|
1
|
Chung HC, Kim SJ, Hwang SJ, Jeon YS, Song MS, Ko SH, Lee J, Choi Y, Chung CU, Lee JM. Identification and characterization of recent retrovirus in Rhinolophus ferrumequinum bats. Microbiol Spectr 2024; 12:e0432323. [PMID: 38687078 DOI: 10.1128/spectrum.04323-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 03/25/2024] [Indexed: 05/02/2024] Open
Abstract
An investigation into retrovirus was conducted in six species of bats (Myotis aurascens, Myotis petax, Myotis macrodactylus, Miniopterus fuliginosus, Rhinolophus ferrumequinum, and Pipistrellus abramus) inhabiting South Korea. Exogenous retroviruses (XRVs) were detected in the tissue samples of R. ferrumequinum individuals by PCR assay. Proviruses were identified in all tissue samples through viral quantification using a digital PCR assay per organ (lung, intestine, heart, brain, wing, kidney, and liver), with viral loads varying greatly between each organ. In phylogenetic analysis based on the whole genome, the Korean bat retroviruses and the R. ferrumequinum retrovirus (RfRV) strain formed a new clade distinct from the Gammaretrovirus clade. The phylogenetic results determined these viruses to be RfRV-like viruses. In the Simplot comparison, Korean RfRV-like viruses exhibited relatively strong fluctuated patterns in the latter part of the envelope gene area compared to other gene areas. Several point mutations within this region (6,878-7,774 bp) of these viruses were observed compared to the RfRV sequence. One Korean RfRV-like virus (named Y4b strain) was successfully recovered in the Raw 264.7 cell line, and virus particles replicated in the cells were confirmed by transmission electron microscopy. RfRVs (or RfRV-like viruses) have been spreading since their first discovery in 2012, and the Korean RfRV-like viruses were assumed to be XRVs that evolved from RfRV.IMPORTANCER. ferrumequinum retrovirus (RfRV)-like viruses were identified in greater horseshoe bats in South Korea. These RfRV-like viruses were considered exogenous retroviruses (XRVs) that emerged from RfRV. Varying amounts of provirus detected in different organs suggest ongoing viral activity, replication, and de novo integration in certain organs. Additionally, the successful recovery of the virus in the Raw 264.7 cell line provides strong evidence supporting their status as XRVs. These viruses have now been identified in South Korea and, more recently, in Kenya since RfRV was discovered in China in 2012, indicating that RfRVs (or RfRV-like viruses) have spread worldwide.
Collapse
Affiliation(s)
- Hee Chun Chung
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
| | - Sung Jae Kim
- Department of Companion Animal Health, Kyungbok University, Namyangju, South Korea
| | - Su Jin Hwang
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Young Shin Jeon
- Department of Life Science, Dongguk University, Gyeongju, South Korea
| | - Min Sik Song
- Bio Institute, OPTOLANE Technologies Inc, Seongnam-si, Gyeonggi-do, South Korea
| | - Si Hwan Ko
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
| | - Jasper Lee
- Department of Microbiology, California University of Science and Medicine, Colton, California, USA
| | - Yoona Choi
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Chul Un Chung
- Department of Life Science, Dongguk University, Gyeongju, South Korea
| | - Jae Myun Lee
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| |
Collapse
|
|
2
|
Hufsky F, Abecasis A, Agudelo-Romero P, Bletsa M, Brown K, Claus C, Deinhardt-Emmer S, Deng L, Friedel CC, Gismondi MI, Kostaki EG, Kühnert D, Kulkarni-Kale U, Metzner KJ, Meyer IM, Miozzi L, Nishimura L, Paraskevopoulou S, Pérez-Cataluña A, Rahlff J, Thomson E, Tumescheit C, van der Hoek L, Van Espen L, Vandamme AM, Zaheri M, Zuckerman N, Marz M. Women in the European Virus Bioinformatics Center. Viruses 2022; 14:1522. [PMID: 35891501 PMCID: PMC9319252 DOI: 10.3390/v14071522] [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: 06/16/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 02/01/2023] Open
Abstract
Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.
Collapse
Affiliation(s)
- Franziska Hufsky
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Ana Abecasis
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, New University of Lisbon, 1349-008 Lisbon, Portugal
| | - Patricia Agudelo-Romero
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Nedlands, WA 6009, Australia
| | - Magda Bletsa
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Katherine Brown
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Claudia Claus
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Medical Microbiology and Virology, Medical Faculty, Leipzig University, 04103 Leipzig, Germany
| | - Stefanie Deinhardt-Emmer
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Medical Microbiology, Jena University Hospital, 07747 Jena, Germany
| | - Li Deng
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Virology, Helmholtz Centre Munich-German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Caroline C. Friedel
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Informatics, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - María Inés Gismondi
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Agrobiotechnology and Molecular Biology (IABIMO), National Institute for Agriculture Technology (INTA), National Research Council (CONICET), Hurlingham B1686IGC, Argentina
- Department of Basic Sciences, National University of Luján, Luján B6702MZP, Argentina
| | - Evangelia Georgia Kostaki
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Denise Kühnert
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Urmila Kulkarni-Kale
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India
| | - Karin J. Metzner
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Irmtraud M. Meyer
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
- Faculty of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
| | - Laura Miozzi
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute for Sustainable Plant Protection, National Research Council of Italy, 10135 Torino, Italy
| | - Luca Nishimura
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Sofia Paraskevopoulou
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Methods Development and Research Infrastructure, Bioinformatics and Systems Biology, Robert Koch Institute, 13353 Berlin, Germany
| | - Alba Pérez-Cataluña
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Janina Rahlff
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linneaus University, 391 82 Kalmar, Sweden
| | - Emma Thomson
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow G51 4TF, UK
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Charlotte Tumescheit
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Lia van der Hoek
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1012 WX Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, 1100 DD Amsterdam, The Netherlands
| | - Lore Van Espen
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Anne-Mieke Vandamme
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal
- Institute for the Future, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Maryam Zaheri
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Neta Zuckerman
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Ramat Gan 52621, Israel
| | - Manja Marz
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
| |
Collapse
|
|
3
|
Verma A, Sharda S, Rathi B, Somvanshi P, Pandey BD. Elucidating potential molecular signatures through host-microbe interactions for reactive arthritis and inflammatory bowel disease using combinatorial approach. Sci Rep 2020; 10:15131. [PMID: 32934294 PMCID: PMC7492238 DOI: 10.1038/s41598-020-71674-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 07/06/2020] [Indexed: 02/08/2023] Open
Abstract
Reactive Arthritis (ReA), a rare seronegative inflammatory arthritis, lacks exquisite classification under rheumatic autoimmunity. ReA is solely established using differential clinical diagnosis of the patient cohorts, where pathogenic triggers linked to enteric and urogenital microorganisms e.g. Salmonella, Shigella, Yersinia, Campylobacter, Chlamydia have been reported. Inflammatory Bowel Disease (IBD), an idiopathic enteric disorder co-evolved and attuned to present gut microbiome dysbiosis, can be correlated to the genesis of enteropathic arthropathies like ReA. Gut microbes symbolically modulate immune system homeostasis and are elementary for varied disease patterns in autoimmune disorders. The gut-microbiota axis structured on the core host-microbe interactions execute an imperative role in discerning the etiopathogenesis of ReA and IBD. This study predicts the molecular signatures for ReA with co-evolved IBD through the enveloped host-microbe interactions and microbe-microbe 'interspecies communication', using synonymous gene expression data for selective microbes. We have utilized a combinatorial approach that have concomitant in-silico work-pipeline and experimental validation to corroborate the findings. In-silico analysis involving text mining, metabolic network reconstruction, simulation, filtering, host-microbe interaction, docking and molecular mimicry studies results in robust drug target/s and biomarker/s for co-evolved IBD and ReA. Cross validation of the target/s or biomarker/s was done by targeted gene expression analysis following a non-probabilistic convenience sampling. Studies were performed to substantiate the host-microbe disease network consisting of protein-marker-symptom/disease-pathway-drug associations resulting in possible identification of vital drug targets, biomarkers, pathways and inhibitors for IBD and ReA.Our study identified Na(+)/H(+) anti-porter (NHAA) and Kynureninase (KYNU) to be robust early and essential host-microbe interacting targets for IBD co-evolved ReA. Other vital host-microbe interacting genes, proteins, pathways and drugs include Adenosine Deaminase (ADA), Superoxide Dismutase 2 (SOD2), Catalase (CAT), Angiotensin I Converting Enzyme (ACE), carbon metabolism (folate biosynthesis) and methotrexate. These can serve as potential prognostic/theranostic biomarkers and signatures that can be extrapolated to stratify ReA and related autoimmunity patient cohorts for further pilot studies.
Collapse
Affiliation(s)
- Anukriti Verma
- Amity Institute of Biotechnology, J-3 Block, Amity University Campus, Sector-125, Noida, UP, 201313, India
| | - Shivani Sharda
- Amity Institute of Biotechnology, J-3 Block, Amity University Campus, Sector-125, Noida, UP, 201313, India.
| | - Bhawna Rathi
- Amity Institute of Biotechnology, J-3 Block, Amity University Campus, Sector-125, Noida, UP, 201313, India
| | - Pallavi Somvanshi
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | - Bimlesh Dhar Pandey
- Fortis Hospital, B-22, Sector 62, Gautam Buddh Nagar, Noida, Uttar Pradesh, 201301, India
| |
Collapse
|
|
4
|
Grandi N, Pisano MP, Demurtas M, Blomberg J, Magiorkinis G, Mayer J, Tramontano E. Identification and characterization of ERV-W-like sequences in Platyrrhini species provides new insights into the evolutionary history of ERV-W in primates. Mob DNA 2020; 11:6. [PMID: 32021657 PMCID: PMC6995185 DOI: 10.1186/s13100-020-0203-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/13/2020] [Indexed: 11/29/2022] Open
Abstract
Background Endogenous Retroviruses (ERVs) constitute approximately 8% of every human genome and are relics of ancestral infections that affected the germ line cells. The ERV-W group contributed to primate physiology by providing an envelope protein (Syncytin-1) that has been adopted for placenta development in hominoids. Expression of Human ERV-W (HERV-W) sequences is investigated for a pathological role in various human diseases. Results We previously characterized ERV-W group genomic sequences in human and non-human Catarrhini species. We now investigated ERV-W-like sequences in the parvorder Platyrrhini, especially regarding two species with complete genome assemblies, namely marmoset (Callithrix jacchus) and squirrel monkey (Saimiri boliviensis). We identified in both species proviral sequences, annotated as ERV1–1 in respective genome assemblies, sharing high sequence similarities with Catarrhini ERV-W. A total of 130 relatively intact proviruses from the genomes of marmoset and squirrel monkey were characterized regarding their structural and evolutionarily relationships with Catarrhini ERV-W elements. Platyrrhini ERV-W sequences share several structural features with Catarrhini ERV-W elements and are closely related phylogenetically with the latter as well as with other ERV-W-related gammaretrovirus-like ERVs. The ERV-W group colonized Platyrrhini primates of both Callitrichidae and Atelidae lineages, with provirus formations having occurred mostly between 25 and 15 mya. Two LTR subgroups were associated with monophyletic proviral bodies. A pre-gag region appears to be a sequence feature common to the ERV-W group: it harbors a putative intron sequence that is missing in some ERV-W loci, holding a putative ORF as well. The presence of a long pre-gag portion was confirmed among all gammaretroviral ERV analyzed, suggesting a role in the latter biology. It is noteworthy that, contrary to Catarrhini ERV-W, there was no evidence of L1-mediated mobilization for Platyrrhini ERV-W sequences. Conclusions Our data establish that ERV-W is not exclusive to Catarrhini primates but colonized both parvorders of Simiiformes, providing further insight into the evolution of ERV-W and the colonization of primate genomes.
Collapse
Affiliation(s)
- Nicole Grandi
- 1Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, Monserrato, Cagliari Italy
| | - Maria Paola Pisano
- 1Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, Monserrato, Cagliari Italy
| | - Martina Demurtas
- 1Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, Monserrato, Cagliari Italy
| | - Jonas Blomberg
- 2Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | | | - Jens Mayer
- 4Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Enzo Tramontano
- 1Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, Monserrato, Cagliari Italy.,5Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Cagliari Italy
| |
Collapse
|
|
5
|
Zhu H, Gifford RJ, Murcia PR. Distribution, Diversity, and Evolution of Endogenous Retroviruses in Perissodactyl Genomes. J Virol 2018; 92:e00927-18. [PMID: 30209175 PMCID: PMC6232481 DOI: 10.1128/jvi.00927-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/01/2018] [Indexed: 01/01/2023] Open
Abstract
The evolution of mammalian genomes has been shaped by interactions with endogenous retroviruses (ERVs). In this study, we investigated the distribution and diversity of ERVs in the mammalian order Perissodactyla, with a view to understanding their impact on the evolution of modern equids (family Equidae). We characterize the major ERV lineages in the horse genome in terms of their genomic distribution, ancestral genome organization, and time of activity. Our results show that subsequent to their ancestral divergence from rhinoceroses and tapirs, equids acquired four novel ERV lineages. We show that two of these ERV lineages proliferated extensively in the lineage leading to modern horses, and one contains loci that are actively transcribed in specific tissues. In addition, we show that the white rhinoceros has resisted germ line colonization by retroviruses for more than 54 million years-longer than any other extant mammalian species. The map of equine ERVs that we provide here will be of great utility to future studies aiming to investigate the potential functional roles of equine ERVs and their impact on equine evolution.IMPORTANCE ERVs in the host genome are highly informative about the long-term interactions of retroviruses and hosts. They are also interesting because they have influenced the evolution of mammalian genomes in various ways. In this study, we derive a calibrated timeline describing the process through which ERV diversity has been generated in the equine germ line. We determined the distribution and diversity of perissodactyl ERV lineages and inferred their retrotranspositional activity during evolution, thereby gaining insight into the long-term coevolutionary history of retroviruses and mammals. Our study provides a platform for future investigations to identify equine ERV loci involved in physiological processes and/or pathological conditions.
Collapse
Affiliation(s)
- Henan Zhu
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | | | - Pablo Ramiro Murcia
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| |
Collapse
|
|
6
|
Gifford RJ, Blomberg J, Coffin JM, Fan H, Heidmann T, Mayer J, Stoye J, Tristem M, Johnson WE. Nomenclature for endogenous retrovirus (ERV) loci. Retrovirology 2018; 15:59. [PMID: 30153831 PMCID: PMC6114882 DOI: 10.1186/s12977-018-0442-1] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 08/20/2018] [Indexed: 11/10/2022] Open
Abstract
Retroviral integration into germline DNA can result in the formation of a vertically inherited proviral sequence called an endogenous retrovirus (ERV). Over the course of their evolution, vertebrate genomes have accumulated many thousands of ERV loci. These sequences provide useful retrospective information about ancient retroviruses, and have also played an important role in shaping the evolution of vertebrate genomes. There is an immediate need for a unified system of nomenclature for ERV loci, not only to assist genome annotation, but also to facilitate research on ERVs and their impact on genome biology and evolution. In this review, we examine how ERV nomenclatures have developed, and consider the possibilities for the implementation of a systematic approach for naming ERV loci. We propose that such a nomenclature should not only provide unique identifiers for individual loci, but also denote orthologous relationships between ERVs in different species. In addition, we propose that-where possible-mnemonic links to previous, well-established names for ERV loci and groups should be retained. We show how this approach can be applied and integrated into existing taxonomic and nomenclature schemes for retroviruses, ERVs and transposable elements.
Collapse
Affiliation(s)
- Robert J Gifford
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
| | - Jonas Blomberg
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - John M Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, USA
| | - Hung Fan
- Department of Molecular Biology and Biochemistry and Cancer Research Institute, University of California, Irvine, CA, 92697, USA
| | - Thierry Heidmann
- Department of Molecular Physiology and Pathology of Infectious and Endogenous Retroviruses, CNRS UMR 9196, Institut Gustave Roussy, 94805, Villejuif, France
| | - Jens Mayer
- Department of Human Genetics, Center of Human and Molecular Biology, Medical Faculty, University of Saarland, Homburg, Germany
| | - Jonathan Stoye
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, UK
| | - Michael Tristem
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
| | - Welkin E Johnson
- Biology Department, Boston College, Chestnut Hill, Massachusetts, 02467, USA.
| |
Collapse
|
|
7
|
Russo AG, Eden JS, Enosi Tuipulotu D, Shi M, Selechnik D, Shine R, Rollins LA, Holmes EC, White PA. Viral Discovery in the Invasive Australian Cane Toad ( Rhinella marina) Using Metatranscriptomic and Genomic Approaches. J Virol 2018; 92:JVI.00768-18. [PMID: 29899109 PMCID: PMC6096826 DOI: 10.1128/jvi.00768-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 06/07/2018] [Indexed: 12/19/2022] Open
Abstract
Cane toads are poisonous amphibians that were introduced to Australia in 1935 for insect control. Since then, their population has increased dramatically, and they now threaten many native Australian species. One potential method to control the population is to release a cane toad virus with high mortality rates, yet few cane toad viruses have been characterized. This study samples cane toads from different Australian locations and uses an RNA sequencing and computational approach to find new viruses. We report novel complete picornavirus and retrovirus sequences that were genetically similar to viruses infecting frogs, reptiles, and fish. Using data generated in other studies, we show that these viral sequences are present in cane toads from distinct Australian locations. Three sequences related to circoviruses were also found in the toad genome. The identification of new viral sequences will aid future studies that investigate their prevalence and potential as agents for biocontrol. Cane toads are a notorious invasive species, inhabiting over 1.2 million km2 of Australia and threatening native biodiversity. The release of pathogenic cane toad viruses is one possible biocontrol strategy yet is currently hindered by the poorly described cane toad virome. Metatranscriptomic analysis of 16 cane toad livers revealed the presence of a novel and full-length picornavirus, Rhimavirus A (RhiV-A), a member of a reptile- and amphibian-specific cluster of the Picornaviridae basal to the Kobuvirus-like group. In the combined liver transcriptome, we also identified a complete genome sequence of a distinct epsilonretrovirus, Rhinella marina endogenous retrovirus (RMERV). The recently sequenced cane toad genome contains 8 complete RMERV proviruses as well as 21 additional truncated insertions. The oldest full-length RMERV provirus was estimated to have inserted 1.9 million years ago (MYA). To screen for these viral sequences in additional toads, we analyzed publicly available transcriptomes from six diverse Australian locations. RhiV-A transcripts were identified in toads sampled from three locations across 1,000 km of Australia, stretching to the current Western Australia (WA) invasion front, while RMERV transcripts were observed at all six sites. Finally, we scanned the cane toad genome for nonretroviral endogenous viral elements, finding three sequences related to small DNA viruses in the family Circoviridae. This shows ancestral circoviral infection with subsequent genomic integration. The identification of these current and past viral infections enriches our knowledge of the cane toad virome, an understanding of which will facilitate future work on infection and disease in this important invasive species. IMPORTANCE Cane toads are poisonous amphibians that were introduced to Australia in 1935 for insect control. Since then, their population has increased dramatically, and they now threaten many native Australian species. One potential method to control the population is to release a cane toad virus with high mortality rates, yet few cane toad viruses have been characterized. This study samples cane toads from different Australian locations and uses an RNA sequencing and computational approach to find new viruses. We report novel complete picornavirus and retrovirus sequences that were genetically similar to viruses infecting frogs, reptiles, and fish. Using data generated in other studies, we show that these viral sequences are present in cane toads from distinct Australian locations. Three sequences related to circoviruses were also found in the toad genome. The identification of new viral sequences will aid future studies that investigate their prevalence and potential as agents for biocontrol.
Collapse
Affiliation(s)
- Alice G. Russo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Disease and Biosecurity, School of Life and Environmental Sciences and Sydney Medical School, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- The Westmead Institute of Medical Research, Centre for Virus Research, Westmead, NSW, Australia
| | - Daniel Enosi Tuipulotu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Mang Shi
- Marie Bashir Institute for Infectious Disease and Biosecurity, School of Life and Environmental Sciences and Sydney Medical School, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Daniel Selechnik
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard Shine
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Lee Ann Rollins
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Disease and Biosecurity, School of Life and Environmental Sciences and Sydney Medical School, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Peter A. White
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| |
Collapse
|
|
8
|
Xu X, Zhao H, Gong Z, Han GZ. Endogenous retroviruses of non-avian/mammalian vertebrates illuminate diversity and deep history of retroviruses. PLoS Pathog 2018; 14:e1007072. [PMID: 29902269 PMCID: PMC6001957 DOI: 10.1371/journal.ppat.1007072] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/03/2018] [Indexed: 02/06/2023] Open
Abstract
The deep history and early diversification of retroviruses remains elusive, largely because few retroviruses have been characterized in vertebrates other than mammals and birds. Endogenous retroviruses (ERVs) documented past retroviral infections and thus provide ‘molecular fossils’ for studying the deep history of retroviruses. Here we perform a comprehensive phylogenomic analysis of ERVs within the genomes of 92 non-avian/mammalian vertebrates, including 72 fishes, 4 amphibians, and 16 reptiles. We find that ERVs are present in all the genomes of jawed vertebrates, revealing the ubiquitous presence of ERVs in jawed vertebrates. We identify a total of >8,000 ERVs and reconstruct ~450 complete or partial ERV genomes, which dramatically expands the phylogenetic diversity of retroviruses and suggests that the diversity of exogenous retroviruses might be much underestimated in non-avian/mammalian vertebrates. Phylogenetic analyses show that retroviruses cluster into five major groups with different host distributions, providing important insights into the classification and diversification of retroviruses. Moreover, we find retroviruses mainly underwent frequent host switches in non-avian/mammalian vertebrates, with exception of spumavirus-related viruses that codiverged with their ray-finned fish hosts. Interestingly, ray-finned fishes and turtles appear to serve as unappreciated hubs for the transmission of retroviruses. Finally, we find retroviruses underwent many independent water-land transmissions, indicating the water-land interface is not a strict barrier for retrovirus transmission. Our analyses provide unprecedented insights into and valuable resources for studying the diversification, key evolutionary transitions, and macroevolution of retroviruses. Retroviruses infect a wide range of vertebrates and cause many diseases, such as AIDS and cancers. To date, retroviruses have been rarely characterized in vertebrates other than mammals and birds, impeding our understanding of the diversity and early evolution of retroviruses. Retroviruses can occasionally integrate into host genomes and become endogenous retroviruses (ERVs), which provide molecular fossils for studying the long-term evolution of retroviruses. Here we performed comparative genomic and evolutionary analyses of ERVs within 92 non-avian/mammalian vertebrates (fishes, amphibians, and reptiles) and uncovered extraordinary diversity of retroviruses in non-avian/mammalian vertebrates. Our analyses reveal an ancient aquatic origin of retroviruses and retroviruses underwent frequent host-switching. Our findings have important implications in understanding the deep history and evolutionary mode of retroviruses.
Collapse
Affiliation(s)
- Xiaoyu Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Huayao Zhao
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Zhen Gong
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Guan-Zhu Han
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
- * E-mail:
| |
Collapse
|
|
9
|
Euphyllophyte Paleoviruses Illuminate Hidden Diversity and Macroevolutionary Mode of Caulimoviridae. J Virol 2018; 92:JVI.02043-17. [PMID: 29491164 DOI: 10.1128/jvi.02043-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 02/16/2018] [Indexed: 12/29/2022] Open
Abstract
Endogenous viral elements (paleoviruses) provide "molecular fossils" for studying the deep history and macroevolution of viruses. Endogenous plant pararetroviruses (EPRVs) are widespread in angiosperms, but little is known about EPRVs in earlier-branching plants. Here we use a large-scale phylogenomic approach to investigate the diversity and macroevolution of plant pararetroviruses (formally known as Caulimoviridae). We uncover an unprecedented and unappreciated diversity of EPRVs within the genomes of gymnosperms and ferns. The known angiosperm viruses constitute only a minor part of the Caulimoviridae diversity. By characterizing the distribution of EPRVs, we show that no major euphyllophyte lineages escape the activity of Caulimoviridae, raising the possibility that many exogenous Caulimoviridae remain to be discovered in euphyllophytes. We find that the copy numbers of EPRVs are generally high, suggesting that EPRVs might define a unique group of repetitive elements and represent important components of euphyllophyte genomes. Evolutionary analyses suggest an ancient origin of Caulimoviridae and at least three independent origins of Caulimoviridae in angiosperms. Our findings reveal the remarkable diversity of Caulimoviridae and have important implications for understanding the origin and macroevolution of plant pararetroviruses.IMPORTANCE Few viruses have been documented in plants outside angiosperms. Viruses can occasionally integrate into host genomes, forming endogenous viral elements (EVEs). Endogenous plant pararetroviruses (EPRVs) are widespread in angiosperms. In this study, we performed comprehensive comparative and phylogenetic analyses of EPRVs and found that EPRVs are present in the genomes of gymnosperms and ferns. We identified numerous EPRVs in gymnosperm and fern genomes, revealing an unprecedented depth in the diversity of plant pararetroviruses. Plant pararetroviruses mainly underwent cross-species transmission, and angiosperm pararetroviruses arose at least three times. Our study provides novel insights into the diversity and macroevolution of plant pararetroviruses.
Collapse
|
|
10
|
Greenwood AD, Ishida Y, O'Brien SP, Roca AL, Eiden MV. Transmission, Evolution, and Endogenization: Lessons Learned from Recent Retroviral Invasions. Microbiol Mol Biol Rev 2018; 82:e00044-17. [PMID: 29237726 PMCID: PMC5813887 DOI: 10.1128/mmbr.00044-17] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Viruses of the subfamily Orthoretrovirinae are defined by the ability to reverse transcribe an RNA genome into DNA that integrates into the host cell genome during the intracellular virus life cycle. Exogenous retroviruses (XRVs) are horizontally transmitted between host individuals, with disease outcome depending on interactions between the retrovirus and the host organism. When retroviruses infect germ line cells of the host, they may become endogenous retroviruses (ERVs), which are permanent elements in the host germ line that are subject to vertical transmission. These ERVs sometimes remain infectious and can themselves give rise to XRVs. This review integrates recent developments in the phylogenetic classification of retroviruses and the identification of retroviral receptors to elucidate the origins and evolution of XRVs and ERVs. We consider whether ERVs may recurrently pressure XRVs to shift receptor usage to sidestep ERV interference. We discuss how related retroviruses undergo alternative fates in different host lineages after endogenization, with koala retrovirus (KoRV) receiving notable interest as a recent invader of its host germ line. KoRV is heritable but also infectious, which provides insights into the early stages of germ line invasions as well as XRV generation from ERVs. The relationship of KoRV to primate and other retroviruses is placed in the context of host biogeography and the potential role of bats and rodents as vectors for interspecies viral transmission. Combining studies of extant XRVs and "fossil" endogenous retroviruses in koalas and other Australasian species has broadened our understanding of the evolution of retroviruses and host-retrovirus interactions.
Collapse
Affiliation(s)
- Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin e.V., Berlin, Germany
| | - Yasuko Ishida
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sean P O'Brien
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Alfred L Roca
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Maribeth V Eiden
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin e.V., Berlin, Germany
| |
Collapse
|
|
11
|
Hayward A. Origin of the retroviruses: when, where, and how? Curr Opin Virol 2017; 25:23-27. [PMID: 28672160 PMCID: PMC5962544 DOI: 10.1016/j.coviro.2017.06.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/11/2017] [Accepted: 06/19/2017] [Indexed: 12/04/2022]
Abstract
Retroviruses are a virus family of considerable medical and veterinary importance. Until recently, very little was known about deep retroviral origins. New research supports a marine origin of retroviruses, ∼460–550 million years ago. The evolutionary events leading to the origin of retroviruses remain obscure. Improved understanding of Metaviridae diversity and evolution are required for this.
Retroviruses are a virus family of considerable medical and veterinary importance. Additionally, it is now clear that endogenous retroviruses (ERVs) comprise significant portions of vertebrate genomes. Until recently, very little was known about the deep evolutionary origins of retroviruses. However, advances in genomics and bioinformatics have opened the way for great strides in understanding. Recent research employing a wide variety of bioinformatic approaches has demonstrated that retroviruses evolved during the early Palaeozoic Era, between 460 and 550 million years ago, providing the oldest inferred date estimate for any virus group. This finding presents an important framework to investigate the evolutionary transitions that led to the emergence of the retroviruses, offering potential insights into the infectious origins of a major group of pathogenic viruses.
Collapse
Affiliation(s)
- Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, TR10 9FE, United Kingdom.
| |
Collapse
|
|
12
|
Affiliation(s)
- Katherine Brown
- Computational Genomics Analysis and Training MRC Centre for Computational Biology Weatherall Institute for Molecular Medicine University of Oxford OX3 9DS UK
| | - Rachael E. Tarlinton
- School of Veterinary Medicine and Science University of Nottingham Sutton Bonington Campus Loughborough LE12 5RD UK
| |
Collapse
|
|
13
|
Vargiu L, Rodriguez-Tomé P, Sperber GO, Cadeddu M, Grandi N, Blikstad V, Tramontano E, Blomberg J. Classification and characterization of human endogenous retroviruses; mosaic forms are common. Retrovirology 2016; 13:7. [PMID: 26800882 PMCID: PMC4724089 DOI: 10.1186/s12977-015-0232-y] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 12/16/2015] [Indexed: 02/06/2023] Open
Abstract
Background Human endogenous retroviruses (HERVs) represent the inheritance of ancient germ-line cell infections by exogenous retroviruses and the subsequent transmission of the integrated proviruses to the descendants. ERVs have the same internal structure as exogenous retroviruses. While no replication-competent HERVs have been recognized, some retain up to three of four intact ORFs. HERVs have been classified before, with varying scope and depth, notably in the RepBase/RepeatMasker system. However, existing classifications are bewildering. There is a need for a systematic, unifying and simple classification. We strived for a classification which is traceable to previous classifications and which encompasses HERV variation within a limited number of clades. Results The human genome assembly GRCh 37/hg19 was analyzed with RetroTector, which primarily detects relatively complete Class I and II proviruses. A total of 3173 HERV sequences were identified. The structure of and relations between these proviruses was resolved through a multi-step classification procedure that involved a novel type of similarity image analysis (“Simage”) which allowed discrimination of heterogeneous (noncanonical) from homogeneous (canonical) HERVs. Of the 3173 HERVs, 1214 were canonical and segregated into 39 canonical clades (groups), belonging to class I (Gamma- and Epsilon-like), II (Beta-like) and III (Spuma-like). The groups were chosen based on (1) sequence (nucleotide and Pol amino acid), similarity, (2) degree of fit to previously published clades, often from RepBase, and (3) taxonomic markers. The groups fell into 11 supergroups. The 1959 noncanonical HERVs contained 31 additional, less well-defined groups. Simage analysis revealed several types of mosaicism, notably recombination and secondary integration. By comparing flanking sequences, LTRs and completeness of gene structure, we deduced that some noncanonical HERVs proliferated after the recombination event. Groups were further divided into envelope subgroups (altogether 94) based on sequence similarity and characteristic “immunosuppressive domain” motifs. Intra and inter(super)group, as well as intraclass, recombination involving envelope genes (“env snatching”) was a common event. LTR divergence indicated that HERV-K(HML2) and HERVFC had the most recent integrations, HERVL and HUERSP3 the oldest. Conclusions A comprehensive HERV classification and characterization approach was undertaken. It should be applicable for classification of all ERVs. Recombination was common among HERV ancestors. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0232-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Laura Vargiu
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy. .,Center for Advanced Studies, Research and Development in Sardinia, CRS4, Pula, Italy. .,Nurideas S.r.l., Cagliari, Italy.
| | - Patricia Rodriguez-Tomé
- Center for Advanced Studies, Research and Development in Sardinia, CRS4, Pula, Italy. .,Nurideas S.r.l., Cagliari, Italy.
| | - Göran O Sperber
- Physiology Unit, Department of Neuroscience, Uppsala University, Uppsala, Sweden.
| | - Marta Cadeddu
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.
| | - Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.
| | - Vidar Blikstad
- Department of Medical Sciences, Uppsala University Hospital, Dag Hammarskjölds Väg 17, Uppsala, 751 85, Sweden.
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.
| | - Jonas Blomberg
- Department of Medical Sciences, Uppsala University Hospital, Dag Hammarskjölds Väg 17, Uppsala, 751 85, Sweden.
| |
Collapse
|
|
14
|
Aiewsakun P, Katzourakis A. Endogenous viruses: Connecting recent and ancient viral evolution. Virology 2015; 479-480:26-37. [PMID: 25771486 DOI: 10.1016/j.virol.2015.02.011] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 12/15/2014] [Accepted: 02/04/2015] [Indexed: 12/17/2022]
Abstract
The rapid rates of viral evolution allow us to reconstruct the recent history of viruses in great detail. This feature, however, also results in rapid erosion of evolutionary signal within viral molecular data, impeding studies of their deep history. Thus, the further back in time, the less accurate the inference becomes. Furthermore, reconstructing complex histories of transmission can be challenging, especially where extinct viral lineages are concerned. This problem has been partially solved by the discovery of viruses embedded in host genomes, known as endogenous viral elements (EVEs). Some of these endogenous viruses are derived from ancient relatives of extant viruses, allowing us to better examine ancient viral host range, geographical distribution and transmission routes. Moreover, our knowledge of viral evolutionary timescales and rate dynamics has also been greatly improved by their discovery, thereby bridging the gap between recent and ancient viral evolution.
Collapse
Affiliation(s)
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
| |
Collapse
|