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Wang X, Cui J. Discovery of an endogenous foamy virus in primitive ruminant chevrotains. Microbiol Spectr 2023; 11:e0209023. [PMID: 37581429 PMCID: PMC10581153 DOI: 10.1128/spectrum.02090-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/28/2023] [Indexed: 08/16/2023] Open
Abstract
Foamy viruses (FVs) are a class of complex retroviruses that could lead to persistent infections in specific species. FVs have two evolutionary characteristics: the first is co-evolution with the host, and the second is difficulty going through the endogenization process. To date, in mammals, only a few species (aye-aye, sloths, and cape golden mole) have been found to have endogenous forms of FVs. In this study, we identified a novel endogenous FV named TraEFV in the genomes of two species of even-toed ungulate chevrotain (genus Tragulus, family Tragulidae) known as mouse-deer. Phylogenetic analysis clustered TraEFVs with an exogenous FV isolated from feline but not with those isolated from cow and horse, and such inconsistent virus-host relationships reflect their complex evolutionary history. Interestingly, TraEFVs could be divided into two lineages, suggesting that TraEFV invaded these hosts at least twice during ancient times. Finally, the molecular clock estimates that TraEFV is approximately 20 million years old, suggesting its ancient nature. Our findings enrich the host taxonomy of spumaretroviruses. IMPORTANCE Foamy viruses (FV) are complex retroviruses that generally codiverge with their hosts. We identified a novel endogenous FV in the genomes of two mouse-deer species, the first endogenous FV found in Artiodactyla. The phylogenetic inconsistency of viruses and hosts suggested that the viruses might have emerged from cross-species transmission in the past. These findings indicate that ancient FVs may have had a wider range of hosts that remain to be expanded.
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Affiliation(s)
- Xiaojing Wang
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Cui
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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2
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Comparison of a Genotype 1 and a Genotype 2 Macaque Foamy Virus env Gene Indicates Distinct Infectivity and Cell-Cell Fusion but Similar Tropism and Restriction of Cell Entry by Interferon-Induced Transmembrane Proteins. Viruses 2023; 15:v15020262. [PMID: 36851478 PMCID: PMC9960098 DOI: 10.3390/v15020262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Foamy viruses (FVs) are naturally found in many different animals and also in primates with the notable exception of humans, but zoonotic infections are common. In several species, two different envelope (env) gene sequence clades or genotypes exist. We constructed a simian FV (SFV) clone containing a reporter gene cassette. In this background, we compared the env genes of the SFVmmu-DPZ9524 (genotype 1) and of the SFVmmu_R289hybAGM (genotype 2) isolates. SFVmmu_R289hybAGM env-driven infection was largely resistant to neutralization by SFVmmu-DPZ9524-neutralizing sera. While SFVmmu_R289hybAGM env consistently effected higher infectivity and cell-cell fusion, we found no differences in the cell tropism conferred by either env across a range of different cells. Infection by both viruses was weakly and non-significantly enhanced by simultaneous knockout of interferon-induced transmembrane proteins (IFITMs) 1, 2, and 3 in A549 cells, irrespective of prior interferon stimulation. Infection was modestly reduced by recombinant overexpression of IFITM3, suggesting that the SFV entry step might be weakly restricted by IFITM3 under some conditions. Overall, our results suggest that the different env gene clades in macaque foamy viruses induce genotype-specific neutralizing antibodies without exhibiting overt differences in cell tropism, but individual env genes may differ significantly with regard to fitness.
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3
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Multiple Infiltration and Cross-Species Transmission of Foamy Viruses across the Paleozoic to the Cenozoic Era. J Virol 2021; 95:e0048421. [PMID: 33910951 DOI: 10.1128/jvi.00484-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Foamy viruses (FVs) are complex retroviruses that can infect humans and other animals. In this study, by integrating transcriptomic and genomic data, we discovered 412 FVs from 6 lineages in amphibians, which significantly increased the known set of FVs in amphibians. Among these lineages, salamander FVs maintained a coevolutionary pattern with their hosts that could be dated back to the Paleozoic era, while in contrast, frog FVs were much more likely acquired from cross-species (class-level) transmission in the Cenozoic era. In addition, we found that three distinct FV lineages had integrated into the genome of a salamander. Unexpectedly, we identified a lineage of endogenous FVs in caecilians that expressed all complete major genes, demonstrating the potential existence of an exogenous form of FV outside of mammals. Our discovery of rare phenomena in amphibian FVs has significantly increased our understanding of the macroevolution of the complex retrovirus. IMPORTANCE Foamy viruses (FVs) represent, more so than other viruses, the best model of coevolution between a virus and a host. This study represents the largest investigation so far of amphibian FVs and reveals 412 FVs of 6 distinct lineages from three major orders of amphibians. Besides a coevolutionary pattern, cross-species and repeated infections were also observed during the evolution of amphibian FVs. Remarkably, expressed FVs including a potential exogenous form were discovered, suggesting that active FVs might be underestimated in nature. These findings revealed that the multiple origins and complex evolution of amphibian FVs started from the Paleozoic era.
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Bergez M, Weber J, Riess M, Erdbeer A, Seifried J, Stanke N, Munz C, Hornung V, König R, Lindemann D. Insights into Innate Sensing of Prototype Foamy Viruses in Myeloid Cells. Viruses 2019; 11:v11121095. [PMID: 31779173 PMCID: PMC6950106 DOI: 10.3390/v11121095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 01/18/2023] Open
Abstract
Foamy viruses (FVs) belong to the Spumaretrovirinae subfamily of retroviruses and are characterized by unique features in their replication strategy. This includes a reverse transcription (RTr) step of the packaged RNA genome late in replication, resulting in the release of particles with a fraction of them already containing an infectious viral DNA (vDNA) genome. Little is known about the immune responses against FVs in their hosts, which control infection and may be responsible for their apparent apathogenic nature. We studied the interaction of FVs with the innate immune system in myeloid cells, and characterized the viral pathogen-associated molecular patterns (PAMPs) and the cellular pattern recognition receptors and sensing pathways involved. Upon cytoplasmic access, full-length but not minimal vector genome containing FVs with active reverse transcriptase, induced an efficient innate immune response in various myeloid cells. It was dependent on cellular cGAS and STING and largely unaffected by RTr inhibition during viral entry. This suggests that RTr products, which are generated during FV morphogenesis in infected cells, and are therefore already present in FV particles taken up by immune cells, are the main PAMPs of FVs with full-length genomes sensed in a cGAS and STING-dependent manner by the innate immune system in host cells of the myeloid lineage.
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Affiliation(s)
- Maïwenn Bergez
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany; (M.B.); (M.R.); (J.S.)
| | - Jakob Weber
- Institute of Virology, Medical Faculty “Carl Gustav Carus”, Technische Universität Dresden, 01307 Dresden, Germany; (J.W.); (A.E.); (N.S.); (C.M.)
- CRTD/DFG-Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
| | - Maximilian Riess
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany; (M.B.); (M.R.); (J.S.)
| | - Alexander Erdbeer
- Institute of Virology, Medical Faculty “Carl Gustav Carus”, Technische Universität Dresden, 01307 Dresden, Germany; (J.W.); (A.E.); (N.S.); (C.M.)
- CRTD/DFG-Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
| | - Janna Seifried
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany; (M.B.); (M.R.); (J.S.)
| | - Nicole Stanke
- Institute of Virology, Medical Faculty “Carl Gustav Carus”, Technische Universität Dresden, 01307 Dresden, Germany; (J.W.); (A.E.); (N.S.); (C.M.)
- CRTD/DFG-Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
| | - Clara Munz
- Institute of Virology, Medical Faculty “Carl Gustav Carus”, Technische Universität Dresden, 01307 Dresden, Germany; (J.W.); (A.E.); (N.S.); (C.M.)
- CRTD/DFG-Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
| | - Veit Hornung
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 München, Germany;
| | - Renate König
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany; (M.B.); (M.R.); (J.S.)
- German Center for Infection Research (DZIF), 63225 Langen, Germany
- Immunity and Pathogenesis Program, SBP Medical Discovery Institute, La Jolla, CA 92037, USA
- Correspondence: (R.K.); (D.L.); Tel.: +49-6103-77-4019 (R.K.); +49-351-458-6210 (D.L.)
| | - Dirk Lindemann
- Institute of Virology, Medical Faculty “Carl Gustav Carus”, Technische Universität Dresden, 01307 Dresden, Germany; (J.W.); (A.E.); (N.S.); (C.M.)
- CRTD/DFG-Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
- Correspondence: (R.K.); (D.L.); Tel.: +49-6103-77-4019 (R.K.); +49-351-458-6210 (D.L.)
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Chen Y, Wei X, Zhang G, Holmes EC, Cui J. Identification and evolution of avian endogenous foamy viruses. Virus Evol 2019; 5:vez049. [PMID: 31777663 PMCID: PMC6875641 DOI: 10.1093/ve/vez049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A history of long-term co-divergence means that foamy viruses (family Retroviridae) provide an ideal framework to understanding virus-host evolution over extended time periods. Endogenous foamy viruses (EndFVs) are rare, and to date have only been described in a limited number of mammals, amphibians, reptiles and fish genomes. By screening 414 avian genomes we identified EndFVs in two bird species: the Maguari Stork (Ciconia maguari) and the Oriental Stork (Ciconia boyciana). Analyses of phylogenetic relationships, genome structures and flanking sequences revealed a single origin of EndFVs in Ciconia species. In addition, the marked incongruence between the virus and host phylogenies suggested that this integration event occurred independently in birds. In sum, by providing evidence that birds can be infected with foamy viruses, we fill the last major gap in the taxonomic distribution of foamy viruses and their animal hosts.
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Affiliation(s)
- Yicong Chen
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoman Wei
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Jie Cui
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
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Simian Foamy Viruses in Central and South America: A New World of Discovery. Viruses 2019; 11:v11100967. [PMID: 31635161 PMCID: PMC6832937 DOI: 10.3390/v11100967] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 12/16/2022] Open
Abstract
Foamy viruses (FVs) are the only exogenous retrovirus to date known to infect neotropical primates (NPs). In the last decade, an increasing number of strains have been completely or partially sequenced, and molecular evolution analyses have identified an ancient co-speciation with their hosts. In this review, the improvement of diagnostic techniques that allowed the determination of a more accurate prevalence of simian FVs (SFVs) in captive and free-living NPs is discussed. Determination of DNA viral load in American primates indicates that oral tissues are the viral replicative site and that buccal swab collection can be an alternative to diagnose SFV infection in NPs. Finally, the transmission potential of NP SFVs to primate workers in zoos and primate centers of the Americas is examined.
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Aiewsakun P, Simmonds P, Katzourakis A. The First Co-Opted Endogenous Foamy Viruses and the Evolutionary History of Reptilian Foamy Viruses. Viruses 2019; 11:v11070641. [PMID: 31336856 PMCID: PMC6669660 DOI: 10.3390/v11070641] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 12/17/2022] Open
Abstract
A recent study reported the discovery of an endogenous reptilian foamy virus (FV), termed ERV-Spuma-Spu, found in the genome of tuatara. Here, we report two novel reptilian foamy viruses also identified as endogenous FVs (EFVs) in the genomes of panther gecko (ERV-Spuma-Ppi) and Schlegel’s Japanese gecko (ERV-Spuma-Gja). Their presence indicates that FVs are capable of infecting reptiles in addition to mammals, amphibians, and fish. Numerous copies of full length ERV-Spuma-Spu elements were found in the tuatara genome littered with in-frame stop codons and transposable elements, suggesting that they are indeed endogenous and are not functional. ERV-Spuma-Ppi and ERV-Spuma-Gja, on the other hand, consist solely of a foamy virus-like env gene. Examination of host flanking sequences revealed that they are orthologous, and despite being more than 96 million years old, their env reading frames are fully coding competent with evidence for strong purifying selection to maintain expression and for them likely being transcriptionally active. These make them the oldest EFVs discovered thus far and the first documented EFVs that may have been co-opted for potential cellular functions. Phylogenetic analyses revealed a complex virus–host co-evolutionary history and cross-species transmission routes of ancient FVs.
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Affiliation(s)
- Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK.
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8
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Wei X, Chen Y, Duan G, Holmes EC, Cui J. A reptilian endogenous foamy virus sheds light on the early evolution of retroviruses. Virus Evol 2019; 5:vez001. [PMID: 30838130 PMCID: PMC6393741 DOI: 10.1093/ve/vez001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Endogenous retroviruses (ERVs) represent host genomic 'fossils' of ancient viruses. Foamy viruses, including those that form endogenous copies, provide strong evidence for virus-host co-divergence across the vertebrate phylogeny. Endogenous foamy viruses (EFVs) have previously been discovered in mammals, amphibians, and fish. Here we report a novel endogenous foamy virus, termed ERV-Spuma-Spu, in genome of the tuatara (Sphenodon punctatus), an endangered reptile species endemic to New Zealand. Phylogenetic analyses revealed that foamy viruses have likely co-diverged with their hosts over many millions of years. The discovery of ERV-Spuma-Spu fills a major gap in the fossil record of foamy viruses and provides important insights into the early evolution of retroviruses.
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Affiliation(s)
- Xiaoman Wei
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yicong Chen
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guangqian Duan
- University of Chinese Academy of Sciences, Beijing, China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Jie Cui
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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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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Marine origin of retroviruses in the early Palaeozoic Era. Nat Commun 2017; 8:13954. [PMID: 28071651 PMCID: PMC5512871 DOI: 10.1038/ncomms13954] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 11/16/2016] [Indexed: 02/03/2023] Open
Abstract
Very little is known about the ancient origin of retroviruses, but owing to the discovery of their ancient endogenous viral counterparts, their early history is beginning to unfold. Here we report 36 lineages of basal amphibian and fish foamy-like endogenous retroviruses (FLERVs). Phylogenetic analyses reveal that ray-finned fish FLERVs exhibit an overall co-speciation pattern with their hosts, while amphibian FLERVs might not. We also observe several possible ancient viral cross-class transmissions, involving lobe-finned fish, shark and frog FLERVs. Sequence examination and analyses reveal two major lineages of ray-finned fish FLERVs, one of which had gained two novel accessory genes within their extraordinarily large genomes. Our phylogenetic analyses suggest that this major retroviral lineage, and therefore retroviruses as a whole, have an ancient marine origin and originated together with, if not before, their jawed vertebrate hosts >450 million years ago in the Ordovician period, early Palaeozoic Era. Endogenous retroviruses are viruses that have become integrated into the genomes of their hosts. Here, the authors investigate the evolution of foamy-like endogenous retroviruses, and, by taking into account the temporal dynamics of the rate of viral evolution, suggest that retroviruses arose at least 450 million years ago in marine vertebrates.
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11
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Abstract
Recent discoveries indicate that the foamy virus (FV) (Spumavirus) ancestor may have been among the first retroviruses to appear during the evolution of vertebrates, demonstrated by foamy endogenous retroviruses present within deeply divergent hosts including mammals, coelacanth, and ray-finned fish. If they indeed existed in ancient marine environments hundreds of millions of years ago, significant undiscovered diversity of foamy-like endogenous retroviruses might be present in fish genomes. By screening published genomes and by applying PCR-based assays of preserved tissues, we discovered 23 novel foamy-like elements in teleost hosts. These viruses form a robust, reciprocally monophyletic sister clade with sarcopterygian host FV, with class III mammal endogenous retroviruses being the sister group to both clades. Some of these foamy-like retroviruses have larger genomes than any known retrovirus, exogenous or endogenous, due to unusually long gag-like genes and numerous accessory genes. The presence of genetic features conserved between mammalian FV and these novel retroviruses attests to a foamy-like replication biology conserved for hundreds of millions of years. We estimate that some of these viruses integrated recently into host genomes; exogenous forms of these viruses may still circulate.
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Affiliation(s)
- Ryan Ruboyianes
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E Lowell St., Tucson, AZ 85721, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E Lowell St., Tucson, AZ 85721, USA
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Muniz CP, Jia H, Shankar A, Troncoso LL, Augusto AM, Farias E, Pissinatti A, Fedullo LP, Santos AF, Soares MA, Switzer WM. An expanded search for simian foamy viruses (SFV) in Brazilian New World primates identifies novel SFV lineages and host age-related infections. Retrovirology 2015; 12:94. [PMID: 26576961 PMCID: PMC4650395 DOI: 10.1186/s12977-015-0217-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 10/20/2015] [Indexed: 11/19/2022] Open
Abstract
Background While simian foamy viruses have co-evolved with their primate hosts for millennia, most scientific studies have focused on understanding infection in Old World primates with little knowledge available on the epidemiology and natural history of SFV infection in New World primates (NWPs). To better understand the geographic and species distribution and evolutionary history of SFV in NWPs we extend our previous studies in Brazil by screening 15 genera consisting of 29 NWP species (140 monkeys total), including five genera (Brachyteles, Cacajao, Callimico, Mico, and Pithecia) not previously analyzed. Monkey blood specimens were tested using a combination of both serology and PCR to more accurately estimate prevalence and investigate transmission patterns. Sequences were phylogenetically analyzed to infer SFV and host evolutionary histories. Results The overall serologic and molecular prevalences were 42.8 and 33.6 %, respectively, with a combined assay prevalence of 55.8 %. Discordant serology and PCR results were observed for 28.5 % of the samples, indicating that both methods are currently necessary for estimating NWP SFV prevalence. SFV prevalence in sexually mature NWPs with a positive result in any of the WB or PCR assays was 51/107 (47.7 %) compared to 20/33 (61 %) for immature animals. Epidemiological analyses revealed an increase in SFV prevalence with age in captive Cebus monkeys. Phylogenetic analysis identified novel SFVs in Cacajao,Leontopithecus, and Chiropotes species that had 6–37 % nucleotide divergence to other NWP SFV. Comparison of host and SFV phylogenies showed an overall cospeciation evolutionary history with rare ancient and contemporaneous host-switching for Saimiri and Leontopithecus and Cebus xanthosternos, respectively. Conclusions We identified novel SFV in four neotropical monkey genera in Brazil and demonstrate that SFV prevalence increases with age in Cebus monkeys. Importantly, our test results suggest that both molecular and serological screening are currently required to accurately determine infection with NWP SFV. Our study significantly expands knowledge of the epidemiology and natural history of NWP SFVs. The tools and information provided in our study will facilitate further investigation of SFV in NWPs and the potential for zoonotic infection with these viruses.
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Affiliation(s)
- Cláudia P Muniz
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil. .,Laboratory Branch, Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd., MS G45, Atlanta, 30329, USA.
| | - Hongwei Jia
- Laboratory Branch, Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd., MS G45, Atlanta, 30329, USA.
| | - Anupama Shankar
- Laboratory Branch, Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd., MS G45, Atlanta, 30329, USA.
| | - Lian L Troncoso
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | | | - Elisabete Farias
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | | | | | - André F Santos
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Marcelo A Soares
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil. .,Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd., MS G45, Atlanta, 30329, USA.
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Troncoso LL, Muniz CP, Siqueira JD, Curty G, Schrago CG, Augusto A, Fedullo L, Soares MA, Santos AF. Characterization and comparative analysis of a simian foamy virus complete genome isolated from Brazilian capuchin monkeys. Virus Res 2015; 208:1-6. [DOI: 10.1016/j.virusres.2015.05.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 05/25/2015] [Indexed: 12/28/2022]
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Aiewsakun P, Katzourakis A. Time dependency of foamy virus evolutionary rate estimates. BMC Evol Biol 2015; 15:119. [PMID: 26111824 PMCID: PMC4480597 DOI: 10.1186/s12862-015-0408-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 06/02/2015] [Indexed: 12/19/2022] Open
Abstract
Background It appears that substitution rate estimates co-vary very strongly with their timescale of measurement; the shorter the timescale, the higher the estimated value. Foamy viruses have a long history of co-speciation with their hosts, and one of the lowest estimated rates of evolution among viruses. However, when their rate of evolution is estimated over short timescales, it is more reminiscent of the rapid rates seen in other RNA viruses. This discrepancy between their short-term and long-term rates could be explained by the time-dependency of substitution rate estimates. Several empirical models have been proposed and used to correct for the time-dependent rate phenomenon (TDRP), such as a vertically-translated exponential rate decay model and a power-law rate decay model. Nevertheless, at present, it is still unclear which model best describes the rate dynamics. Here, we use foamy viruses as a case study to empirically describe the phenomenon and to determine how to correct rate estimates for its effects. Four empirical models were investigated: (i) a vertically-translated exponential rate decay model, (ii) a simple exponential rate decay model, (iii) a vertically-translated power-law rate decay model, and (iv) a simple power-law rate decay model. Results Our results suggest that the TDRP is likely responsible for the large discrepancy observed in foamy virus short-term and long-term rate estimates, and the simple power-law rate decay model is the best model for inferring evolutionary timescales. Furthermore, we demonstrated that, within the Bayesian phylogenetic framework, currently available molecular clocks can severely bias evolutionary date estimates, indicating that they are inadequate for correcting for the TDRP. Our analyses also suggest that different viral lineages may have different TDRP dynamics, and this may bias date estimates if it is unaccounted for. Conclusions As evolutionary rate estimates are dependent on their measurement timescales, their values must be used and interpreted under the context of the timescale of rate estimation. Extrapolating rate estimates across large timescales for evolutionary inferences can severely bias the outcomes. Given that the TDRP is widespread in nature but has been noted only recently the estimated timescales of many viruses may need to be reconsidered and re-estimated. Our models could be used as a guideline to further improve current phylogenetic inference tools. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0408-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pakorn Aiewsakun
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
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Tenth International Foamy Virus Conference 2014--achievements and perspectives. Viruses 2015; 7:1651-66. [PMID: 25835535 PMCID: PMC4411671 DOI: 10.3390/v7041651] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 01/10/2023] Open
Abstract
For the past two decades, scientists from around the world, working on different aspects of foamy virus (FV) research, have gathered in different research institutions almost every two years to present their recent results in formal talks, to discuss their ongoing studies informally, and to initiate fruitful collaborations. In this report we review the 2014 anniversary conference to share the meeting summary with the virology community and hope to arouse interest by other researchers to join this exciting field. The topics covered included epidemiology, virus molecular biology, and immunology of FV infection in non-human primates, cattle, and humans with zoonotic FV infections, as well as recent findings on endogenous FVs. Several topics focused on virus replication and interactions between viral and cellular proteins. Use of FV in biomedical research was highlighted with presentations on using FV vectors for gene therapy and FV proteins as scaffold for vaccine antigen presentation. On behalf of the FV community, this report also includes a short tribute to commemorate Prof. Axel Rethwilm, one of the leading experts in the field of retrovirology and foamy viruses, who passed away 29 July 2014.
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