Ortervirales: New Virus Order Unifying Five Families of Reverse-Transcribing Viruses

Mart Krupovic¹, Jonas Blomberg², John M Coffin³, Indranil Dasgupta⁴, Hung Fan⁵, Andrew D Geering⁶, Robert Gifford⁷, Balázs Harrach⁸, Roger Hull⁹, Welkin Johnson¹⁰, Jan F Kreuze¹¹, Dirk Lindemann¹², Carlos Llorens¹³, Ben Lockhart¹⁴, Jens Mayer¹⁵, Emmanuelle Muller^{16

17}, Neil E Olszewski¹⁸, Hanu R Pappu¹⁹, Mikhail M Pooggin²⁰, Katja R Richert-Pöggeler²¹, Sead Sabanadzovic²², Hélène Sanfaçon²³, James E Schoelz²⁴, Susan Seal²⁵, Livia Stavolone^{26

27}, Jonathan P Stoye²⁸, Pierre-Yves Teycheney^{29

30}, Michael Tristem³¹, Eugene V Koonin³², Jens H Kuhn³³

Affiliations

¹ Department of Microbiology, Institut Pasteur, Paris, France krupovic@pasteur.fr.
² Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
³ Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA.
⁴ Department of Plant Molecular Biology, University of Delhi, New Delhi, India.
⁵ Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA.
⁶ Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia.
⁷ MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom.
⁸ Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary.
⁹ Child Okeford, Blandford Forum, Dorset, United Kingdom.
¹⁰ Biology Department, Boston College, Chestnut Hill, Massachusetts, USA.
¹¹ Crop and System Sciences Division, International Potato Center (CIP), Lima, Peru.
¹² Institute of Virology, Technische Universität Dresden, Dresden, Germany.
¹³ Biotechvana, Parc Cientific, Universitat de Valencia, Valencia, Spain.
¹⁴ Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA.
¹⁵ Institute of Human Genetics, University of Saarland, Homburg, Germany.
¹⁶ CIRAD, UMR BGPI, Montpellier, France.
¹⁷ BGPI, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
¹⁸ Department of Microbial and Plant Biology, University of Minnesota, St. Paul, Minnesota, USA.
¹⁹ Department of Plant Pathology, Washington State University, Pullman, Washington, USA.
²⁰ INRA, UMR BGPI, Montpellier, France.
²¹ Julius Kühn-Institut, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany.
²² Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, USA.
²³ Agriculture and Agri-Food Canada, Summerland Research and Development Centre, Summerland, BC, Canada.
²⁴ Division of Plant Sciences, University of Missouri, Columbia, Missouri, USA.
²⁵ Natural Resources Institute, University of Greenwich, Chatham, Kent, United Kingdom.
²⁶ Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy.
²⁷ International Institute of Tropical Agriculture, Ibadan, Nigeria.
²⁸ The Francis Crick Institute and Department of Medicine, Faculty of Medicine, Imperial College London, London, United Kingdom.
²⁹ CIRAD, UMR AGAP, Capesterre Belle Eau, Guadeloupe, France.
³⁰ AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
³¹ Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom.
³² National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
³³ Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA.

PMID: 29618642
PMCID: PMC5974489
DOI: 10.1128/JVI.00515-18

Ortervirales: New Virus Order Unifying Five Families of Reverse-Transcribing Viruses

Mart Krupovic et al. J Virol. 2018.

. 2018 May 29;92(12):e00515-18.

doi: 10.1128/JVI.00515-18. Print 2018 Jun 15.

Authors

Affiliations

¹ Department of Microbiology, Institut Pasteur, Paris, France krupovic@pasteur.fr.
² Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
³ Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA.
⁴ Department of Plant Molecular Biology, University of Delhi, New Delhi, India.
⁵ Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA.
⁶ Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia.
⁷ MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom.
⁸ Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary.
⁹ Child Okeford, Blandford Forum, Dorset, United Kingdom.
¹⁰ Biology Department, Boston College, Chestnut Hill, Massachusetts, USA.
¹¹ Crop and System Sciences Division, International Potato Center (CIP), Lima, Peru.
¹² Institute of Virology, Technische Universität Dresden, Dresden, Germany.
¹³ Biotechvana, Parc Cientific, Universitat de Valencia, Valencia, Spain.
¹⁴ Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA.
¹⁵ Institute of Human Genetics, University of Saarland, Homburg, Germany.
¹⁶ CIRAD, UMR BGPI, Montpellier, France.
¹⁷ BGPI, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
¹⁸ Department of Microbial and Plant Biology, University of Minnesota, St. Paul, Minnesota, USA.
¹⁹ Department of Plant Pathology, Washington State University, Pullman, Washington, USA.
²⁰ INRA, UMR BGPI, Montpellier, France.
²¹ Julius Kühn-Institut, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany.
²² Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, USA.
²³ Agriculture and Agri-Food Canada, Summerland Research and Development Centre, Summerland, BC, Canada.
²⁴ Division of Plant Sciences, University of Missouri, Columbia, Missouri, USA.
²⁵ Natural Resources Institute, University of Greenwich, Chatham, Kent, United Kingdom.
²⁶ Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy.
²⁷ International Institute of Tropical Agriculture, Ibadan, Nigeria.
²⁸ The Francis Crick Institute and Department of Medicine, Faculty of Medicine, Imperial College London, London, United Kingdom.
²⁹ CIRAD, UMR AGAP, Capesterre Belle Eau, Guadeloupe, France.
³⁰ AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
³¹ Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom.
³² National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
³³ Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA.

PMID: 29618642
PMCID: PMC5974489
DOI: 10.1128/JVI.00515-18

No abstract available

Keywords: Belpaoviridae; Caulimoviridae; Hepadnaviridae; International Committee on Taxonomy of Viruses (ICTV); Metaviridae; Pseudoviridae; Retroviridae; Ty3/Gypsy and Ty1/Copia LTR retrotransposons; retroviruses; virus classification; virus evolution.

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Figures

**FIG 1**
Maximum-likelihood phylogeny of viral reverse transcriptases. The tree includes sequences of 290 viruses belonging to all ICTV-recognized genera of reverse-transcribing viruses. The phylogeny was inferred using PhyML (27) with the LG+G+F substitution model and is rooted with sequences from nonviral retroelements (bacterial group II introns and eukaryotic LINE retroelements). Genomic organizations of selected representatives of reverse-transcribing viruses are shown next to the corresponding branches. Long terminal repeats are shown as black triangles. Note that members of the virus families display considerable variation in gene/domain content (5), which is not captured in this figure. Abbreviations: 6, 6-kDa protein; ATF, aphid transmission factor; CA/CP, capsid protein; CHR, chromodomain (present only in the integrase of particular clades of metaviruses of plants, fungi, and several vertebrates); *gag*, group-specific antigen; *env*, envelope genes; INT, integrase; LTR, long terminal repeat; MA, matrix protein; MP, movement protein; NC, nucleocapsid; *nef*, *tat*, *rev*, *vif*, *vpr*, and *vpu*, genes that express regulatory proteins via spliced mRNAs; P, polymerase; *pol*, polymerase gene; PR, protease; PreS, presurface protein (envelope); PX/TA, protein X/transcription activator; RH, RNase H; RT, reverse transcriptase; SU, surface glycoprotein; TM, transmembrane glycoprotein; TP, terminal protein domain; TT/SR, translation *trans*-activator/suppressor of RNA interference; VAP, virion-associated protein.

See this image and copyright information in PMC

References

1. Llorens C, Futami R, Covelli L, Dominguez-Escriba L, Viu JM, Tamarit D, Aguilar-Rodriguez J, Vicente-Ripolles M, Fuster G, Bernet GP, Maumus F, Munoz-Pomer A, Sempere JM, Latorre A, Moya A. 2011. The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Res 39:D70–D74. doi:10.1093/nar/gkq1061. - DOI - PMC - PubMed
1. Ahlquist P. 2006. Parallels among positive-strand RNA viruses, reverse-transcribing viruses and double-stranded RNA viruses. Nat Rev Microbiol 4:371–382. doi:10.1038/nrmicro1389. - DOI - PMC - PubMed
1. Koonin EV, Dolja VV, Krupovic M. 2015. Origins and evolution of viruses of eukaryotes: the ultimate modularity. Virology 479-480:2–25. doi:10.1016/j.virol.2015.02.039. - DOI - PMC - PubMed
1. Geering ADW. 2014. Caulimoviridae (plant pararetroviruses). In eLS John Wiley & Sons, Ltd, Chichester, United Kingdom. doi:10.1002/9780470015902.a0000746.pub3. - DOI
1. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ. 2011. Virus taxonomy. Ninth report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press, San Diego, CA.

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Ortervirales: New Virus Order Unifying Five Families of Reverse-Transcribing Viruses

Affiliations

Ortervirales: New Virus Order Unifying Five Families of Reverse-Transcribing Viruses

Authors

Affiliations

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