Retrovirus Phylogeny and Evolution

  • R. F. Doolittle
  • D. F. Feng
  • M. A. McClure
  • M. S. Johnson
Part of the Current Topics in Microbiology and Immunology book series (CT MICROBIOLOGY, volume 157)


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.


Transposable Element Simian Immunodeficiency Virus Bovine Leukemia Virus African Green Monkey Equine Infectious Anemia Virus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. 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: 111–119PubMedCrossRefGoogle Scholar
  2. 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: 366–368PubMedCrossRefGoogle Scholar
  3. Clark SP, Mak TW (1984) Fluidity of a retrovirus genome. J Virol 50: 759–765PubMedGoogle Scholar
  4. 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: 623–633PubMedCrossRefGoogle Scholar
  5. 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: 543–547PubMedCrossRefGoogle Scholar
  6. 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: 1201–1204PubMedCrossRefGoogle Scholar
  7. 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 7–16Google Scholar
  8. Doolittle RF, Feng D-F (1990) Nearest Neighbour Procedure for Relating Progressively Aligned Amino Acid Sequences. Methods Enzymol 183: 659–669PubMedCrossRefGoogle Scholar
  9. Doolittle RF, Feng D-F, Johnson MS, McClure MA (1989) Origins and evolutionary relationships of retroviruses. Q Rev Biol 64: 1–30PubMedCrossRefGoogle Scholar
  10. Feng D-F, Doolittle RF (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol 25: 351–360PubMedCrossRefGoogle Scholar
  11. Finnegan DJ (1983) Retroviruses and transposable elements-which came first? Nature 302: 105–106PubMedCrossRefGoogle Scholar
  12. Fitch WM (1981) A non-sequential method for constructing trees and hierarchical classifications. J Mol Evol 18: 30–37PubMedCrossRefGoogle Scholar
  13. Fitch WM, Margoliash (1967) Construction of phylogenetic trees. Science 15: 279–284CrossRefGoogle Scholar
  14. 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: 539–543PubMedCrossRefGoogle Scholar
  15. 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: 457–461PubMedCrossRefGoogle Scholar
  16. 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: 388–391PubMedCrossRefGoogle Scholar
  17. Hansen J, Schulze T, Meliert W, Moelling K (1988) Identification and characterization of HIV-specific RNase H by monoclonal antibody. EMBO J 7: 239–243PubMedGoogle Scholar
  18. Holland J, Spindler K, Horodyski F, Grabau E, Nichol S, VandePol S (1982) Rapid evolution of RNA genomes. Science 215: 1577–1585PubMedCrossRefGoogle Scholar
  19. 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: 7648–7652PubMedCrossRefGoogle Scholar
  20. 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: 238–243PubMedCrossRefGoogle Scholar
  21. 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: 619–622PubMedCrossRefGoogle Scholar
  22. Klotz LC, Blanken RL (1981) A practical method for calculating evolutionary trees from sequence data. J Theor Biol 91: 261–272PubMedCrossRefGoogle Scholar
  23. 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: 1808–1809PubMedGoogle Scholar
  24. Levy JA (1978) Xenotropic Type C Viruses. Curr Top Microbiol Immunol 79: 111–118PubMedCrossRefGoogle Scholar
  25. 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. 649–783Google Scholar
  26. 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: 1590–1597PubMedGoogle Scholar
  27. McClure MA, Johnson MS, Doolittle RF (1987) Relocation of a protease-like gene segment between two retroviruses. Proc Natl Acad Sci USA 84: 2693–2697PubMedCrossRefGoogle Scholar
  28. 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: 2469–2473PubMedCrossRefGoogle Scholar
  29. Mulder C (1988) Human AIDS virus not from monkeys. Nature 333: 396PubMedCrossRefGoogle Scholar
  30. 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: 225–235CrossRefGoogle Scholar
  31. 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: 589–598PubMedGoogle Scholar
  32. 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: 1567–1572PubMedCrossRefGoogle Scholar
  33. 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: 277–283PubMedCrossRefGoogle Scholar
  34. 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: 677–681PubMedCrossRefGoogle Scholar
  35. Shiba T, Saigo K (1983) Retrovirus-like particles containing RNA homologous to the transposable element copia in Drosophila melanogaster. Nature 302: 119–124PubMedCrossRefGoogle Scholar
  36. Smith TF, Srinivasan A, Schochetman G, Marcus M, Myers G (1988) The phylogenetic age of AIDS. Nature 333: 573–575PubMedCrossRefGoogle Scholar
  37. Steele PE, Martin MA, Rabson AB, Bryan T, O’Brien SJ (1986) Amplification and chromosomal dispersion of human endogenous retroviral sequences. J Virol 59: 545–550PubMedGoogle Scholar
  38. 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: 1777–1781PubMedCrossRefGoogle Scholar
  39. 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 25–207Google Scholar
  40. Temin H (1980) Origin of retroviruses from cellular moveable genetic elements. Cell 21: 599–600PubMedCrossRefGoogle Scholar
  41. Temin H (1985) Reverse transcription in the eukaryotic genome: retroviruses, pararetroviruses, retrotransposons and retrotranscripts. Mol Biol Evol 6: 455–468Google Scholar
  42. 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: 317–329CrossRefGoogle Scholar
  43. Todaro GJ (1975) Evolution and modes of transmission of RNA tumor viruses. Am J Pathol 81: 590–605PubMedGoogle Scholar
  44. Wain-Hobson S, Alizon M, Montagnier L (1985) Relationship of AIDS to other retroviruses. Nature 313:743PubMedCrossRefGoogle Scholar
  45. 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: 59–65CrossRefGoogle Scholar
  46. Yokoyama S, Gojobori T (1987) Molecular evolution and phylogeny of the Human AIDS viruses LAV, HTLV-III, and ARV. J Mol Evol 24: 330–336PubMedCrossRefGoogle Scholar
  47. Yokoyama S, Chung L, Gojobori T (1988) Molecular evolution of the human immunodeficiency and related viruses. Mol Biol Evol 5: 237–251PubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin · Heidelberg 1990

Authors and Affiliations

  • R. F. Doolittle
    • 1
  • D. F. Feng
    • 1
  • M. A. McClure
    • 1
  • M. S. Johnson
    • 1
  1. 1.Department of Chemistry, Center for Molecular Genetics M-034University of CaliforniaSan Diego, La JollaUSA

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