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Dunay E, Rukundo J, Atencia R, Cole MF, Cantwell A, Emery Thompson M, Rosati AG, Goldberg TL. Viruses in saliva from sanctuary chimpanzees (Pan troglodytes) in Republic of Congo and Uganda. PLoS One 2023; 18:e0288007. [PMID: 37384730 PMCID: PMC10310015 DOI: 10.1371/journal.pone.0288007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/16/2023] [Indexed: 07/01/2023] Open
Abstract
Pathogen surveillance for great ape health monitoring has typically been performed on non-invasive samples, primarily feces, in wild apes and blood in sanctuary-housed apes. However, many important primate pathogens, including known zoonoses, are shed in saliva and transmitted via oral fluids. Using metagenomic methods, we identified viruses in saliva samples from 46 wild-born, sanctuary-housed chimpanzees at two African sanctuaries in Republic of Congo and Uganda. In total, we identified 20 viruses. All but one, an unclassified CRESS DNA virus, are classified in five families: Circoviridae, Herpesviridae, Papillomaviridae, Picobirnaviridae, and Retroviridae. Overall, viral prevalence ranged from 4.2% to 87.5%. Many of these viruses are ubiquitous in primates and known to replicate in the oral cavity (simian foamy viruses, Retroviridae; a cytomegalovirus and lymphocryptovirus; Herpesviridae; and alpha and gamma papillomaviruses, Papillomaviridae). None of the viruses identified have been shown to cause disease in chimpanzees or, to our knowledge, in humans. These data suggest that the risk of zoonotic viral disease from chimpanzee oral fluids in sanctuaries may be lower than commonly assumed.
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Affiliation(s)
- Emily Dunay
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Joshua Rukundo
- Ngamba Island Chimpanzee Sanctuary / Chimpanzee Trust, Entebbe, Uganda
| | - Rebeca Atencia
- Jane Goodall Institute Congo, Pointe-Noire, Republic of Congo
| | - Megan F. Cole
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Averill Cantwell
- Department of Psychology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Melissa Emery Thompson
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Alexandra G. Rosati
- Department of Psychology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Anthropology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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Dynesen LT, Fernandez I, Coquin Y, Delaplace M, Montange T, Njouom R, Bilounga-Ndongo C, Rey FA, Gessain A, Backovic M, Buseyne F. Neutralization of zoonotic retroviruses by human antibodies: Genotype-specific epitopes within the receptor-binding domain from simian foamy virus. PLoS Pathog 2023; 19:e1011339. [PMID: 37093892 PMCID: PMC10159361 DOI: 10.1371/journal.ppat.1011339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/04/2023] [Accepted: 03/31/2023] [Indexed: 04/25/2023] Open
Abstract
Infection with viruses of animal origin pose a significant threat to human populations. Simian foamy viruses (SFVs) are frequently transmitted to humans, in which they establish a life-long infection, with the persistence of replication-competent virus. However, zoonotic SFVs do not induce severe disease nor are they transmitted between humans. Thus, SFVs represent a model of zoonotic retroviruses that lead to a chronic infection successfully controlled by the human immune system. We previously showed that infected humans develop potent neutralizing antibodies (nAbs). Within the viral envelope (Env), the surface protein (SU) carries a variable region that defines two genotypes, overlaps with the receptor binding domain (RBD), and is the exclusive target of nAbs. However, its antigenic determinants are not understood. Here, we characterized nAbs present in plasma samples from SFV-infected individuals living in Central Africa. Neutralization assays were carried out in the presence of recombinant SU that compete with SU at the surface of viral vector particles. We defined the regions targeted by the nAbs using mutant SU proteins modified at the glycosylation sites, RBD functional subregions, and genotype-specific sequences that present properties of B-cell epitopes. We observed that nAbs target conformational epitopes. We identified three major epitopic regions: the loops at the apex of the RBD, which likely mediate interactions between Env protomers to form Env trimers, a loop located in the vicinity of the heparan binding site, and a region proximal to the highly conserved glycosylation site N8. We provide information on how nAbs specific for each of the two viral genotypes target different epitopes. Two common immune escape mechanisms, sequence variation and glycan shielding, were not observed. We propose a model according to which the neutralization mechanisms rely on the nAbs to block the Env conformational change and/or interfere with binding to susceptible cells. As the SFV RBD is structurally different from known retroviral RBDs, our data provide fundamental knowledge on the structural basis for the inhibition of viruses by nAbs. Trial registration: The study was registered at www.clinicaltrials.gov: https://clinicaltrials.gov/ct2/show/NCT03225794/.
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Affiliation(s)
- Lasse Toftdal Dynesen
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Ignacio Fernandez
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, Paris, France
| | - Youna Coquin
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Manon Delaplace
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Thomas Montange
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | | | | | - Félix A Rey
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, Paris, France
| | - Antoine Gessain
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Marija Backovic
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, Paris, France
| | - Florence Buseyne
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
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Fernández I, Dynesen LT, Coquin Y, Pederzoli R, Brun D, Haouz A, Gessain A, Rey FA, Buseyne F, Backovic M. The crystal structure of a simian Foamy Virus receptor binding domain provides clues about entry into host cells. Nat Commun 2023; 14:1262. [PMID: 36878926 PMCID: PMC9988990 DOI: 10.1038/s41467-023-36923-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 02/21/2023] [Indexed: 03/08/2023] Open
Abstract
The surface envelope glycoprotein (Env) of all retroviruses mediates virus binding to cells and fusion of the viral and cellular membranes. A structure-function relationship for the HIV Env that belongs to the Orthoretrovirus subfamily has been well established. Structural information is however largely missing for the Env of Foamy viruses (FVs), the second retroviral subfamily. In this work we present the X-ray structure of the receptor binding domain (RBD) of a simian FV Env at 2.57 Å resolution, revealing two subdomains and an unprecedented fold. We have generated a model for the organization of the RBDs within the trimeric Env, which indicates that the upper subdomains form a cage-like structure at the apex of the Env, and identified residues K342, R343, R359 and R369 in the lower subdomain as key players for the interaction of the RBD and viral particles with heparan sulfate.
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Affiliation(s)
- Ignacio Fernández
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015, Paris, France
| | - Lasse Toftdal Dynesen
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, 75015, Paris, France
| | - Youna Coquin
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, 75015, Paris, France
| | - Riccardo Pederzoli
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015, Paris, France
| | - Delphine Brun
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015, Paris, France
| | - Ahmed Haouz
- Institut Pasteur, Université Paris Cité, Plateforme de cristallographie-C2RT, CNRS UMR 3528, 75015, Paris, France
| | - Antoine Gessain
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, 75015, Paris, France
| | - Félix A Rey
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015, Paris, France
| | - Florence Buseyne
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, 75015, Paris, France
| | - Marija Backovic
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015, Paris, France.
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Zhang F, Chase-Topping M, Guo CG, Woolhouse MEJ. Predictors of human-infective RNA virus discovery in the United States, China, and Africa, an ecological study. eLife 2022; 11:e72123. [PMID: 35666108 PMCID: PMC9278958 DOI: 10.7554/elife.72123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Background The variation in the pathogen type as well as the spatial heterogeneity of predictors make the generality of any associations with pathogen discovery debatable. Our previous work confirmed that the association of a group of predictors differed across different types of RNA viruses, yet there have been no previous comparisons of the specific predictors for RNA virus discovery in different regions. The aim of the current study was to close the gap by investigating whether predictors of discovery rates within three regions-the United States, China, and Africa-differ from one another and from those at the global level. Methods Based on a comprehensive list of human-infective RNA viruses, we collated published data on first discovery of each species in each region. We used a Poisson boosted regression tree (BRT) model to examine the relationship between virus discovery and 33 predictors representing climate, socio-economics, land use, and biodiversity across each region separately. The discovery probability in three regions in 2010-2019 was mapped using the fitted models and historical predictors. Results The numbers of human-infective virus species discovered in the United States, China, and Africa up to 2019 were 95, 80, and 107 respectively, with China lagging behind the other two regions. In each region, discoveries were clustered in hotspots. BRT modelling suggested that in all three regions RNA virus discovery was better predicted by land use and socio-economic variables than climatic variables and biodiversity, although the relative importance of these predictors varied by region. Map of virus discovery probability in 2010-2019 indicated several new hotspots outside historical high-risk areas. Most new virus species since 2010 in each region (6/6 in the United States, 19/19 in China, 12/19 in Africa) were discovered in high-risk areas as predicted by our model. Conclusions The drivers of spatiotemporal variation in virus discovery rates vary in different regions of the world. Within regions virus discovery is driven mainly by land-use and socio-economic variables; climate and biodiversity variables are consistently less important predictors than at a global scale. Potential new discovery hotspots in 2010-2019 are identified. Results from the study could guide active surveillance for new human-infective viruses in local high-risk areas. Funding FFZ is funded by the Darwin Trust of Edinburgh (https://darwintrust.bio.ed.ac.uk/). MEJW has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 874735 (VEO) (https://www.veo-europe.eu/).
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Affiliation(s)
- Feifei Zhang
- Usher Institute, University of EdinburghEdinburghUnited Kingdom
| | - Margo Chase-Topping
- Usher Institute, University of EdinburghEdinburghUnited Kingdom
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghEdinburghUnited Kingdom
| | - Chuan-Guo Guo
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong KongHong KongChina
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5
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Couteaudier M, Montange T, Njouom R, Bilounga-Ndongo C, Gessain A, Buseyne F. Plasma antibodies from humans infected with zoonotic simian foamy virus do not inhibit cell-to-cell transmission of the virus despite binding to the surface of infected cells. PLoS Pathog 2022; 18:e1010470. [PMID: 35605011 PMCID: PMC9166401 DOI: 10.1371/journal.ppat.1010470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/03/2022] [Accepted: 03/25/2022] [Indexed: 01/23/2023] Open
Abstract
Zoonotic simian foamy viruses (SFV) establish lifelong infection in their human hosts. Despite repeated transmission of SFV from nonhuman primates to humans, neither transmission between human hosts nor severe clinical manifestations have been reported. We aim to study the immune responses elicited by chronic infection with this retrovirus and previously reported that SFV-infected individuals generate potent neutralizing antibodies that block cell infection by viral particles. Here, we assessed whether human plasma antibodies block SFV cell-to-cell transmission and present the first description of cell-to-cell spreading of zoonotic gorilla SFV. We set-up a microtitration assay to quantify the ability of plasma samples from 20 Central African individuals infected with gorilla SFV and 9 uninfected controls to block cell-associated transmission of zoonotic gorilla SFV strains. We used flow-based cell cytometry and fluorescence microscopy to study envelope protein (Env) localization and the capacity of plasma antibodies to bind to infected cells. We visualized the cell-to-cell spread of SFV by real-time live imaging of a GFP-expressing prototype foamy virus (CI-PFV) strain. None of the samples neutralized cell-associated SFV infection, despite the inhibition of cell-free virus. We detected gorilla SFV Env in the perinuclear region, cytoplasmic vesicles and at the cell surface. We found that plasma antibodies bind to Env located at the surface of cells infected with primary gorilla SFV strains. Extracellular labeling of SFV proteins by human plasma samples showed patchy staining at the base of the cell and dense continuous staining at the cell apex, as well as staining in the intercellular connections that formed when previously connected cells separated from each other. In conclusion, SFV-specific antibodies from infected humans do not block cell-to-cell transmission, at least in vitro, despite their capacity to bind to the surface of infected cells. Trial registration: Clinical trial registration: www.clinicaltrials.gov, https://clinicaltrials.gov/ct2/show/NCT03225794/. Foamy viruses are the oldest known retroviruses and have been mostly described to be nonpathogenic in their natural animal hosts. Simian foamy viruses (SFVs) can be transmitted to humans, in whom they establish persistent infection, as have the simian viruses that led to the emergence of two major human pathogens, human immunodeficiency virus type 1 (HIV-1) and human T lymphotropic virus type 1 (HTLV-1). Such cross-species transmission of SFV is ongoing in many parts of the world where humans have contact with nonhuman primates. We previously showed high titers of neutralizing antibodies in the plasma of most SFV-infected individuals. These antiviral antibodies can inhibit cell-free virus entry. However, SFV efficiently spread from one cell to another. Here, we demonstrate that plasma antibodies do not block such cell-to-cell transmission, despite their capacity to bind to the surface of infected cells. In addition, we document for the first time the cell-to-cell spread of primary zoonotic gorilla SFV.
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Affiliation(s)
- Mathilde Couteaudier
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d’Epidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Thomas Montange
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d’Epidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | | | | | - Antoine Gessain
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d’Epidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Florence Buseyne
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d’Epidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
- * E-mail:
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6
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Evaluation of the stability and intratumoral delivery of foreign transgenes encoded by an oncolytic Foamy Virus vector. Cancer Gene Ther 2022; 29:1240-1251. [PMID: 35145270 PMCID: PMC9363555 DOI: 10.1038/s41417-022-00431-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 12/21/2021] [Accepted: 01/25/2022] [Indexed: 11/12/2022]
Abstract
Foamy Viruses are cell cycle-dependent retroviruses capable of persisting unintegrated in quiescent cells until cell division occurs. This unique ability allows them to target slowly dividing human tumor cells which remains an unmet need in oncolytic virotherapy. We have previously reported the generation of oncolytic Foamy Virus (oFV) vector system and demonstrated its superiority over oncolytic Murine Leukemia Virus vectors in infecting slowly dividing cancer cells. In the present study we evaluated (i) the ability of oFV to carry foreign transgenes and (ii) the genetic stability of these vectors upon serial passage. The thymidine kinase (TK) and inducible caspase 9 (iCasp9) cDNAs could be detected in the oFV backbone for up to 3 in vitro passages. In vivo, GFP-, TK- and iCasp9- carrying oFV vectors propagated efficiently in subcutaneous xenograft glioblastoma tumors and drove transgene expression for up to 66 days. However, in vivo oFV vector spread eventually resulted in complete loss of the iCasp9 cDNA, minor loss of the TK cDNA and negligible loss of the GFP. Our results suggest that oFV is a promising gene delivery platform and that transgenes smaller than 1 kb might be most suitable for oFV arming.
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Oncolytic Foamy Virus - generation and properties of a nonpathogenic replicating retroviral vector system that targets chronically proliferating cancer cells. J Virol 2021; 95:JVI.00015-21. [PMID: 33692205 PMCID: PMC8139661 DOI: 10.1128/jvi.00015-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nonpathogenic retroviruses of the Spumaretrovirinae subfamily can persist long-term in the cytoplasm of infected cells, completing their lifecycle only after the nuclear membrane dissolves at the time of cell division. Since the targeting of slowly dividing cancer cells remains an unmet need in oncolytic virotherapy we constructed a replication competent Foamy Virus vector (oFV) from the genomes of two chimpanzee Simian Foamy Viruses (PAN1 and PAN2) and inserted a GFP transgene in place of the bel-2 open reading frame. oFV-GFP infected and propagated with slow kinetics in multiple human tumor cell lines, inducing a syncytial cytopathic effect. Infection of growth arrested MRC5 cells was not productive, but oFV genomes persisted in the cytoplasm and the productive viral lifecycle resumed when cell division was later restored. In vivo, the virus propagated extensively in intraperitoneal ovarian cancer xenografts, slowing tumor growth, significantly prolonging survival of the treated mice and sustaining GFP transgene expression for at least 45 days. Our data indicate that oFV is a promising new replication-competent viral and gene delivery platform for efficient targeting of the most fundamental trait of cancer cells, their ability to sustain chronic proliferation.Significance:The infectivity of certain retroviruses is limited to dividing cells, which makes them attractive tools for targeting cancer cell proliferation. Previously developed replication-competent gammaretroviral vectors spread efficiently in rapidly dividing cancer cells, but not in cancer cells that divide more slowly. In contrast to rapidly proliferating transplantable mouse tumors, slow proliferation is a hallmark of human cancers and may have contributed to the clinical failure of the preclinically promising Murine Leukemia Virus vector Toca511 which failed to show efficacy in a phase 3 clinical trial in patients with glioblastoma. The studies presented in our manuscript show that oncolytic Foamy Virus (oFV) vectors are capable of persisting unintegrated in quiescent cells and resuming their life cycle once the cells start dividing again. This property of oFVs, together with their lack of pathogenicity and their ability to catalyze the fusion of infected cancer cells, makes them an attractive platform for further investigation.
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Gessain A, Montange T, Betsem E, Bilounga Ndongo C, Njouom R, Buseyne F. Case-Control Study of the Immune Status of Humans Infected With Zoonotic Gorilla Simian Foamy Viruses. J Infect Dis 2021; 221:1724-1733. [PMID: 31822908 DOI: 10.1093/infdis/jiz660] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/10/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Zoonotic simian foamy viruses (SFVs) establish persistent infections in humans, for whom the long-term consequences for health are poorly described. In this study, we aimed to characterize blood-cell phenotypes and plasma biomarkers associated with gorilla SFV infection in humans. METHODS We used a case-control design to compare 15 Cameroonian hunters infected with gorilla SFV (cases) to 15 controls matched for age and ethnicity. A flow cytometry-based phenotypic study and quantification of plasma immune biomarkers were carried out on blood samples from all participants. Wilcoxon signed-rank tests were used to compare cases and controls. RESULTS Cases had a significantly higher percentage of CD8 T lymphocytes than controls (median, 17.6% vs 13.7%; P = .03) but similar levels of B, natural killer, and CD4 T lymphocytes. Cases also had a lower proportion of recent CD4 thymic emigrants (10.9% vs 18.6%, P = .05), a higher proportion of programmed death receptor 1 (PD-1) expressing memory CD4 T lymphocytes (31.7% vs 24.7%, P = .01), and higher plasma levels of the soluble CD163 scavenger receptor (0.84 vs .59 µg/mL, P = .003) than controls. CONCLUSIONS We show, for the first time, that chronic infection with SFV is associated with T lymphocyte differentiation and monocyte activation.
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Affiliation(s)
- Antoine Gessain
- Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, Paris, France.,Unité Mixte de Recherche du Centre National de la Recherche Scientifique 3569, Paris, France
| | - Thomas Montange
- Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, Paris, France.,Unité Mixte de Recherche du Centre National de la Recherche Scientifique 3569, Paris, France
| | | | | | | | - Florence Buseyne
- Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, Paris, France.,Unité Mixte de Recherche du Centre National de la Recherche Scientifique 3569, Paris, France
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Complete Genome Sequence of a Baboon Simian Foamy Virus Isolated from an Infected Human. Microbiol Resour Announc 2020; 9:9/27/e00522-20. [PMID: 32616640 PMCID: PMC7330242 DOI: 10.1128/mra.00522-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We obtained the full-length genome of a simian foamy virus (SFV) from an infected human. This virus originated from a baboon (Papio species, strain SFVpxx_hu9406). The genome is 13,113 nucleotides long with the canonical SFV genome structure. Phylogenetically, SFVpxx_hu9406 clustered closely with SFVpan_V909/03F from a captive baboon and other Cercopithecidae SFVs. We obtained the full-length genome of a simian foamy virus (SFV) from an infected human. This virus originated from a baboon (Papio species, strain SFVpxx_hu9406). The genome is 13,113 nucleotides long with the canonical SFV genome structure. Phylogenetically, SFVpxx_hu9406 clustered closely with SFVpan_V909/03F from a captive baboon and other Cercopithecidae SFVs.
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10
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Inhibitors of the interferon response increase the replication of gorilla simian foamy viruses. Virology 2019; 541:25-31. [PMID: 31826843 DOI: 10.1016/j.virol.2019.11.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/17/2022]
Abstract
Simian foamy viruses (SFVs) are complex retroviruses that are widespread throughout nonhuman primates. SFVs can also be transmitted to humans, mostly through bites. We previously observed that primary zoonotic gorilla SFV strains grow much more slowly than laboratory-adapted chimpanzee strains. Here, we tested the hypothesis that the growth of SFV is limited by interferon (IFN) using inhibitors of cellular pathways involved in the induction or action of type I IFN. Inhibitors of JAK1/2 (Ruxolitinib) and TBK-1 (BX795) led to a 2- to 4-fold higher percentage of cells infected with zoonotic gorilla SFVs but did not affect the replication of laboratory-adapted chimpanzee SFVs. IKK2 inhibitors (TPCA-1 and BMS345541) had no effect on any of the SFV strains. In conclusion, the addition of molecules that inhibit the type I IFN response to the culture medium can be used as a simple and efficient method to enhance the replication of zoonotic gorilla SFVs.
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Materniak-Kornas M, Tan J, Heit-Mondrzyk A, Hotz-Wagenblatt A, Löchelt M. Bovine Foamy Virus: Shared and Unique Molecular Features In Vitro and In Vivo. Viruses 2019; 11:E1084. [PMID: 31766538 PMCID: PMC6950176 DOI: 10.3390/v11121084] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 12/18/2022] Open
Abstract
The retroviral subfamily of Spumaretrovirinae consists of five genera of foamy (spuma) viruses (FVs) that are endemic in some mammalian hosts [1]. Closely related species may be susceptible to the same or highly related FVs. FVs are not known to induce overt disease and thus do not pose medical problems to humans and livestock or companion animals. A robust lab animal model is not available or is a lab animal a natural host of a FV. Due to this, research is limited and often focused on the simian FVs with their well-established zoonotic potential. The authors of this review and their groups have conducted several studies on bovine FV (BFV) in the past with the intention of (i) exploring the risk of zoonotic infection via beef and raw cattle products, (ii) studying a co-factorial role of BFV in different cattle diseases with unclear etiology, (iii) exploring unique features of FV molecular biology and replication strategies in non-simian FVs, and (iv) conducting animal studies and functional virology in BFV-infected calves as a model for corresponding studies in primates or small lab animals. These studies gained new insights into FV-host interactions, mechanisms of gene expression, and transcriptional regulation, including miRNA biology, host-directed restriction of FV replication, spread and distribution in the infected animal, and at the population level. The current review attempts to summarize these findings in BFV and tries to connect them to findings from other FVs.
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Affiliation(s)
| | - Juan Tan
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China;
| | - Anke Heit-Mondrzyk
- German Cancer Research Center DKFZ, Core Facility Omics IT and Data Management, 69120 Heidelberg, Germany; (A.H.-M.); (A.H.-W.)
| | - Agnes Hotz-Wagenblatt
- German Cancer Research Center DKFZ, Core Facility Omics IT and Data Management, 69120 Heidelberg, Germany; (A.H.-M.); (A.H.-W.)
| | - Martin Löchelt
- German Cancer Research Center DKFZ, Program Infection, Inflammation and Cancer, Div. Viral Transformation Mechanisms, 69120 Heidelberg, Germany
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12
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Aiewsakun P, Richard L, Gessain A, Mouinga-Ondémé A, Vicente Afonso P, Katzourakis A. Modular nature of simian foamy virus genomes and their evolutionary history. Virus Evol 2019; 5:vez032. [PMID: 31636999 PMCID: PMC6795992 DOI: 10.1093/ve/vez032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Among all known retroviruses, foamy viruses (FVs) have the most stable virus–host co-speciation history, co-diverging in concert with their vertebrate hosts for hundreds of millions of years. However, detailed molecular analyses indicate that different parts of their genome might have different evolutionary histories. While their polymerase gene displays a robust and straightforward virus–host co-speciation pattern, the evolutionary history of their envelope (env) gene, is much more complicated. Here, we report eleven new FV env sequences in two mandrill populations in Central Africa, geographically separated by the Ogooué River into the North and the South populations. Phylogenetic reconstruction of the polymerase gene shows that the two virus populations are distinct, and each contains two variants of env genes co-existing with one another. The distinction between the two env variants can be mapped to the surface domain, flanked by two recombination hotspots, as previously reported for chimpanzee and gorilla FVs. Our analyses suggest that the two env variants originated during the diversification of Old World monkeys and apes, ∼30 million years ago. We also show that this env gene region forms two phylogenetically distinct clades, each displaying a host co-divergence and geographical separation pattern, while the rest of the genome of the two strains is phylogenetically indistinguishable in each of the host-specific groups. We propose possible evolutionary mechanisms to explain the modular nature of the FV genome.
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Affiliation(s)
- Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Léa Richard
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, UMR3569 CNRS, Paris, France.,Université Paris Diderot - Paris7, Sorbonne Paris Cité, Paris, France
| | - Antoine Gessain
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, UMR3569 CNRS, Paris, France
| | - Augustin Mouinga-Ondémé
- Unité des Infections Rétrovirales et Pathologies Associées, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Philippe Vicente Afonso
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, UMR3569 CNRS, Paris, France
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
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Shankar A, Sibley SD, Goldberg TL, Switzer WM. Molecular Analysis of the Complete Genome of a Simian Foamy Virus Infecting Hylobates pileatus (pileated gibbon) Reveals Ancient Co-Evolution with Lesser Apes. Viruses 2019; 11:E605. [PMID: 31277268 PMCID: PMC6669568 DOI: 10.3390/v11070605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/27/2019] [Accepted: 06/30/2019] [Indexed: 02/07/2023] Open
Abstract
Foamy viruses (FVs) are complex retroviruses present in many mammals, including nonhuman primates, where they are called simian foamy viruses (SFVs). SFVs can zoonotically infect humans, but very few complete SFV genomes are available, hampering the design of diagnostic assays. Gibbons are lesser apes widespread across Southeast Asia that can be infected with SFV, but only two partial SFV sequences are currently available. We used a metagenomics approach with next-generation sequencing of nucleic acid extracted from the cell culture of a blood specimen from a lesser ape, the pileated gibbon (Hylobates pileatus), to obtain the complete SFVhpi_SAM106 genome. We used Bayesian analysis to co-infer phylogenetic relationships and divergence dates. SFVhpi_SAM106 is ancestral to other ape SFVs with a divergence date of ~20.6 million years ago, reflecting ancient co-evolution of the host and SFVhpi_SAM106. Analysis of the complete SFVhpi_SAM106 genome shows that it has the same genetic architecture as other SFVs but has the longest recorded genome (13,885-nt) due to a longer long terminal repeat region (2,071 bp). The complete sequence of the SFVhpi_SAM106 genome fills an important knowledge gap in SFV genetics and will facilitate future studies of FV infection, transmission, and evolutionary history.
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Affiliation(s)
- Anupama Shankar
- Laboratory Branch, Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Samuel D Sibley
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, GA 30329, USA.
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14
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An Immunodominant and Conserved B-Cell Epitope in the Envelope of Simian Foamy Virus Recognized by Humans Infected with Zoonotic Strains from Apes. J Virol 2019; 93:JVI.00068-19. [PMID: 30894477 DOI: 10.1128/jvi.00068-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/13/2019] [Indexed: 11/20/2022] Open
Abstract
Cross-species transmission of simian foamy viruses (SFVs) from nonhuman primates (NHPs) to humans is currently ongoing. These zoonotic retroviruses establish lifelong persistent infection in their human hosts. SFV are apparently nonpathogenic in vivo, with ubiquitous in vitro tropism. Here, we aimed to identify envelope B-cell epitopes that are recognized following a zoonotic SFV infection. We screened a library of 169 peptides covering the external portion of the envelope from the prototype foamy virus (SFVpsc_huHSRV.13) for recognition by samples from 52 Central African hunters (16 uninfected and 36 infected with chimpanzee, gorilla, or Cercopithecus SFV). We demonstrate the specific recognition of peptide N96-V110 located in the leader peptide, gp18LP Forty-three variant peptides with truncations, alanine substitutions, or amino acid changes found in other SFV species were tested. We mapped the epitope between positions 98 and 108 and defined six amino acids essential for recognition. Most plasma samples from SFV-infected humans cross-reacted with sequences from apes and Old World monkey SFV species. The magnitude of binding to peptide N96-V110 was significantly higher for samples of individuals infected with a chimpanzee or gorilla SFV than those infected with a Cercopithecus SFV. In conclusion, we have been the first to define an immunodominant B-cell epitope recognized by humans following zoonotic SFV infection.IMPORTANCE Foamy viruses are the oldest known retroviruses and have been mostly described to be nonpathogenic in their natural animal hosts. SFVs can be transmitted to humans, in whom they establish persistent infection, like the simian lenti- and deltaviruses that led to the emergence of two major human pathogens, human immunodeficiency virus type 1 and human T-lymphotropic virus type 1. This is the first identification of an SFV-specific B-cell epitope recognized by human plasma samples. The immunodominant epitope lies in gp18LP, probably at the base of the envelope trimers. The NHP species the most genetically related to humans transmitted SFV strains that induced the strongest antibody responses. Importantly, this epitope is well conserved across SFV species that infect African and Asian NHPs.
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15
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Lambert C, Couteaudier M, Gouzil J, Richard L, Montange T, Betsem E, Rua R, Tobaly-Tapiero J, Lindemann D, Njouom R, Mouinga-Ondémé A, Gessain A, Buseyne F. Potent neutralizing antibodies in humans infected with zoonotic simian foamy viruses target conserved epitopes located in the dimorphic domain of the surface envelope protein. PLoS Pathog 2018; 14:e1007293. [PMID: 30296302 PMCID: PMC6193739 DOI: 10.1371/journal.ppat.1007293] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 10/18/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022] Open
Abstract
Human diseases of zoonotic origin are a major public health problem. Simian foamy viruses (SFVs) are complex retroviruses which are currently spilling over to humans. Replication-competent SFVs persist over the lifetime of their human hosts, without spreading to secondary hosts, suggesting the presence of efficient immune control. Accordingly, we aimed to perform an in-depth characterization of neutralizing antibodies raised by humans infected with a zoonotic SFV. We quantified the neutralizing capacity of plasma samples from 58 SFV-infected hunters against primary zoonotic gorilla and chimpanzee SFV strains, and laboratory-adapted chimpanzee SFV. The genotype of the strain infecting each hunter was identified by direct sequencing of the env gene amplified from the buffy coat with genotype-specific primers. Foamy virus vector particles (FVV) enveloped by wild-type and chimeric gorilla SFV were used to map the envelope region targeted by antibodies. Here, we showed high titers of neutralizing antibodies in the plasma of most SFV-infected individuals. Neutralizing antibodies target the dimorphic portion of the envelope protein surface domain. Epitopes recognized by neutralizing antibodies have been conserved during the cospeciation of SFV with their nonhuman primate host. Greater neutralization breadth in plasma samples of SFV-infected humans was statistically associated with smaller SFV-related hematological changes. The neutralization patterns provide evidence for persistent expression of viral proteins and a high prevalence of coinfection. In conclusion, neutralizing antibodies raised against zoonotic SFV target immunodominant and conserved epitopes located in the receptor binding domain. These properties support their potential role in restricting the spread of SFV in the human population.
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Affiliation(s)
- Caroline Lambert
- Unité d’Épidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, Paris, France
- UMR CNRS 3569, Institut Pasteur, Paris, France
- Sorbonne Paris Cité, Cellule Pasteur, Université Paris Diderot, Institut Pasteur, Paris, France
| | - Mathilde Couteaudier
- Unité d’Épidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, Paris, France
- UMR CNRS 3569, Institut Pasteur, Paris, France
| | - Julie Gouzil
- Unité d’Épidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, Paris, France
- UMR CNRS 3569, Institut Pasteur, Paris, France
| | - Léa Richard
- Unité d’Épidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, Paris, France
- UMR CNRS 3569, Institut Pasteur, Paris, France
- Sorbonne Paris Cité, Cellule Pasteur, Université Paris Diderot, Institut Pasteur, Paris, France
| | - Thomas Montange
- Unité d’Épidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, Paris, France
- UMR CNRS 3569, Institut Pasteur, Paris, France
| | - Edouard Betsem
- Unité d’Épidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, Paris, France
- UMR CNRS 3569, Institut Pasteur, Paris, France
- University of Yaounde I, Yaounde, Cameroon
| | - Réjane Rua
- Unité d’Épidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, Paris, France
- UMR CNRS 3569, Institut Pasteur, Paris, France
| | - Joelle Tobaly-Tapiero
- CNRS UMR 7212, INSERM U944, Institut Universitaire d’Hématologie, Hôpital Saint-Louis, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Dirk Lindemann
- Institute of Virology, Medical Faculty “Carl Gustav Carus”, Technische Universität Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Richard Njouom
- Laboratoire de Virologie, Centre Pasteur du Cameroun, Yaoundé, Cameroon
| | - Augustin Mouinga-Ondémé
- Unité de Rétrovirologie, Centre International de Recherche Médicale de Franceville, Franceville, Gabon
| | - Antoine Gessain
- Unité d’Épidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, Paris, France
- UMR CNRS 3569, Institut Pasteur, Paris, France
| | - Florence Buseyne
- Unité d’Épidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, Paris, France
- UMR CNRS 3569, Institut Pasteur, Paris, France
- * E-mail:
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16
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Khan AS, Bodem J, Buseyne F, Gessain A, Johnson W, Kuhn JH, Kuzmak J, Lindemann D, Linial ML, Löchelt M, Materniak-Kornas M, Soares MA, Switzer WM. Spumaretroviruses: Updated taxonomy and nomenclature. Virology 2018; 516:158-164. [PMID: 29407373 DOI: 10.1016/j.virol.2017.12.035] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 12/29/2017] [Accepted: 12/29/2017] [Indexed: 01/28/2023]
Abstract
Spumaretroviruses, commonly referred to as foamy viruses, are complex retroviruses belonging to the subfamily Spumaretrovirinae, family Retroviridae, which naturally infect a variety of animals including nonhuman primates (NHPs). Additionally, cross-species transmissions of simian foamy viruses (SFVs) to humans have occurred following exposure to tissues of infected NHPs. Recent research has led to the identification of previously unknown exogenous foamy viruses, and to the discovery of endogenous spumaretrovirus sequences in a variety of host genomes. Here, we describe an updated spumaretrovirus taxonomy that has been recently accepted by the International Committee on Taxonomy of Viruses (ICTV) Executive Committee, and describe a virus nomenclature that is generally consistent with that used for other retroviruses, such as lentiviruses and deltaretroviruses. This taxonomy can be applied to distinguish different, but closely related, primate (e.g., human, ape, simian) foamy viruses as well as those from other hosts. This proposal accounts for host-virus co-speciation and cross-species transmission.
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Affiliation(s)
- Arifa S Khan
- Laboratory of Retroviruses, US Food and Drug Administration, Silver Spring, MD 20993, USA.
| | - Jochen Bodem
- Institut für Virologie und Immunbiologie, Universität Würzburg, Würzburg, Germany
| | - Florence Buseyne
- Unit of Epidemiology and Physiopathology of Oncogenic Viruses, Institut Pasteur, Paris, France; Centre National de la Recherche Scientifique, CNRS UMR3569, Paris, France
| | - Antoine Gessain
- Unit of Epidemiology and Physiopathology of Oncogenic Viruses, Institut Pasteur, Paris, France; Centre National de la Recherche Scientifique, CNRS UMR3569, Paris, France
| | - Welkin Johnson
- Biology Department, Boston College, Chestnut Hill, MA 02467, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Jacek Kuzmak
- Department of Biochemistry, National Veterinary Research Institute, Puławy, Poland
| | - Dirk Lindemann
- Institute of Virology, Technische Universität Dresden, Dresden, Germany
| | - Maxine L Linial
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Martin Löchelt
- Research Program Infection, Inflammation and Cancer, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | | | - Marcelo A Soares
- Instituto Nacional de Câncer and Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
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17
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Lambert C, Rua R, Gessain A, Buseyne F. A new sensitive indicator cell line reveals cross-transactivation of the viral LTR by gorilla and chimpanzee simian foamy viruses. Virology 2016; 496:219-226. [PMID: 27348053 DOI: 10.1016/j.virol.2016.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/13/2016] [Accepted: 06/14/2016] [Indexed: 12/25/2022]
Abstract
The majority of currently identified simian foamy virus (SFV)-infected Cameroonian and Gabonese individuals harbor SFV from the gorilla lineage. We constructed an indicator cell line for the quantification of gorilla SFVs, in which the U3 sequence of a gorilla SFV directs the expression of the β-galactosidase protein. The gorilla foamy virus activated β-galactosidase (GFAB) cells efficiently quantified two zoonotic primary gorilla isolates and SFVs from three chimpanzee subspecies. Primary gorilla SFVs replicated more slowly and at lower levels than primary chimpanzee SFVs. Analysis of previously described motifs of Tas proteins and U3 LTRs involved in viral gene synthesis revealed conservation of such motifs in Tas proteins from gorilla and chimpanzee SFVs, but little sequence homology in the LTR regions previously shown to interact with viral and cellular factors.
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Affiliation(s)
- Caroline Lambert
- Unité d'épidémiologie et physiopathologie des virus oncogènes, Institut Pasteur, 28 rue du Dr Roux, 75015 Paris, France; UMR CNRS 3569, Institut Pasteur, Paris 75015, France; Sorbonne Paris Cité, Cellule Pasteur, Université Paris Diderot, Institut Pasteur, 75015 Paris, France
| | - Réjane Rua
- Unité d'épidémiologie et physiopathologie des virus oncogènes, Institut Pasteur, 28 rue du Dr Roux, 75015 Paris, France
| | - Antoine Gessain
- Unité d'épidémiologie et physiopathologie des virus oncogènes, Institut Pasteur, 28 rue du Dr Roux, 75015 Paris, France; UMR CNRS 3569, Institut Pasteur, Paris 75015, France
| | - Florence Buseyne
- Unité d'épidémiologie et physiopathologie des virus oncogènes, Institut Pasteur, 28 rue du Dr Roux, 75015 Paris, France; UMR CNRS 3569, Institut Pasteur, Paris 75015, France.
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18
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Varki NM, Varki A. On the apparent rarity of epithelial cancers in captive chimpanzees. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0225. [PMID: 26056369 DOI: 10.1098/rstb.2014.0225] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Malignant neoplasms arising from epithelial cells are called carcinomas. Such cancers are diagnosed in about one in three humans in 'developed' countries, with the most common sites affected being lung, breast, prostate, colon, ovary and pancreas. By contrast, carcinomas are said to be rare in captive chimpanzees, which share more than 99% protein sequence homology with humans (and possibly in other related 'great apes'-bonobos, gorillas and orangutans). Simple ascertainment bias is an unlikely explanation, as these nonhuman hominids are recipients of excellent veterinary care in research facilities and zoos, and are typically subjected to necropsies when they die. In keeping with this notion, benign tumours and cancers that are less common in humans are well documented in this population. In this brief overview, we discuss other possible explanations for the reported rarity of carcinomas in our closest evolutionary cousins, including inadequacy of numbers surveyed, differences in life expectancy, diet, genetic susceptibility, immune responses or their microbiomes, and other potential environmental factors. We conclude that while relative carcinoma risk is a likely difference between humans and chimpanzees (and possibly other 'great apes'), a more systematic survey of available data is required for validation of this claim.
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Affiliation(s)
- Nissi M Varki
- Department of Pathology, Center for Academic Research and Training in Anthropogeny (CARTA), University of California, San Diego, La Jolla, CA 92093, USA
| | - Ajit Varki
- Department of Pathology, Center for Academic Research and Training in Anthropogeny (CARTA), University of California, San Diego, La Jolla, CA 92093, USA Department of Medicine, Center for Academic Research and Training in Anthropogeny (CARTA), University of California, San Diego, La Jolla, CA 92093, USA Department of Cellular and Molecular Medicine, Center for Academic Research and Training in Anthropogeny (CARTA), University of California, San Diego, La Jolla, CA 92093, USA
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19
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Cocirculation of Two env Molecular Variants, of Possible Recombinant Origin, in Gorilla and Chimpanzee Simian Foamy Virus Strains from Central Africa. J Virol 2015; 89:12480-91. [PMID: 26446599 DOI: 10.1128/jvi.01798-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/28/2015] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED Simian foamy virus (SFV) is a ubiquitous retrovirus in nonhuman primates (NHPs) that can be transmitted to humans, mostly through severe bites. In the past few years, our laboratory has identified more than 50 hunters from central Africa infected with zoonotic SFVs. Analysis of the complete sequences of five SFVs obtained from these individuals revealed that env was the most variable gene. Furthermore, recombinant SFV strains, some of which involve sequences in the env gene, were recently identified. Here, we investigated the variability of the env genes of zoonotic SFV strains and searched for possible recombinants. We sequenced the complete env gene or its surface glycoprotein region (SU) from DNA amplified from the blood of (i) a series of 40 individuals from Cameroon or Gabon infected with a gorilla or chimpanzee foamy virus (FV) strain and (ii) 1 gorilla and 3 infected chimpanzees living in the same areas as these hunters. Phylogenetic analyses revealed the existence of two env variants among both the gorilla and chimpanzee FV strains that were present in zoonotic and NHP strains. These variants differ greatly (>30% variability) in a 753-bp-long region located in the receptor-binding domain of SU, whereas the rest of the gene is very conserved. Although the organizations of the Env protein sequences are similar, the potential glycosylation patterns differ between variants. Analysis of recombination suggests that the variants emerged through recombination between different strains, although all parental strains could not be identified. IMPORTANCE SFV infection in humans is a great example of a zoonotic retroviral infection that has not spread among human populations, in contrast to human immunodeficiency viruses (HIVs) and human T-lymphotropic viruses (HTLVs). Recombination was a major mechanism leading to the emergence of HIV. Here, we show that two SFV molecular envelope gene variants circulate among ape populations in Central Africa and that both can be transmitted to humans. These variants differ greatly in the SU region that corresponds to the part of the Env protein in contact with the environment. These variants may have emerged through recombination between SFV strains infecting different NHP species.
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20
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Rua R, Gessain A. Origin, evolution and innate immune control of simian foamy viruses in humans. Curr Opin Virol 2015; 10:47-55. [PMID: 25698621 PMCID: PMC7185842 DOI: 10.1016/j.coviro.2014.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 12/04/2014] [Accepted: 12/10/2014] [Indexed: 12/23/2022]
Abstract
Simian foamy viruses (SFV) are transmitted to humans after contact, mainly bites, with infected monkeys and apes. Contexts of transmission include mainly hunting activities and monkeys’ sympatry. In humans, active immune response probably explains SFV latency in blood and saliva. It is a model of restriction of retroviral emergence after cross-species transmission.
Most viral pathogens that have emerged in humans have originated from various animal species. Emergence is a multistep process involving an initial spill-over of the infectious agent into single individuals and its subsequent dissemination into the human population. Similar to simian immunodeficiency viruses and simian T lymphotropic viruses, simian foamy viruses (SFV) are retroviruses that are widespread among non-human primates and can be transmitted to humans, giving rise to a persistent infection, which seems to be controlled in the case of SFV. In this review, we present current data on the discovery, cross-species transmission, and molecular evolution of SFV in human populations initially infected and thus at risk for zoonotic emergence.
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Affiliation(s)
- Rejane Rua
- Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, 28 Rue du Dr. Roux, 75015 Paris, France; Département de Virologie, Institut Pasteur, 25-28 rue du Dr Roux, 75724 Paris, Cedex 15, France; CNRS, UMR369, 28 Rue du Dr. Roux, F-75015 Paris, France; Université Paris Diderot, Cellule Pasteur, Paris, France.
| | - Antoine Gessain
- Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, 28 Rue du Dr. Roux, 75015 Paris, France; Département de Virologie, Institut Pasteur, 25-28 rue du Dr Roux, 75724 Paris, Cedex 15, France; CNRS, UMR369, 28 Rue du Dr. Roux, F-75015 Paris, France
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21
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In vivo cellular tropism of gorilla simian foamy virus in blood of infected humans. J Virol 2014; 88:13429-35. [PMID: 25210185 DOI: 10.1128/jvi.01801-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
UNLABELLED Simian foamy viruses (SFV) are retroviruses that are widespread among nonhuman primates. SFV can be transmitted to humans, giving rise to a persistent infection. Only a few data are available concerning the distribution of SFV in human blood cells. Here we purified blood mononuclear cell subsets from 11 individuals infected with a Gorilla gorilla SFV strain and quantified SFV DNA levels by quantitative PCR. SFV DNA was detected in the majority of the CD8(+), CD4(+), and CD19(+) lymphocyte samples and rarely in CD14(+) monocyte and CD56(+) NK lymphocyte samples. The median (interquartile range [IQR]) SFV DNA counts were 16.0 (11.0 to 49.8), 11.3 (5.9 to 28.3), and 17.2 (2.0 to 25.2) copies/10(5) cells in CD8(+) T lymphocytes, CD4(+) T lymphocytes, and CD19(+) B lymphocytes, respectively. In the CD4 compartment, SFV DNA was detected in both memory and naive CD4(+) T lymphocytes. SFV DNA levels in CD4(+) T cells were positively correlated with the duration of the infection. Our study shows with a quantitative method that CD8(+), CD4(+), and B lymphocytes are major cellular targets of SFV in the blood of infected humans. IMPORTANCE Investigation of SFV infections in humans is important due to the origin of human immunodeficiency viruses (HIV) and human T cell lymphotropic viruses (HTLV) from cross-species transmission of their simian counterparts to humans. Surprisingly little is known about many aspects of the biology of SFV in infected humans, including quantitative data concerning the cellular targets of SFV in vivo. Here we show that the distribution of SFV DNA among the different leukocyte populations is not homogeneous and that viral load in CD4(+) T lymphocytes is correlated with the duration of infection. These new data will help in understanding the biology of retroviral infections in humans and can be useful in the growing field of SFV-based gene therapy.
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Abstract
Foamy viruses (FV) are complex retroviruses that naturally infect all nonhuman primates (NHP) studied to date. Zoonotic transmission of Old World NHP simian foamy viruses (SFV) has been documented, leading to nonpathogenic persistent infections. To date, there have been no reports concerning zoonotic transmission of New World monkey (NWM) SFV to humans and resulting infection. In this study, we developed a Western blot assay to detect antibodies to NWM SFV, a nested PCR assay to detect NWM SFV DNA, and a β-galactosidase-containing indicator cell line to assay replication of NWM SFV. Using these tools, we analyzed the plasma and blood of 116 primatologists, of whom 69 had reported exposures to NWM. While 8 of the primatologists tested were seropositive for SFV from a NWM, the spider monkey, none had detectable levels of viral DNA in their blood. We found that SFV isolated from three different species of NWM replicated in some, but not all, human cell lines. From our data, we conclude that while humans exposed to NWM SFV produce antibodies, there is no evidence for long-term viral persistence.
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23
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Rua R, Betsem E, Gessain A. Viral latency in blood and saliva of simian foamy virus-infected humans. PLoS One 2013; 8:e77072. [PMID: 24116202 PMCID: PMC3792900 DOI: 10.1371/journal.pone.0077072] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 09/06/2013] [Indexed: 12/31/2022] Open
Abstract
Simian foamy viruses (SFV) are widespread retroviruses among non-human primates (NHP). SFV actively replicate in the oral cavity and can be transmitted to humans through NHP bites, giving rise to a persistent infection. We aimed at studying the natural history of SFV infection in human. We have analyzed viral load and gene expression in 14 hunters from Cameroon previously shown to be infected with a gorilla SFV strain. Viral DNA could be detected by quantitative polymerase chain reaction (q-PCR) targeting the pol-in region, in most samples of peripheral blood mononuclear cells (PBMCs) (7.1 ± 6.0 SFV DNA copies/105 PBMCs) and saliva (2.4 ± 4.3 SFV DNA copies/105 cells) derived from the hunters. However, quantitative real-time reverse-transcription polymerase chain reaction (RT)-qPCR revealed the absence of SFV viral gene expression in both PBMCs and saliva, suggesting that SFV was latent in the human samples. Our study demonstrates that a latent infection can occur in humans and persist for years, both in PBMCs and saliva. Such a scenario may contribute to the putative lack of secondary human-to-human transmissions of SFV.
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Affiliation(s)
- Rejane Rua
- Department of Virology, Unit of Epidemiology and Physiopathology of Oncogenic Viruses, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique (CNRS), Institut Pasteur, Paris, France
- Paris Diderot University, Cellule Pasteur, Paris, France
| | - Edouard Betsem
- Department of Virology, Unit of Epidemiology and Physiopathology of Oncogenic Viruses, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique (CNRS), Institut Pasteur, Paris, France
- Department of Microbiology, Parasitology, Hematology, Faculty of Medicine and Biomedical Sciences, University of Yaounde I, Yaounde, Cameroun
| | - Antoine Gessain
- Department of Virology, Unit of Epidemiology and Physiopathology of Oncogenic Viruses, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique (CNRS), Institut Pasteur, Paris, France
- * E-mail:
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Rethwilm A, Bodem J. Evolution of foamy viruses: the most ancient of all retroviruses. Viruses 2013; 5:2349-74. [PMID: 24072062 PMCID: PMC3814592 DOI: 10.3390/v5102349] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 08/27/2013] [Accepted: 09/18/2013] [Indexed: 12/24/2022] Open
Abstract
Recent evidence indicates that foamy viruses (FVs) are the oldest retroviruses (RVs) that we know and coevolved with their hosts for several hundred million years. This coevolution may have contributed to the non-pathogenicity of FVs, an important factor in development of foamy viral vectors in gene therapy. However, various questions on the molecular evolution of FVs remain still unanswered. The analysis of the spectrum of animal species infected by exogenous FVs or harboring endogenous FV elements in their genome is pivotal. Furthermore, animal studies might reveal important issues, such as the identification of the FV in vivo target cells, which than require a detailed characterization, to resolve the molecular basis of the accuracy with which FVs copy their genome. The issues of the extent of FV viremia and of the nature of the virion genome (RNA vs. DNA) also need to be experimentally addressed.
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Affiliation(s)
- Axel Rethwilm
- Universität Würzburg, Institut für Virologie und Immunbiologie, Versbacher Str.7, Würzburg 97078, Germany.
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25
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Kehl T, Tan J, Materniak M. Non-simian foamy viruses: molecular virology, tropism and prevalence and zoonotic/interspecies transmission. Viruses 2013; 5:2169-209. [PMID: 24064793 PMCID: PMC3798896 DOI: 10.3390/v5092169] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 09/04/2013] [Accepted: 09/05/2013] [Indexed: 12/27/2022] Open
Abstract
Within the field of retrovirus, our knowledge of foamy viruses (FV) is still limited. Their unique replication strategy and mechanism of viral persistency needs further research to gain understanding of the virus-host interactions, especially in the light of the recent findings suggesting their ancient origin and long co-evolution with their nonhuman hosts. Unquestionably, the most studied member is the primate/prototype foamy virus (PFV) which was originally isolated from a human (designated as human foamy virus, HFV), but later identified as chimpanzee origin; phylogenetic analysis clearly places it among other Old World primates. Additionally, the study of non-simian animal FVs can contribute to a deeper understanding of FV-host interactions and development of other animal models. The review aims at highlighting areas of special interest regarding the structure, biology, virus-host interactions and interspecies transmission potential of primate as well as non-primate foamy viruses for gaining new insights into FV biology.
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Affiliation(s)
- Timo Kehl
- German Cancer Research Center, INF242, Heidelberg 69120, Germany
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +49-6221-42-4935; Fax: +49-6221-42-4932
| | - Juan Tan
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; E-Mail:
| | - Magdalena Materniak
- Department of Biochemistry, National Veterinary Research Institute, Partyzantow Ave. 57, Pulawy 24-100, Poland; E-Mail:
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Gessain A, Rua R, Betsem E, Turpin J, Mahieux R. HTLV-3/4 and simian foamy retroviruses in humans: discovery, epidemiology, cross-species transmission and molecular virology. Virology 2013; 435:187-99. [PMID: 23217627 PMCID: PMC7111966 DOI: 10.1016/j.virol.2012.09.035] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 09/28/2012] [Indexed: 12/20/2022]
Abstract
Non-human primates are considered to be likely sources of viruses that can infect humans and thus pose a significant threat to human population. This is well illustrated by some retroviruses, as the simian immunodeficiency viruses and the simian T lymphotropic viruses, which have the ability to cross-species, adapt to a new host and sometimes spread. This leads to a pandemic situation for HIV-1 or an endemic one for HTLV-1. Here, we present the available data on the discovery, epidemiology, cross-species transmission and molecular virology of the recently discovered HTLV-3 and HTLV-4 deltaretroviruses, as well as the simian foamy retroviruses present in different human populations at risk, especially in central African hunters. We discuss also the natural history in humans of these retroviruses of zoonotic origin (magnitude and geographical distribution, possible inter-human transmission). In Central Africa, the increase of the bushmeat trade during the last decades has opened new possibilities for retroviral emergence in humans, especially in immuno-compromised persons.
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Affiliation(s)
- Antoine Gessain
- Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, France, Département de Virologie, Institut Pasteur, 25-28 rue du Dr Roux, 75724 Paris, Cedex 15, France.
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Similar patterns of infection with bovine foamy virus in experimentally inoculated calves and sheep. J Virol 2013; 87:3516-25. [PMID: 23325680 DOI: 10.1128/jvi.02447-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Foamy viruses (FVs) are the least known retroviruses commonly found in primates, cats, horses, and cattle. Although FVs are considered apathogenic, simian and feline FVs have been shown to be associated with some transient health abnormalities in animal models. Currently, data regarding the course of infection with bovine FV (BFV) are not available. In this study, we conducted experimental infections of natural (cattle) and heterologous (sheep) hosts with the BFV(100) isolate and monitored infection patterns in both hosts during the early phase postinoculation as well as after long-term infection. Four calves and six sheep inoculated with BFV(100) showed no signs of pathology but developed persistent infection, as confirmed by virus rescue, consistent detection of BFV-specific antibodies, and presence of viral DNA. In both hosts, antibodies against BFV Gag and Bet appeared early after infection and persisted at high and stable levels while seroreactivity toward Env was consistently detectable only in BFV-infected sheep. Interestingly, the BFV proviral DNA load was highest in lung, spleen, and liver and moderate in leukocytes, while salivary glands contained either low or undetectable DNA loads in calves or sheep, respectively. Additionally, comparison of partial BFV sequences from inoculum and infected animals demonstrated very limited changes after long-term infection in the heterologous host, clearly less than those found in BFV field isolates. The persistence of BFV infection in both hosts suggests full replication competence of the BFV(100) isolate with no requirement of genetic adaptation for productive replication in the authentic and even in a heterologous host.
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