Skip to main content
SpringerLink
Log in

Retrovirus Phylogeny and Evolution

  • Conference paper
Retroviruses

Part of the book series: Current Topics in Microbiology and Immunology ((CT MICROBIOLOGY,volume 157))

Abstract

During the past few years the nucleic sequences of a large number of retroviruses have been determined, making it possible to quantify how they are related to each other and to trace their evolutionary origins. There are two factors that complicate such studies, however. First, retroviruses, like other RNA viruses, mutate at a very rapid rate (Holland et al. 1982) and as a consequence evolve very rapidly. Second, retroviruses can recombine with each other (see for example Clark and Mak 1984; reviewed in Linial and Blair 1984), raising the possibility that simple phylogenies may be confounded by mosaic genomes.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Adams SE, Mellor J., Gull K, Sim RB, Tuite MF, Kingsman AJ (1987) The functions and relationships of Ty-VLP proteins in yeast reflect those of mammalian retroviral proteins. Cell 49: 111–119

    Article  PubMed  CAS  Google Scholar 

  • Chiu I-M, Yaniv A, Dahlberg JE, Gazit A, Skuntz SF, Tronick ST, Aaronson SA (1985) Nucleotide sequence evidence for relationship of AIDS retrovirus to lentiviruses. Nature 317: 366–368

    Article  PubMed  CAS  Google Scholar 

  • Clark SP, Mak TW (1984) Fluidity of a retrovirus genome. J Virol 50: 759–765

    PubMed  CAS  Google Scholar 

  • Covey SN (1986) Amino acid sequence homology in gag region of reverse transcribing elements and the coat protein gene of cauliflower mosaic virus. Nucleic Acids Res 14: 623–633

    Article  PubMed  CAS  Google Scholar 

  • Chakrabarti L, Guyader M, Alizon M, Daniel MD, Desrosiers RC, Tiollais P, Sonigo P (1987) Sequence of simian immunodeficiency virus from macaque and its relationship to other human and simian retroviruses. Nature 328: 543–547

    Article  PubMed  CAS  Google Scholar 

  • Daniel MD, Letvin NL, King NW, Kannagi M, Sehgal PK, Hunt RD (1985) Isolation of T-cell tropic HTLV-III-like retrovirus from macaques. Science 228: 1201–1204

    Article  PubMed  CAS  Google Scholar 

  • Dayhoff MO, Park CM, McLaughlin PJ (1972) Building a phylogenetic tree: cytochrome c, In: Dayhoff MO (ed) Atlas of protein sequence and structure, vol 5. National Biomedical Research Foundation, Washington DC pp 7–16

    Google Scholar 

  • Doolittle RF, Feng D-F (1990) Nearest Neighbour Procedure for Relating Progressively Aligned Amino Acid Sequences. Methods Enzymol 183: 659–669

    Article  PubMed  CAS  Google Scholar 

  • Doolittle RF, Feng D-F, Johnson MS, McClure MA (1989) Origins and evolutionary relationships of retroviruses. Q Rev Biol 64: 1–30

    Article  PubMed  CAS  Google Scholar 

  • Feng D-F, Doolittle RF (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol 25: 351–360

    Article  PubMed  CAS  Google Scholar 

  • Finnegan DJ (1983) Retroviruses and transposable elements-which came first? Nature 302: 105–106

    Article  PubMed  CAS  Google Scholar 

  • Fitch WM (1981) A non-sequential method for constructing trees and hierarchical classifications. J Mol Evol 18: 30–37

    Article  PubMed  CAS  Google Scholar 

  • Fitch WM, Margoliash (1967) Construction of phylogenetic trees. Science 15: 279–284

    Article  Google Scholar 

  • Franchini G, Gurgo C, Guo H-G, Gallo RC, Collalti E, Fargnoli KA, Hall LF, Wong-Staal, Reitz Jr, MS (1987) Sequence of simian immunodeficiency virus and its relationship to the human immunodeficiency viruses. Nature 328: 539–543

    Article  PubMed  CAS  Google Scholar 

  • Fukasawa M, Miura T, Hasegawa A, Morikawa S, Tsujimoto H, Miki K, Kitamura T, Hayami M (1988) Sequence of simian immunodeficiency virus from African green monkey, a new member of the HIV/SIV group. Nature 333: 457–461

    Article  PubMed  CAS  Google Scholar 

  • Gonda MA, Braun MJ, Carter SG, Kost TA, Bess Jr, JW, Arthur LO, Van Der Maaten MJ (1987) Characterization and molecular cloning of a bovine lentivirus related to human immunodeficiency virus. Nature 330: 388–391

    Article  PubMed  CAS  Google Scholar 

  • Hansen J, Schulze T, Meliert W, Moelling K (1988) Identification and characterization of HIV-specific RNase H by monoclonal antibody. EMBO J 7: 239–243

    PubMed  CAS  Google Scholar 

  • Holland J, Spindler K, Horodyski F, Grabau E, Nichol S, VandePol S (1982) Rapid evolution of RNA genomes. Science 215: 1577–1585

    Article  PubMed  CAS  Google Scholar 

  • Johnson MS, McClure MA, Feng D-F, Gray J, Doolittle RF (1986) Computer analysis of retroviral pol genes: assignment of enzymatic functions to specific sequences and homologies with non-viral enzymes. Proc Natl Acad Sci USA 83: 7648–7652

    Article  PubMed  CAS  Google Scholar 

  • Kanki PJ, Barin F, M’Boup S, Allan JS, Romet-Lemonne JL, Marlink R, McLane MF, Lee T-H, Arbeille B, Denis F, Essex M (1986) New human T-lymphotropic retrovirus related to simian T-lymphotropic virus type III (STLV-IIIAGM). Science 232: 238–243

    Article  PubMed  CAS  Google Scholar 

  • Kestler III, HW, Li Y, Naidu YM, Butler CV, Ochs MF, Jaenel G, King NW, Daniel MD, Desrosiers RC (1988) Comparison of simian immunodeficiency virus isolates. Nature 331: 619–622

    Article  PubMed  Google Scholar 

  • Klotz LC, Blanken RL (1981) A practical method for calculating evolutionary trees from sequence data. J Theor Biol 91: 261–272

    Article  PubMed  CAS  Google Scholar 

  • Leis J, Baltimore D, Bishop JM, Coffin J, Fleissner E, Goff SP, Oroszlan S, Robinson H, Skalka AM, Temin HM, Vogt V (1988) Standardized and simplified nomenclature for proteins common to all retroviruses. J Virol 62: 1808–1809

    PubMed  CAS  Google Scholar 

  • Levy JA (1978) Xenotropic Type C Viruses. Curr Top Microbiol Immunol 79: 111–118

    Article  PubMed  CAS  Google Scholar 

  • Lineal M, Blair D (1984) Genetics of Retroviruses. In: Weiss R, Teich N, Varmus H, Coffin J (eds) Molecular Biology of Tumor Virus: RNA Tumor Viruses. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, pp. 649–783

    Google Scholar 

  • Maurer B, Bannert H, Darai G, Flugel RM (1988) Analysis of the primary structure of the long terminal repeat and the gag and pol genes of the human spumaretrovirus. J Virol 62: 1590–1597

    PubMed  CAS  Google Scholar 

  • McClure MA, Johnson MS, Doolittle RF (1987) Relocation of a protease-like gene segment between two retroviruses. Proc Natl Acad Sci USA 84: 2693–2697

    Article  PubMed  CAS  Google Scholar 

  • McClure MA, Johnson MS, Feng D-F, Doolittle RF (1988) Sequence comparisons of retroviral proteins: relative rate of change and general phylogeny. Proc Natl Acad Sci USA 85: 2469–2473

    Article  PubMed  CAS  Google Scholar 

  • Mulder C (1988) Human AIDS virus not from monkeys. Nature 333: 396

    Article  PubMed  CAS  Google Scholar 

  • O’Connell C, O’Brien S, Nash WG, Cohen M (1984) ER V3, a full-length human endogenous provirus: chromosomal localization and evolutionary relationships. Virol 138: 225–235

    Article  Google Scholar 

  • Ono M, Yasunaga T, Miyata T, Ushikubo H (1986) Nucleotide sequence of human endogenous retrovirus genome related to the mouse mammary tumor virus genome. J Virol 60: 589–598

    PubMed  CAS  Google Scholar 

  • Power MD, Marx PA, Bryant ML, Gardner MS, Barr PJ, Luciw PA (1986) Nucleotide sequence of SRV-I, a type D simian acquired immune deficiency syndrome retrovirus. Science 231: 1567–1572

    Article  PubMed  CAS  Google Scholar 

  • Ratner L, Haseltine W, Patarca R, Livak KJ, Starcich B, Josephs SF, Doran ER, Rafalski JA, Whitehorn EA, Baumeister K, Ivanoff L, Retteway Jr, SR, Pearson ML, Lautenberger JA, Papas TS, Ghrayeb J, Chang NT, Gallo RC, Wong-Staal F (1985) Complete nucleotide sequence of the AIDS virus, HTLV-III. Nature 313: 277–283

    Article  PubMed  CAS  Google Scholar 

  • Sagata N, Yasunaga T, Tsuzuku-Kawamura T, Ohishi K, Ogawa Y, Ikawa Y (1985) Complete Nucleotide sequence of the genome of Bovine Leukemia virus: its evolutionary relationship to other retroviruses. Proc Natl Acad Sci USA 82: 677–681

    Article  PubMed  CAS  Google Scholar 

  • Shiba T, Saigo K (1983) Retrovirus-like particles containing RNA homologous to the transposable element copia in Drosophila melanogaster. Nature 302: 119–124

    Article  PubMed  CAS  Google Scholar 

  • Smith TF, Srinivasan A, Schochetman G, Marcus M, Myers G (1988) The phylogenetic age of AIDS. Nature 333: 573–575

    Article  PubMed  CAS  Google Scholar 

  • Steele PE, Martin MA, Rabson AB, Bryan T, O’Brien SJ (1986) Amplification and chromosomal dispersion of human endogenous retroviral sequences. J Virol 59: 545–550

    PubMed  CAS  Google Scholar 

  • Tanese N, Goff SP (1988) Domain structure of the Moloney Murine leukemia virus reverse transcriptase: mutational analysis and separate expression of the DNA polymerase and RNase H activities. Proc Natl Acad Sci USA 85: 1777–1781

    Article  PubMed  CAS  Google Scholar 

  • Teich N (1984) Taxonomy of Retroviruses. In: Weiss R et al. (eds) RNA Tumor Viruses. 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, pp 25–207

    Google Scholar 

  • Temin H (1980) Origin of retroviruses from cellular moveable genetic elements. Cell 21: 599–600

    Article  PubMed  CAS  Google Scholar 

  • Temin H (1985) Reverse transcription in the eukaryotic genome: retroviruses, pararetroviruses, retrotransposons and retrotranscripts. Mol Biol Evol 6: 455–468

    Google Scholar 

  • Thayer RM, Power MD, Bryant M, Gardner MB, Barr PJ, Luciw PA (1987) Sequence relationships of type D retroviruses which cause simian acquired immunodeficiency syndrome. Virol 157: 317–329

    Article  CAS  Google Scholar 

  • Todaro GJ (1975) Evolution and modes of transmission of RNA tumor viruses. Am J Pathol 81: 590–605

    PubMed  CAS  Google Scholar 

  • Wain-Hobson S, Alizon M, Montagnier L (1985) Relationship of AIDS to other retroviruses. Nature 313:743

    Article  PubMed  CAS  Google Scholar 

  • Watanabe T, Seiki M, Tsujimoto H, Miyoshi I, Hayami M, Yoshida M (1985) Sequence homology of the simian retrovirus genome with human T-cell leukemia virus type I. Virol 144: 59–65

    Article  CAS  Google Scholar 

  • Yokoyama S, Gojobori T (1987) Molecular evolution and phylogeny of the Human AIDS viruses LAV, HTLV-III, and ARV. J Mol Evol 24: 330–336

    Article  PubMed  CAS  Google Scholar 

  • Yokoyama S, Chung L, Gojobori T (1988) Molecular evolution of the human immunodeficiency and related viruses. Mol Biol Evol 5: 237–251

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Chemistry, Center for Molecular Genetics M-034, University of California, San Diego, La Jolla, CA, 92093, USA

    R. F. Doolittle, D. F. Feng, M. A. McClure & M. S. Johnson

Authors
  1. R. F. Doolittle
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. D. F. Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. M. A. McClure
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. M. S. Johnson
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Dept. of Biochemistry, Lineberger Cancer Research Ctr., University of North Carolina at Chapel Hill, CB #7295, 246 Lineberger Bldg., Chapel Hill, NC, 27599, USA

    Ronald Swanstrom Ph.D. (Associate Professor of Biochemistry) (Associate Professor of Biochemistry)

  2. Dept. of Microbiology, School of Medicine, University of Southern California, 2011 Zone Avenue HMR 401, Los Angeles, CA, 90033, USA

    Peter K. Vogt M.D.

Rights and permissions

Reprints and permissions

Copyright information

© 1990 Springer-Verlag Berlin · Heidelberg

About this paper

Cite this paper

Doolittle, R.F., Feng, D.F., McClure, M.A., Johnson, M.S. (1990). Retrovirus Phylogeny and Evolution. In: Swanstrom, R., Vogt, P.K. (eds) Retroviruses. Current Topics in Microbiology and Immunology, vol 157. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-75218-6_1

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-75218-6_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-75220-9

  • Online ISBN: 978-3-642-75218-6

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation