant and neutralizing epitope on hepatitis A virus antigen. Arch Virol 1990; 113:95-8. [PMID: 1696807 DOI: 10.1007/bf01318357] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Two monoclonal antibodies (813 and 10.09) were raised against hepatitis A virus (HAV). They recognize an immunodominant epitope and a neutralizing site on HAV.
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Affiliation(s)
- D Crevat
- Unité d'immunologie Clonatec, Paris, France
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