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Stapleton JT. Human Pegivirus Type 1: A Common Human Virus That Is Beneficial in Immune-Mediated Disease? Front Immunol 2022; 13:887760. [PMID: 35707535 PMCID: PMC9190258 DOI: 10.3389/fimmu.2022.887760] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/03/2022] [Indexed: 12/25/2022] Open
Abstract
Two groups identified a novel human flavivirus in the mid-1990s. One group named the virus hepatitis G virus (HGV) and the other named it GB Virus type C (GBV-C). Sequence analyses found these two isolates to be the same virus, and subsequent studies found that the virus does not cause hepatitis despite sharing genome organization with hepatitis C virus. Although HGV/GBV-C infection is common and may cause persistent infection in humans, the virus does not appear to directly cause any other known disease state. Thus, the virus was renamed “human pegivirus 1” (HPgV-1) for “persistent G” virus. HPgV-1 is found primarily in lymphocytes and not hepatocytes, and several studies found HPgV-1 infection associated with prolonged survival in people living with HIV. Co-infection of human lymphocytes with HPgV-1 and HIV inhibits HIV replication. Although three viral proteins directly inhibit HIV replication in vitro, the major effects of HPgV-1 leading to reduced HIV-related mortality appear to result from a global reduction in immune activation. HPgV-1 specifically interferes with T cell receptor signaling (TCR) by reducing proximal activation of the lymphocyte specific Src kinase LCK. Although TCR signaling is reduced, T cell activation is not abolished and with sufficient stimulus, T cell functions are enabled. Consequently, HPgV-1 is not associated with immune suppression. The HPgV-1 immunomodulatory effects are associated with beneficial outcomes in other diseases including Ebola virus infection and possibly graft-versus-host-disease following stem cell transplantation. Better understanding of HPgV-1 immune escape and mechanisms of inflammation may identify novel therapies for immune-based diseases.
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Affiliation(s)
- Jack T. Stapleton
- Medicine Service, Iowa City Veterans Administration Healthcare, Iowa City, IA, United States
- Departments of Internal Medicine, Microbiology & Immunology, University of Iowa, Iowa City, IA, United States
- *Correspondence: Jack T. Stapleton,
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2
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Porter AF, Pettersson JHO, Chang WS, Harvey E, Rose K, Shi M, Eden JS, Buchmann J, Moritz C, Holmes EC. Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates. Virus Evol 2020; 6:veaa064. [PMID: 33240526 PMCID: PMC7673076 DOI: 10.1093/ve/veaa064] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Flaviviridae family of positive-sense RNA viruses contains important pathogens of humans and other animals, including Zika virus, dengue virus, and hepatitis C virus. The Flaviviridae are currently divided into four genera-Hepacivirus, Pegivirus, Pestivirus, and Flavivirus-each with a diverse host range. Members of the genus Hepacivirus are associated with an array of animal species, including humans, non-human primates, other mammalian species, as well as birds and fish, while the closely related pegiviruses have been identified in a variety of mammalian taxa, also including humans. Using a combination of total RNA and whole-genome sequencing we identified four novel hepaci-like viruses and one novel variant of a known hepacivirus in five species of Australian wildlife. The hosts infected comprised native Australian marsupials and birds, as well as a native gecko (Gehyra lauta). From these data we identified a distinct marsupial clade of hepaci-like viruses that also included an engorged Ixodes holocyclus tick collected while feeding on Australian long-nosed bandicoots (Perameles nasuta). Distinct lineages of hepaci-like viruses associated with geckos and birds were also identified. By mining the SRA database we similarly identified three new hepaci-like viruses from avian and primate hosts, as well as two novel pegi-like viruses associated with primates. The phylogenetic history of the hepaci- and pegi-like viruses as a whole, combined with co-phylogenetic analysis, provided support for virus-host co-divergence over the course of vertebrate evolution, although with frequent cross-species virus transmission. Overall, our work highlights the diversity of the Hepacivirus and Pegivirus genera as well as the uncertain phylogenetic distinction between.
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Affiliation(s)
- Ashleigh F Porter
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - John H-O Pettersson
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Wei-Shan Chang
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Erin Harvey
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Karrie Rose
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman 2088, Australia
| | - Mang Shi
- School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - John-Sebastian Eden
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Jan Buchmann
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Craig Moritz
- Research School of Biology, Centre for Biodiversity Analysis, Australian National University, Acton, ACT, Australia
| | - Edward C Holmes
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
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Lu G, Huang J, Yang Q, Xu H, Wu P, Fu C, Li S. Identification and genetic characterization of hepacivirus and pegivirus in commercial equine serum products in China. PLoS One 2017; 12:e0189208. [PMID: 29216266 PMCID: PMC5720783 DOI: 10.1371/journal.pone.0189208] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 11/21/2017] [Indexed: 01/29/2023] Open
Abstract
Equine hepacivirus (EqHV), equine pegivirus (EPgV) and Theiler’s disease-associated virus (TDAV) are three novel equine viruses in the family Flaviviridae. EqHV and EPgV have been identified to circulate in the equine population worldwide, whereas TDAV has not been detected in equines since the first reported case. To date, no studies have focused on investigating EqHV, EPgV and TDAV in commercial equine sera or equine blood products in China. Considering the potential threat of EqHV, EPgV and TDAV to biosecurity and considering their possible influences on research results, equine sera for cell culture propagation and pregnant mare serum gonadotropin (PMSG) were purchased from different companies in China and investigated for EqHV, EPgV and TDAV in this study. By performing nested PCR or two rounds of PCR targeting the viral NS3 gene, four serum samples were confirmed to be EqHV-, EPgV-, or TDAV-RNA positive; all of the PMSG samples were negative for these three viruses. Subsequent sequencing results indicated that the serum samples contained multiple viral variants of EqHV, EPgV or TDAV, and a genetic analysis based on the partial NS3 gene of the three equine viruses was performed. Our study is the first to confirm the presence of EqHV, EPgV and TDAV in equine sera for cell culture propagation that is commercially available in China and provides the first demonstration of the presence of TDAV in China.
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Affiliation(s)
- Gang Lu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Technological Engineering Research Center for Pet Guangzhou, Guangdong Province, People’s Republic of China
| | - Ji Huang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Technological Engineering Research Center for Pet Guangzhou, Guangdong Province, People’s Republic of China
| | - Qiliang Yang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Technological Engineering Research Center for Pet Guangzhou, Guangdong Province, People’s Republic of China
| | - Haibin Xu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Technological Engineering Research Center for Pet Guangzhou, Guangdong Province, People’s Republic of China
| | - Peixin Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Technological Engineering Research Center for Pet Guangzhou, Guangdong Province, People’s Republic of China
| | - Cheng Fu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Technological Engineering Research Center for Pet Guangzhou, Guangdong Province, People’s Republic of China
| | - Shoujun Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Technological Engineering Research Center for Pet Guangzhou, Guangdong Province, People’s Republic of China
- * E-mail:
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First Description of Hepacivirus and Pegivirus Infection in Domestic Horses in China: A Study in Guangdong Province, Heilongjiang Province and Hong Kong District. PLoS One 2016; 11:e0155662. [PMID: 27182887 PMCID: PMC4868292 DOI: 10.1371/journal.pone.0155662] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/02/2016] [Indexed: 02/06/2023] Open
Abstract
Since 2012, three viruses, known as equine hepacivirus (EqHV), equine pegivirus (EPgV) and Theiler’s disease-associated virus (TDAV), have been discovered in equines. Given that these viruses are the newest members of the Flaviviridae family, genomic information concerning circulating EqHV, EPgV and TDAV strains around the world is limited. To date, no genetic surveillance studies have been performed on these three viruses in the equine population of China. Here, a total of 177 serum samples were collected from equines across China between 2014 and 2015. Using PCR, we detected viral RNA in the serum samples, six of which were EqHV positive and two of which were EPgV positive. Co-infection with the two viruses was not observed among the Chinese equines studied, and TDAV RNA was not detected in the equine serum samples collected for this study. Phylogenetic analysis of partial NS5B open reading frame (ORF), NS3 ORF, and 5’ untranslated region nucleotide sequences from EqHV as well as partial NS3 ORF sequence from EPgV indicated that EqHV and EPgV have evolved into two main clades by themselves, both of which are circulating in China. Based on the partial NS5B and NS3 ORF sequences of EqHV, the sequences of one clade were also split into two subclades. This study enriches our knowledge of the geographic distribution of these three equine viruses.
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Sibley SD, Lauck M, Bailey AL, Hyeroba D, Tumukunde A, Weny G, Chapman CA, O’Connor DH, Goldberg TL, Friedrich TC. Discovery and characterization of distinct simian pegiviruses in three wild African Old World monkey species. PLoS One 2014; 9:e98569. [PMID: 24918769 PMCID: PMC4053331 DOI: 10.1371/journal.pone.0098569] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 05/05/2014] [Indexed: 01/08/2023] Open
Abstract
Within the Flaviviridae, the recently designated genus Pegivirus has expanded greatly due to new discoveries in bats, horses, and rodents. Here we report the discovery and characterization of three simian pegiviruses (SPgV) that resemble human pegivirus (HPgV) and infect red colobus monkeys (Procolobus tephrosceles), red-tailed guenons (Cercopithecus ascanius) and an olive baboon (Papio anubis). We have designated these viruses SPgVkrc, SPgVkrtg and SPgVkbab, reflecting their host species' common names, which include reference to their location of origin in Kibale National Park, Uganda. SPgVkrc and SPgVkrtg were detected in 47% (28/60) of red colobus and 42% (5/12) red-tailed guenons, respectively, while SPgVkbab infection was observed in 1 of 23 olive baboons tested. Infections were not associated with any apparent disease, despite the generally high viral loads observed for each variant. These viruses were monophyletic and equally divergent from HPgV and pegiviruses previously identified in chimpanzees (SPgVcpz). Overall, the high degree of conservation of genetic features among the novel SPgVs, HPgV and SPgVcpz suggests conservation of function among these closely related viruses. Our study describes the first primate pegiviruses detected in Old World monkeys, expanding the known genetic diversity and host range of pegiviruses and providing insight into the natural history of this genus.
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Affiliation(s)
- Samuel D. Sibley
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Michael Lauck
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Adam L. Bailey
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | | | | | | | - Colin A. Chapman
- Makerere University, Kampala, Uganda
- Department of Anthropology and McGill School of Environment, Montreal, Quebec, Canada
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Makerere University, Kampala, Uganda
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
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6
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Patel MR, Loo YM, Horner SM, Gale M, Malik HS. Convergent evolution of escape from hepaciviral antagonism in primates. PLoS Biol 2012; 10:e1001282. [PMID: 22427742 PMCID: PMC3302847 DOI: 10.1371/journal.pbio.1001282] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 01/30/2012] [Indexed: 12/30/2022] Open
Abstract
Escape from antagonism by hepatitis C and related viruses has repeatedly evolved in antiviral factor MAVS via convergent evolution, revealing an ancient history of previous viral encounters in primates. The ability to mount an interferon response on sensing viral infection is a critical component of mammalian innate immunity. Several viruses directly antagonize viral sensing pathways to block activation of the host immune response. Here, we show that recurrent viral antagonism has shaped the evolution of the host protein MAVS—a crucial component of the viral-sensing pathway in primates. From sequencing and phylogenetic analyses of MAVS from 21 simian primates, we found that MAVS has evolved under strong positive selection. We focused on how this positive selection has shaped MAVS' susceptibility to Hepatitis C virus (HCV). We functionally tested MAVS proteins from diverse primate species for their ability to resist antagonism by HCV, which uses its protease NS3/4A to cleave human MAVS. We found that MAVS from multiple primates are resistant to inhibition by the HCV protease. This resistance maps to single changes within the protease cleavage site in MAVS, which protect MAVS from getting cleaved by the HCV protease. Remarkably, most of these changes have been independently acquired at a single residue 506 that evolved under positive selection. We show that “escape” mutations lower affinity of the NS3 protease for MAVS and allow it to better restrict HCV replication. We further show that NS3 proteases from all other primate hepaciviruses, including the highly divergent GBV-A and GBV-C viruses, are functionally similar to HCV. We conclude that convergent evolution at residue 506 in multiple primates has resulted in escape from antagonism by hepaciviruses. Our study provides a model whereby insights into the ancient history of viral infections in primates can be gained using extant host and virus genes. Our analyses also provide a means by which primates might clear infections by extant hepaciviruses like HCV. Hepatitis C virus (HCV) causes chronic liver disease and is estimated to infect 170 million people worldwide. HCV is able to establish a persistent infection in part by inhibiting the innate immune response. It does so by using its protease, NS3, to cleave the host's antiviral factor MAVS, which normally activates the interferon response. Using an assay that measures MAVS activity, we found that multiple primate species contain a version of MAVS that is resistant to HCV antagonism. Surprisingly, most of these primates have independently converged on changes in the same amino acid residue of MAVS to escape cleavage by the HCV protease. We found that the HCV protease has lower binding affinity for these resistant MAVS variants, which consequently are more effective at restricting HCV infection. Using a combination of phylogenetic and functional analyses of proteases from other HCV-related viruses, we infer that ancestral primates were likely exposed to and adapted to HCV-like viruses. One consequence of this adaptation is that changes that have given rise to extant MAVS variants may now provide protection from modern-day viruses.
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Affiliation(s)
- Maulik R. Patel
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Yueh-Ming Loo
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Stacy M. Horner
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Michael Gale
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Harmit S. Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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7
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Stapleton JT, Foung S, Muerhoff AS, Bukh J, Simmonds P. The GB viruses: a review and proposed classification of GBV-A, GBV-C (HGV), and GBV-D in genus Pegivirus within the family Flaviviridae. J Gen Virol 2010; 92:233-46. [PMID: 21084497 PMCID: PMC3081076 DOI: 10.1099/vir.0.027490-0] [Citation(s) in RCA: 212] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In 1967, it was reported that experimental inoculation of serum from a surgeon (G.B.) with acute hepatitis into tamarins resulted in hepatitis. In 1995, two new members of the family Flaviviridae, named GBV-A and GBV-B, were identified in tamarins that developed hepatitis following inoculation with the 11th GB passage. Neither virus infects humans, and a number of GBV-A variants were identified in wild New World monkeys that were captured. Subsequently, a related human virus was identified [named GBV-C or hepatitis G virus (HGV)], and recently a more distantly related virus (named GBV-D) was discovered in bats. Only GBV-B, a second species within the genus Hepacivirus (type species hepatitis C virus), has been shown to cause hepatitis; it causes acute hepatitis in experimentally infected tamarins. The other GB viruses have however not been assigned to a genus within the family Flaviviridae. Based on phylogenetic relationships, genome organization and pathogenic features of the GB viruses, we propose to classify GBV-A-like viruses, GBV-C and GBV-D as members of a fourth genus in the family Flaviviridae, named Pegivirus (pe, persistent; g, GB or G). We also propose renaming 'GB' viruses within the tentative genus Pegivirus to reflect their host origin.
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Affiliation(s)
- Jack T Stapleton
- Department of Internal Medicine, Veterans Administration Medical Center and the University of Iowa, Iowa City, IA, USA.
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Epstein JH, Quan PL, Briese T, Street C, Jabado O, Conlan S, Ali Khan S, Verdugo D, Hossain MJ, Hutchison SK, Egholm M, Luby SP, Daszak P, Lipkin WI. Identification of GBV-D, a novel GB-like flavivirus from old world frugivorous bats (Pteropus giganteus) in Bangladesh. PLoS Pathog 2010; 6:e1000972. [PMID: 20617167 PMCID: PMC2895649 DOI: 10.1371/journal.ppat.1000972] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 05/27/2010] [Indexed: 11/19/2022] Open
Abstract
Bats are reservoirs for a wide range of zoonotic agents including lyssa-, henipah-, SARS-like corona-, Marburg-, Ebola-, and astroviruses. In an effort to survey for the presence of other infectious agents, known and unknown, we screened sera from 16 Pteropus giganteus bats from Faridpur, Bangladesh, using high-throughput pyrosequencing. Sequence analyses indicated the presence of a previously undescribed virus that has approximately 50% identity at the amino acid level to GB virus A and C (GBV-A and -C). Viral nucleic acid was present in 5 of 98 sera (5%) from a single colony of free-ranging bats. Infection was not associated with evidence of hepatitis or hepatic dysfunction. Phylogenetic analysis indicates that this first GBV-like flavivirus reported in bats constitutes a distinct species within the Flaviviridae family and is ancestral to the GBV-A and -C virus clades.
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Affiliation(s)
- Jonathan H. Epstein
- Conservation Medicine Program, Wildlife Trust, New York, New York, United States of America
| | - Phenix-Lan Quan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Craig Street
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Omar Jabado
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Sean Conlan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Shahneaz Ali Khan
- Conservation Medicine Program, Wildlife Trust, New York, New York, United States of America
- Chittagong Veterinary & Animal Sciences University, Chittagong, Bangladesh
| | - Dawn Verdugo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - M. Jahangir Hossain
- Programme on Infectious Disease and Vaccine Sciences, International Centre for Diarrheal Disease Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | | | - Michael Egholm
- 454 Life Sciences, Branford, Connecticut, United States of America
| | - Stephen P. Luby
- Programme on Infectious Disease and Vaccine Sciences, International Centre for Diarrheal Disease Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | - Peter Daszak
- Conservation Medicine Program, Wildlife Trust, New York, New York, United States of America
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
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Bukh J, Engle RE, Govindarajan S, Purcell RH. Immunity against the GBV-B hepatitis virus in tamarins can prevent productive infection following rechallenge and is long-lived. J Med Virol 2008; 80:87-94. [PMID: 18041000 DOI: 10.1002/jmv.21013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
GB virus-B (GBV-B) is the virus most closely related to hepatitis C virus (HCV). Thus, we have used GBV-B infection of tamarins, which develop acute hepatitis following experimental infection, as a surrogate model to study protective immunity. As challenge virus, we first produced a GBV-B pool from an infected tamarin, which was not infected with the related GBV-A viruses. Its infectivity titer was 10(6.6) tamarin 50% infectious doses per ml. Next, two tamarins that were convalescent from recombinant GBV-B infection were re-challenged. In the original infection viremia persisted for 8 and 12 weeks, respectively, and both animals developed moderately severe hepatitis. Each tamarin was re-challenged four times with 10(4.3) tamarin 50% infectious doses of the GBV-B challenge virus. In one animal, each re-challenge produced 1-2 weeks of viremia; hepatitis was observed following the first re-challenge. In the other animal, however, only the first re-challenge produced viremia, lasting 1 week. During the primary infection, peak GBV-B titers were about 10(8) genome equivalents/ml in both animals; following re-challenges, peak titers ranged from 10(3) to 10(6) genome equivalents/ml. Analysis of the polyprotein sequence of viruses recovered from both animals following the first re-challenge demonstrated that these did not represent immune escape variants since mutations were not detected. Neutralization studies suggested that the immunity was not humoral in nature. We also demonstrated that the immunity was long-lived: 1 year after the fourth challenge, the animal with sterilizing immunity had low titer viremia for only 1 week following an additional challenge.
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Affiliation(s)
- Jens Bukh
- Hepatitis Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-8009, USA.
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10
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Welsch C, Albrecht M, Maydt J, Herrmann E, Welker MW, Sarrazin C, Scheidig A, Lengauer T, Zeuzem S. Structural and functional comparison of the non-structural protein 4B in flaviviridae. J Mol Graph Model 2007; 26:546-57. [PMID: 17507273 DOI: 10.1016/j.jmgm.2007.03.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2006] [Revised: 03/23/2007] [Accepted: 03/28/2007] [Indexed: 12/27/2022]
Abstract
Flaviviridae are evolutionarily related viruses, comprising the hepatitis C virus (HCV), with the non-structural protein 4B (NS4B) as one of the least characterized proteins. NS4B is located in the endoplasmic reticulum membrane and is assumed to be a multifunctional protein. However, detailed structure information is missing. The hydrophobic nature of NS4B is a major difficulty for many experimental techniques. We applied bioinformatics methods to analyse structural and functional properties of NS4B in different viruses. We distinguish a central non-globular membrane portion with four to five transmembrane regions from an N- and C-terminal part with non-transmembrane helical elements. We demonstrate high similarity in sequence and structure for the C-terminal part within the flaviviridae family. A palmitoylation site contained in the C-terminal part of HCV is equally conserved in GB virus B. Furthermore, we identify and characterize an N-terminal basic leucine zipper (bZIP) motif in HCV, which is suggestive of a functionally important interaction site. In addition, we model the interaction of the bZIP region with the recently identified interaction partner CREB-RP/ATF6beta, a human activating transcription factor involved in ER-stress. In conclusion, the versatile structure, together with functional sites and motifs, possibly enables NS4B to adopt a role as protein hub in the membranous web interaction network of virus and host proteins. Important structural and functional properties of NS4B are predicted with implications for ER-stress response, altered gene expression and replication efficacy.
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Affiliation(s)
- Christoph Welsch
- Internal Medicine II, Saarland University Hospital, Kirrberger Strasse, 66421 Homburg/Saar, Germany.
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Abstract
GB viruses A and B (GBV-A and GBV-B) are members of the Flaviviridae family and are isolated from tamarins injected with serum from a human hepatitis patient. Along with a related human virus, GB virus C, or alternatively, hepatitis G virus (GBV-C/HGV), the three viruses represent the GB agents. Of the three viruses, GBV-B has been proposed as a potential surrogate model for the study of hepatitis C virus (HCV) infections of humans. GBV-B is phylogenetically most closely related to HCV and causes an acute, self-resolving hepatitis in tamarins as indicated by an increase in alanine aminotransferase and changes in liver histology. Similarities between GBV-B and HCV are found at the nucleotide sequence level with the two viruses sharing 28% amino acid homology over the lengths of their open reading frames. Short regions have even higher levels of homology that are functionally significant as shown by the ability of the GBV-B NS3 protease to cleave recombinant HCV polyprotein substrates. The shared protease substrate specificities suggest that GBV-B may be useful in testing antiviral compounds for activity against HCV. Although there are numerous similarities between GBV-B and HCV, there are important differences in that HCV frequently causes chronic infections in people, whereas GBV-B appears to cause only acute infections. The acute versus chronic course of infection may point to important differences between the two viruses that, along with the numerous similarities, will make GBV-B in tamarins a good surrogate model for HCV.
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Affiliation(s)
- B Beames
- Department of Virology and Immunology, Southwest Foundation for Biomedical Research and Southwest Regional Primate Research Center, San Antonio, Texas, 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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Smith DB, Basaras M, Frost S, Haydon D, Cuceanu N, Prescott L, Kamenka C, Millband D, Sathar MA, Simmonds P. Phylogenetic analysis of GBV-C/hepatitis G virus. J Gen Virol 2000; 81:769-80. [PMID: 10675415 DOI: 10.1099/0022-1317-81-3-769] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Comparison of 33 epidemiologically distinct GBV-C/hepatitis G virus complete genome sequences suggests the existence of four major phylogenetic groupings that are equally divergent from the chimpanzee isolate GBV-C(tro) and have distinct geographical distributions. These four groupings are not consistently reproduced by analysis of the virus 5'-noncoding region (5'-NCR), or of individual genes or subgenomic fragments with the exception of the E2 gene as a whole or of 200-600 nucleotide fragments from its 3' half. This region is upstream of a proposed anti-sense reading frame and contains conserved potential RNA secondary structures that may be capable of directing the internal initiation of translation. Phylogenetic analysis of this region from certain South African isolates is consistent with previous analysis of the 5'-NCR suggesting that these belong to a fifth group. The geographical distribution of virus variants is consistent with a long evolutionary history that may parallel that of pre-historic human migrations, implying that the long-term evolution of this RNA virus is extremely slow.
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Affiliation(s)
- D B Smith
- Department of Medical Microbiology, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, UK.
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15
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Charrel RN, De Micco P, de Lamballerie X. Phylogenetic analysis of GB viruses A and C: evidence for cospeciation between virus isolates and their primate hosts. J Gen Virol 1999; 80 ( Pt 9):2329-2335. [PMID: 10501484 DOI: 10.1099/0022-1317-80-9-2329] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
GB viruses A and C (GBV-A and GBV-C) have been isolated from humans and non-human primates. Phylogenetic analysis based on full-length polyproteins suggests that these two viruses have a common ancestor. It has now been determined that analysis of subgenomic amino acid sequences in the E2 and NS5 regions of GBV-A and a 345 nucleotide segment in the 5' non-coding (5'NC) region was able to reproduce the phylogenetic relationships obtained by complete polyprotein sequences analysis. Using 5'NC sequences from databases, GBV-A isolates were discriminated into eight genetic groups, each one closely associated with specific primate hosts. Phylogenetic analyses performed on sequences from the epsilon-globin genes of primate hosts on one hand and complete polyprotein sequences from GBV-A and GBV-C isolates on the other suggest that a mechanism of cospeciation could be involved in virus evolution over a period of 35 million years.
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Affiliation(s)
- Rémi N Charrel
- Dept of Pathology, Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA2
- Laboratoire de Virologie moléculaire, transfusionnelle et tropicale, Faculté de Médecine, 13385 Marseille, France1
| | - Philippe De Micco
- Laboratoire de Virologie moléculaire, transfusionnelle et tropicale, Faculté de Médecine, 13385 Marseille, France1
| | - Xavier de Lamballerie
- Laboratoire de Virologie moléculaire, transfusionnelle et tropicale, Faculté de Médecine, 13385 Marseille, France1
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16
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Leary TP, Erker JC, Chalmers ML, Desai SM, Mushahwar IK. Improved detection systems for TT virus reveal high prevalence in humans, non-human primates and farm animals. J Gen Virol 1999; 80 ( Pt 8):2115-2120. [PMID: 10466810 DOI: 10.1099/0022-1317-80-8-2115] [Citation(s) in RCA: 170] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
TT virus is a newly described agent infecting humans. Initially isolated from a patient (initials T.T.) with unexplained hepatitis, the virus has since been found in both normal and diseased individuals. In the present study, we utilized genomic-length sequences from distinct genotypes of TT virus to design PCR-based assays using conserved oligonucleotide primers from three independent regions of the virus genome. Each of the three assays was found to be superior to the PCR-based assays previously published. The most sensitive of the new assays was utilized to demonstrate the prevalence of TT virus to be at least 34.1% in volunteer blood donors, 39.6% in commercial blood donors, 59.6% in non-A-GB hepatitis cases, 81.7% in injectable drug users and 95.9% in haemophiliacs. In an attempt to identify a possible source of human infection, we found TT virus sequences to be present in 19% of chickens, 20% of pigs, 25% of cows and 30% of sheep. Sequence determination and phylogenetic analyses demonstrated that isolates from farm animals were not genetically distinct from those found in humans. This study clearly demonstrates that previously reported PCR assays dramatically underestimate the true prevalence of TT virus within the human population. Due to the high rate of infection in both blood donors and those with non-A-GB hepatitis, these results question the causal role of TT virus in cases of unexplained hepatitis. Further, it is possible that domesticated farm animals serve as a source of human infection.
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Affiliation(s)
- Thomas P Leary
- Virus Discovery Group, Experimental Biology Research, Dept 90D, Bldg L3, Abbott Laboratories, 1401 Sheridan Road, North Chicago, IL 60064-6269, USA1
| | - James C Erker
- Virus Discovery Group, Experimental Biology Research, Dept 90D, Bldg L3, Abbott Laboratories, 1401 Sheridan Road, North Chicago, IL 60064-6269, USA1
| | - Michelle L Chalmers
- Virus Discovery Group, Experimental Biology Research, Dept 90D, Bldg L3, Abbott Laboratories, 1401 Sheridan Road, North Chicago, IL 60064-6269, USA1
| | - Suresh M Desai
- Virus Discovery Group, Experimental Biology Research, Dept 90D, Bldg L3, Abbott Laboratories, 1401 Sheridan Road, North Chicago, IL 60064-6269, USA1
| | - Isa K Mushahwar
- Virus Discovery Group, Experimental Biology Research, Dept 90D, Bldg L3, Abbott Laboratories, 1401 Sheridan Road, North Chicago, IL 60064-6269, USA1
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17
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Birkenmeyer LG, Desai SM, Muerhoff AS, Leary TP, Simons JN, Montes CC, Mushahwar IK. Isolation of a GB virus-related genome from a chimpanzee. J Med Virol 1998; 56:44-51. [PMID: 9700632 DOI: 10.1002/(sici)1096-9071(199809)56:1<44::aid-jmv8>3.0.co;2-n] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Recently, two new flaviviruses, GB virus A (GBV-A) and GB virus B (GBV-B), were identified in the plasma of a tamarin infected with the hepatitis GB agent. A third virus, GB virus C (GBV-C), was subsequently identified in humans. In the current study, representational difference analysis (RDA) was used to search for a new virus in the serum of a chimpanzee that developed acute resolving hepatitis following inoculation with a pool of chimpanzee plasma. The plasma pool originated from serial passages of a human sample containing virus-like particles. Numerous cDNA clones were obtained that exhibited 62-80% identity with GBV-C. With the exception of the extreme 5' and 3' ends, the complete viral genome was sequenced, revealing a single large open reading frame encoding a 2833 amino acid polyprotein that contains two envelope proteins, two proteases, a helicase, and an RNA-dependent RNA polymerase. Phylogenetic analysis of the new virus indicates that it is closely related to GBV-C, yet still sufficiently divergent as to be placed in a separate group, tentatively labeled GB virus Ctroglodytes (GBV-Ctro). Numerous human samples were screened by reverse transcriptase-polymerase chain reaction (RT-PCR), but GBV-Ctro sequence was not detected. However, a second chimpanzee inoculated with the same plasma pool was shown to develop a GBV-Ctro infection. Although isolated from an Old World primate with hepatitis, the primary host of GBV-Ctro and any association with disease remains to be determined.
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Affiliation(s)
- L G Birkenmeyer
- Virus Discovery Group, Experimental Biology Research, Abbott Laboratories, North Chicago, Illinois, USA
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Hadlock KG, Foung SK. GBV-C/HGV: a new virus within the Flaviviridae and its clinical implications. Transfus Med Rev 1998; 12:94-108. [PMID: 9566077 DOI: 10.1016/s0887-7963(98)80032-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- K G Hadlock
- Department of Pathology, Stanford University, CA, USA
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19
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Abstract
Molecular techniques have been used to investigate the epidemiology of hepatitis C virus (HCV) at several different levels. At a global level, the time of divergence of the diverse HCV genotypes isolated from different geographical regions has been estimated from the rate of divergence observed among a cohort of individuals infected from a common source. Estimates of more than 300 years for virus subtypes and more than 500-2000 years for virus types are consistent with their current geographical distributions. Analysis of virus sequences has also provided evidence for a common source of infection in several large-scale outbreaks of HCV infection, although where there is evidence that the implicated source contains more than one variant it may be difficult to distinguish individuals infected by different sources. Finally, sequence analysis has been used to investigate the vertical or horizontal transmission of HCV between pairs of individuals. The hypervariable region of the E2 gene is the most informative region to study if samples are available soon after the transmission event, but evidence for more distant events can still be obtained from analysis of genes such as NS5b and E1. Interpretation of some studies is complicated by the conservation of the gene region studied, or by the failure to make comparisons with sequences from epidemiologically unrelated viruses.
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Affiliation(s)
- D B Smith
- Department of Medical Microbiology, University of Edinburgh, Scotland, United Kingdom
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Bukh J, Apgar CL. Five new or recently discovered (GBV-A) virus species are indigenous to New World monkeys and may constitute a separate genus of the Flaviviridae. Virology 1997; 229:429-36. [PMID: 9126255 DOI: 10.1006/viro.1997.8461] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In previous studies, human hepatitis viruses have been experimentally transmitted to New World monkeys of the genus Saguinus (tamarins). Recently, two Flaviviridae-like agents (GBV-A and GBV-B) were identified in tamarins that developed hepatitis following inoculation with serum of the 11th tamarin passage of a potentially new human hepatitis agent. However, it was not shown that these viruses originated from the initial inoculum. We here report the discovery of indigenous species-specific viruses related to GBV-A in several species of New World monkeys and suggest that GBV-A virus was fortuitously acquired during passage in tamarins. Sera or plasma from 98 wild-caught New World monkeys representing 10 different species was tested by RT-PCR with conserved degenerate primers to the 5' noncoding region of the genome. Viral sequences were identified in 33 animals and sequence analysis was performed on the amplicons. In addition, the genomic region corresponding to the putative NS3 RNA helicase of GBV-A was amplified from most positive animals and sequenced. We detected GBV-A-like viruses in 13 (35%) of 37 S. mystax, 7 (78%) of 9 S. nigricollis, 3 (25%) of 12 S. labiatus, 2 (50%) of 4 S. oedipus, 2 (100%) of 2 Callithrix jacchus, and 6 (50%) of 12 Aotus trivirgatus monkeys. Each positive animal was infected with a unique strain of the GBV-A-like viruses. Analysis of the 5' NC and NS3 helicase sequences revealed that these viruses could be classified into 5 major genetic groups with genetic distances equivalent to or greater than those found among major genetic groups of hepatitis C virus. Species-specific GBV-A-like viruses were found in S. mystax, S. nigricollis, S. oedipus, C. jacchus, and A. trivirgatus species. The viruses specific for S. nigricollis were closely related to GBV-A, suggesting that GBV-A was acquired by passage through this species during the initial transmission studies. The natural history of the GBV-A-like viruses was studied in serial serum samples from 9 S. mystax and 2 A. trivirgatus monkeys. Each animal was chronically infected and the viral strain did not vary during 9-27 months of follow-up. Finally, we demonstrated that four S. mystax were positive upon arrival to the United States from the country of origin. No apparent disease was associated with chronic infection of the GBV-A-like viruses. In conclusion, many New World monkeys are persistently infected with indigenous species-specific viruses that may represent a new genus within the virus family Flaviviridae.
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Affiliation(s)
- J Bukh
- Hepatitis Viruses Section, National Institute of Allergy and infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-0740, USA
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21
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Farci P, Bukh J, Purcell RH. The quasispecies of hepatitis C virus and the host immune response. SPRINGER SEMINARS IN IMMUNOPATHOLOGY 1997; 19:5-26. [PMID: 9266628 DOI: 10.1007/bf00945022] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- P Farci
- Istituto di Medicina Interna, University of Cagliari, Italy
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