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Abstract
During millions of years, viruses have emerged and reemerged, with imbalance of photogenicity and transmissivity overtime. This letter describes that sometimes the nomenclature is uncertain what may actually happen during retrovirus evolution nowadays. This article discusses a possibility that human T-lymphotropic virus type 2 (HTLV-2) has been processed to incorporate the human genome in the last millions of years. Persistent viruses such as human immunodeficiency virus type 1 (HIV-1), HIV-2, and human T cell lymphotropic type 2 may also have potential of endogenization instead of a cytolytic process in a long time.
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Affiliation(s)
- Jorge Casseb
- Laboratory of Dermatology and Immunodeficiencies, Department of Dermatology, University of São Paulo Medical School, Brazil/Institute of Tropical Medicine of São Paulo, São Paulo, Brazil
| | - Luciano Rodrigo Lopes
- Bioinformatics and Biomedical Data Science Division, Health Informatics Department, Federal University of Sao Paulo-Unifesp, São Paulo, Brazil
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2
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Blyton MDJ, Young PR, Moore BD, Chappell KJ. Geographic patterns of koala retrovirus genetic diversity, endogenization, and subtype distributions. Proc Natl Acad Sci U S A 2022; 119:e2122680119. [PMID: 35943984 DOI: 10.1073/pnas.2122680119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Koala retrovirus (KoRV) subtype A (KoRV-A) is currently in transition from exogenous virus to endogenous viral element, providing an ideal system to elucidate retroviral-host coevolution. We characterized KoRV geography using fecal DNA from 192 samples across 20 populations throughout the koala's range. We reveal an abrupt change in KoRV genetics and incidence at the Victoria/New South Wales state border. In northern koalas, pol gene copies were ubiquitously present at above five per cell, consistent with endogenous KoRV. In southern koalas, pol copies were detected in only 25.8% of koalas and always at copy numbers below one, while the env gene was detected in all animals and in a majority at copy numbers above one per cell. These results suggest that southern koalas carry partial endogenous KoRV-like sequences. Deep sequencing of the env hypervariable region revealed three putatively endogenous KoRV-A sequences in northern koalas and a single, distinct sequence present in all southern koalas. Among northern populations, env sequence diversity decreased with distance from the equator, suggesting infectious KoRV-A invaded the koala genome in northern Australia and then spread south. The exogenous KoRV subtypes (B to K), two novel subtypes, and intermediate subtypes were detected in all northern koala populations but were strikingly absent from all southern animals tested. Apart from KoRV subtype D, these exogenous subtypes were generally locally prevalent but geographically restricted, producing KoRV genetic differentiation among northern populations. This suggests that sporadic evolution and local transmission of the exogenous subtypes have occurred within northern Australia, but this has not extended into animals within southern Australia.
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Hannat S, Pontarotti P, Colson P, Kuhn ML, Galiana E, La Scola B, Aherfi S, Panabières F. Diverse Trajectories Drive the Expression of a Giant Virus in the Oomycete Plant Pathogen Phytophthora parasitica. Front Microbiol 2021; 12:662762. [PMID: 34140938 PMCID: PMC8204020 DOI: 10.3389/fmicb.2021.662762] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/07/2021] [Indexed: 11/13/2022] Open
Abstract
Giant viruses of amoebas, recently classified in the class Megaviricetes, are a group of viruses that can infect major eukaryotic lineages. We previously identified a set of giant virus sequences in the genome of Phytophthora parasitica, an oomycete and a devastating major plant pathogen. How viral insertions shape the structure and evolution of the invaded genomes is unclear, but it is known that the unprecedented functional potential of giant viruses is the result of an intense genetic interplay with their hosts. We previously identified a set of giant virus sequences in the genome of P. parasitica, an oomycete and a devastating major plant pathogen. Here, we show that viral pieces are found in a 550-kb locus and are organized in three main clusters. Viral sequences, namely RNA polymerases I and II and a major capsid protein, were identified, along with orphan sequences, as a hallmark of giant viruses insertions. Mining of public databases and phylogenetic reconstructions suggest an ancient association of oomycetes and giant viruses of amoeba, including faustoviruses, African swine fever virus (ASFV) and pandoraviruses, and that a single viral insertion occurred early in the evolutionary history of oomycetes prior to the Phytophthora–Pythium radiation, estimated at ∼80 million years ago. Functional annotation reveals that the viral insertions are located in a gene sparse region of the Phytophthora genome, characterized by a plethora of transposable elements (TEs), effectors and other genes potentially involved in virulence. Transcription of viral genes was investigated through analysis of RNA-Seq data and qPCR experiments. We show that most viral genes are not expressed, and that a variety of mechanisms, including deletions, TEs insertions and RNA interference may contribute to transcriptional repression. However, a gene coding a truncated copy of RNA polymerase II along a set of neighboring sequences have been shown to be expressed in a wide range of physiological conditions, including responses to stress. These results, which describe for the first time the endogenization of a giant virus in an oomycete, contribute to challenge our view of Phytophthora evolution.
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Affiliation(s)
- Sihem Hannat
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,MEPHI, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Pierre Pontarotti
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,MEPHI, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France.,CNRS SNC5039, Marseille, France
| | - Philippe Colson
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,MEPHI, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France.,Assistance Publique - Hôpitaux de Marseille, Marseille, France
| | - Marie-Line Kuhn
- INRAE, Université Côte d'Azur, CNRS, ISA, Sophia Antipolis, France
| | - Eric Galiana
- INRAE, Université Côte d'Azur, CNRS, ISA, Sophia Antipolis, France
| | - Bernard La Scola
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,MEPHI, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Sarah Aherfi
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,MEPHI, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France.,Assistance Publique - Hôpitaux de Marseille, Marseille, France
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Iida A, Takemae H, Tarigan R, Kobayashi R, Kato H, Shimoda H, Omatsu T, Supratikno, Basri C, Mayasari NLPI, Agungpriyono S, Maeda K, Mizutani T, Hondo E. Viral-derived DNA invasion and individual variation in an Indonesian population of large flying fox Pteropus vampyrus. J Vet Med Sci 2021; 83:1068-1074. [PMID: 33994419 PMCID: PMC8349802 DOI: 10.1292/jvms.21-0115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Here, we performed next-generation sequencing (NGS) on six large flying foxes (Pteropus vampyrus) collected in Indonesia. Seventy-five virus species in the liver tissue of each specimen were listed. Viral homologous sequences in the bat genome were identified from the listed viruses. This finding provides collateral evidence of viral endogenization into the host genome. We found that two of the six specimens bore partial sequences that were homologous to the plant pathogens Geminiviridae and Luteoviridae. These sequences were absent in the P. vampyrus chromosomal sequences. Hence, plant viral homologous sequences were localized to the hepatocytes as extrachromosomal DNA fragments. Therefore, this suggests that the bat is a potential carrier or vector of plant viruses. The present investigation on wild animals offered novel perspectives on viral invasion, variation, and host interaction.
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Affiliation(s)
- Atsuo Iida
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Hitoshi Takemae
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8602, Japan.,Laboratory of Veterinary Microbiology, Cooperative Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Sawai, Fuchu, Tokyo 183-8509, Japan
| | - Ronald Tarigan
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Ryosuke Kobayashi
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Hirokazu Kato
- Biology and Somatology Related Support Section, Nagoya University, Nagoya 464-8602, Japan
| | - Hiroshi Shimoda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Tsutomu Omatsu
- Laboratory of Veterinary Microbiology, Cooperative Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Sawai, Fuchu, Tokyo 183-8509, Japan
| | - Supratikno
- Faculty of Veterinary Medicine Bogor Agricultural University-IPB University, Bogor 16680, Indonesia
| | - Chaerul Basri
- Faculty of Veterinary Medicine Bogor Agricultural University-IPB University, Bogor 16680, Indonesia
| | - Ni Luh Putu Ika Mayasari
- Faculty of Veterinary Medicine Bogor Agricultural University-IPB University, Bogor 16680, Indonesia
| | - Srihadi Agungpriyono
- Faculty of Veterinary Medicine Bogor Agricultural University-IPB University, Bogor 16680, Indonesia
| | - Ken Maeda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi 753-8515, Japan.,Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Tetsuya Mizutani
- Laboratory of Veterinary Microbiology, Cooperative Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Sawai, Fuchu, Tokyo 183-8509, Japan
| | - Eiichi Hondo
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8602, Japan
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Mahé D, Matusali G, Deleage C, Alvarenga RLLS, Satie AP, Pagliuzza A, Mathieu R, Lavoué S, Jégou B, de França LR, Chomont N, Houzet L, Rolland AD, Dejucq-Rainsford N. Potential for Virus Endogenization in Humans through Testicular Germ Cell Infection: the Case of HIV. J Virol 2020; 94:e01145-20. [PMID: 32999017 PMCID: PMC7925188 DOI: 10.1128/jvi.01145-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022] Open
Abstract
Viruses have colonized the germ line of our ancestors on several occasions during evolution, leading to the integration in the human genome of viral sequences from over 30 retroviral groups and a few nonretroviruses. Among the recently emerged viruses infecting humans, several target the testis (e.g., human immunodeficiency virus [HIV], Zika virus, and Ebola virus). Here, we aimed to investigate whether human testicular germ cells (TGCs) can support integration by HIV, a contemporary retrovirus that started to spread in the human population during the last century. We report that albeit alternative receptors enabled HIV-1 binding to TGCs, HIV virions failed to infect TGCs in vitro Nevertheless, exposure of TGCs to infected lymphocytes, naturally present in the testis from HIV+ men, led to HIV-1 entry, integration, and early protein expression. Similarly, cell-associated infection or bypassing viral entry led to HIV-1 integration in a spermatogonial cell line. Using DNAscope, HIV-1 and simian immunodeficiency virus (SIV) DNA were detected within a few TGCs in the testis from one infected patient, one rhesus macaque, and one African green monkey in vivo Molecular landscape analysis revealed that early TGCs were enriched in HIV early cofactors up to integration and had overall low antiviral defenses compared with testicular macrophages and Sertoli cells. In conclusion, our study reveals that TGCs can support the entry and integration of HIV upon cell-associated infection. This could represent a way for this contemporary virus to integrate into our germ line and become endogenous in the future, as happened during human evolution for a number of viruses.IMPORTANCE Viruses have colonized the host germ line on many occasions during evolution to eventually become endogenous. Here, we aimed at investigating whether human testicular germ cells (TGCs) can support such viral invasion by studying HIV interactions with TGCs in vitro Our results indicate that isolated primary TGCs express alternative HIV-1 receptors, allowing virion binding but not entry. However, HIV-1 entered and integrated into TGCs upon cell-associated infection and produced low levels of viral proteins. In vivo, HIV-1 and SIV DNA was detected in a few TGCs. Molecular landscape analysis showed that TGCs have overall weak antiviral defenses. Altogether, our results indicate that human TGCs can support HIV-1 early replication, including integration, suggesting potential for endogenization in future generations.
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Affiliation(s)
- Dominique Mahé
- Université Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - Giulia Matusali
- Université Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - Claire Deleage
- Université Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - Raquel L L S Alvarenga
- Laboratory of Cellular Biology, Department of Morphology, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Anne-Pascale Satie
- Université Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - Amélie Pagliuzza
- Department of Microbiology, Infectiology and Immunology, Faculty of Medecine, Université de Montréal, and Centre de Recherche du CHUM, Montréal, Quebec, Canada
| | - Romain Mathieu
- Centre Hospitalier Universitaire de Pontchaillou, Service Urologie, Rennes, France
| | - Sylvain Lavoué
- Centre Hospitalier Universitaire de Pontchaillou, Centre de Coordination des Prélèvements, Rennes, France
| | - Bernard Jégou
- Université Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - Luiz R de França
- Laboratory of Cellular Biology, Department of Morphology, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Nicolas Chomont
- Department of Microbiology, Infectiology and Immunology, Faculty of Medecine, Université de Montréal, and Centre de Recherche du CHUM, Montréal, Quebec, Canada
| | - Laurent Houzet
- Université Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - Antoine D Rolland
- Université Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - Nathalie Dejucq-Rainsford
- Université Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
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Colson P, Ravaux I, Tamalet C, Glazunova O, Baptiste E, Chabriere E, Wiedemann A, Lacabaratz C, Chefrour M, Picard C, Stein A, Levy Y, Raoult D. HIV infection en route to endogenization: two cases. Clin Microbiol Infect 2014; 20:1280-8. [PMID: 25366539 PMCID: PMC4360783 DOI: 10.1111/1469-0691.12807] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 10/28/2014] [Accepted: 10/28/2014] [Indexed: 12/30/2022]
Abstract
The long-term spontaneous evolution of humans and the human immunodeficiency virus (HIV) is not well characterized; many vertebrate species, including humans, exhibit remnants of other retroviruses in their genomes that question such possible endogenization of HIV. We investigated two HIV-infected patients with no HIV-related disease and no detection with routine tests of plasma HIV RNA or cell-associated HIV DNA. We used Sanger and deep sequencing to retrieve HIV DNA sequences integrated in the human genome and tested the host humoral and cellular immune responses. We noticed that viruses from both patients were inactivated by the high prevalence of the transformation of tryptophan codons into stop codons (25% overall (3-100% per gene) and 24% overall (0-50% per gene)). In contrast, the humoral and/or cellular responses were strong for one patient and moderate for the other, indicating that a productive infection occurred at one stage of the infection. We speculate that the stimulation of APOBEC, the enzyme group that exchanges G for A in viral nucleic acids and is usually inhibited by the HIV protein Vif, has been amplified and made effective from the initial stage of the infection. Furthermore, we propose that a cure for HIV may occur through HIV endogenization in humans, as observed for many other retroviruses in mammals, rather than clearance of all traces of HIV from human cells, which defines viral eradication.
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Affiliation(s)
- P Colson
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1095, Aix-Marseille Université, Marseille, France; Fondation Institut Hospitalo-Universitaire (IHU) MéiterranéInfection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France
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Touret F, Guiguen F, Terzian C. Un rétrovirus endogène actif et infectieux : le cas gypsy chez Drosophila melanogaster. Virologie (Montrouge) 2012; 16:381-9. [PMID: 31910556 DOI: 10.1684/vir.2012.0471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Retroviruses are viruses that have the ability to synthesize a DNA copy from their RNA genome and to integrate it in the host genome. Sequencing of eukaryotic genomes has revealed the presence of many of these endogenous retrovirus sequences. The mechanisms by which these sequences colonize the genome are still unknown, and the endogenous retrovirus gypsy of Drosophila melanogaster (D. melanogaster) is a powerful experimental model deciphering this process. Gypsy is expressed in gonadic somatic cells and transferred into the oocyte. This critical step is the first one of the endogenization process. Moreover, gypsy has been shown to possess infectious properties, probably due to its envelope gene that is suspected to have been acquired from baculovirus. So far, gypsy is a unique model to understand endogenization of retroviruses.
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