Journal of Molecular Evolution

, Volume 24, Issue 4, pp 330–336 | Cite as

Molecular evolution and phylogeny of the human AIDS viruses LAV, HTLV-III, and ARV

  • Shozo Yokoyama
  • Takashi Gojobori


A phylogenetic tree for the human lymphadenopathy-associated virus (LAV), the human T-cell lymphotrophic virus type III (HTLV-III), and the acquired immune deficiency syndrome (AIDS)-associated retrovirus (ARV) has been constructed from comparisons of the amino acid sequences of their gag proteins. A method is proposed for estimating the divergence times among these AIDS viruses and the rates of nucleotide substitution for their RNA genomes. The analysis indicates that the LAV and HTLV-III strains diverged from one another after 1977 and that their common ancestor diverged from the ARV virus no more than 10 years earlier. Hence, the evolutionary diversity among strains of the AIDS viruses apparently has been generated within the last 20 years. It is estimated that the genome of the AIDS virus has a nucleotide substitution rate on the order of 10−3 per site per year, with the rate in the second half of the genome being double that in the first half.

Key words

Human AIDS viruses Molecular evolution Phylogeny 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Air GM (1981) Sequence relationships among the hemagglutinin genes of 12 subtypes of influenza A virus. Proc Natl Acad Sci USA 78:7639–7643PubMedGoogle Scholar
  2. Barre-Sinoussi F, Chermann JC, Rey F, Nugeyre MT, Chamaret S, Gruest J, Dauguet C, Axler-Blin C, Vezinet-Brun F, Rouzioux C, Rozenbaum W, Montagnier L (1983) Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Science 220:868–871PubMedGoogle Scholar
  3. Chiu I-M, Yaniv A, Dahlberg JE, Gazit A, Skuntz SF, Tronick SR, Aaronson SA (1985) Nucleotide sequence evidence for relationship of AIDS retrovirus to lentiviruses. Nature 317:366–368CrossRefPubMedGoogle Scholar
  4. Gojobori T, Yokoyama S (1985) Rates of evolution of the retroviral oncogene of Moloney murine sarcoma virus and of its cellular homologues. Proc Natl Acad Sci USA 82:4198–4201Google Scholar
  5. Gojobori T, Ishii K, Nei M (1982) Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide. J Mol Evol 18:414–423CrossRefPubMedGoogle Scholar
  6. Gojobori T, Yokoyama S, Maruyama T (1985) DNA polymorphism of acquired immune deficiency syndrome virus. Genetics 110:s91Google Scholar
  7. Gonda MA, Wong-Staal F, Gallo RC, Clements JE, Narayan O, Gilden RV (1985) Sequence homology and morphologic similarity of HTLV-III and visna virus, a pathogenic lentivirus. Science 227:173–177PubMedGoogle Scholar
  8. Holland J, Spindler K, Horodyski F, Grabau E, Nicol S, Vande Pol S (1982) Rapid evolution of RNA genomes. Science 215:1577–1589PubMedGoogle Scholar
  9. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian Protein Metabolism II. Acdemic Press, New York, p 21Google Scholar
  10. Kanki PJ, Alroy J, Essex M (1985) Isolation of T-lymphotropic retrovirus related to HTLV-III/LAV from wild-caught African green monkeys. Science 230:951–954PubMedGoogle Scholar
  11. Kanki PJ, Barin F, M'Boup S, Allan JS, Romet-Lemmone 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 232:238–243PubMedGoogle Scholar
  12. Kimura M (1969) The rate of molecular evolution considered from the standpoint of population genetics. Proc Natl Acad Sci USA 63:1181–1188PubMedGoogle Scholar
  13. Kimura M (1981) Estimation of evolutionary distances between homologous nucleotide sequences. Proc Natl Acad Sci USA 78:454–458PubMedGoogle Scholar
  14. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge, EnglandGoogle Scholar
  15. Krystal M, Buonagurio D, Young JF, Palese P (1983) Sequential mutations in the NS genes of influenza virus field strains. J Virol 45:547–554PubMedGoogle Scholar
  16. Levy JA, Hoffman AD, Kramer SM, Landis JA, Shimabukuro JM, Oshiro LS (1984) Isolation of lymphocytopathic retroviruses from San Francisco patients with AIDS. Science 225:840–842PubMedGoogle Scholar
  17. Martinez C, Del Rio L, Portela A, Domingo E, Ortin J (1983) Evolution of the influenza virus neuraminidase gene during drift of the N2 subtype. Virology 130539–545CrossRefPubMedGoogle Scholar
  18. Miyata T, Yasanaga T (1980) Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application. J Mol Evol 16:23–36CrossRefPubMedGoogle Scholar
  19. Moloney JB (1966) A virus-induced rhabdomyosarcoma of mice. Natl Cancer Inst Monogr 22:139–142PubMedGoogle Scholar
  20. Muesing MA, Smith DH, Cabradilla CD, Benton CV, Lasky LA, Capon DJ (1985) Nucleic acid structure and expression of the human AIDS/lymphadenopathy retrovirus. Nature 313:450–458CrossRefPubMedGoogle Scholar
  21. Nei M (1983) Genetic polymorphism and the role of mutation in evolution. In: Nei M, Koehn RK (eds) Evolution of genes and proteins. Sinauer Associates, Sunderland, Massachusetts, p 165Google Scholar
  22. Popovic M, Sarngadharan MG, Read E, Gallo RC (1984) Detection, isolation, and continuous production of cytopathic retroviruses (HTLV-III) from patients with AIDS and pre-AIDS. Science 224:497–500PubMedGoogle Scholar
  23. Ratner L, Gallo RC, Wong-Staal F (1985a) HTLV-III, LAV, ARV are variants of the same AIDS virus. Nature 313:636–637CrossRefGoogle Scholar
  24. Ratner L, Haseltine W, Patarca R, Livak KJ, Starcich B, Josephs SF, Doran ER, Rafalski JA, Whitehorn EA, Baumeister K, Ivanoff L, Petteway SR, Pearson ML, Lautenberger JA, Papas TS, Ghrayeb J, Chang NT, Gallo RC, Wong-Staal F (1985b) Complete nucleotide sequence of the AIDS virus, HTLV-III. Nature 313:277–284CrossRefPubMedGoogle Scholar
  25. Reddy EP, Smith MJ, Aaronson SA (1981) Complete nucleotide sequence and organization of the Moloney murine sarcoma virus genome. Science 214:445–450PubMedGoogle Scholar
  26. Sanchez-Pescador R, Power MD, Barr PJ, Steimer KS, Stempien MM, Brown-Shimer SL, Gee WW, Renard A, Randolph A, Levy JA, Dina D, Luciw PA (1985) Nucleotide sequence and expression of an AIDS-associated retrovirus (ARV-2). Science 484–492Google Scholar
  27. Shaw GM, Hahn BH, Arya SK, Groopman JE, Gallo RC, Wong-Staal F (1984) Molecular characterization of human T-cell leukemia (lymphotropic) virus type III in the acquired immune deficiency syndrome. Science 226:1165–1171PubMedGoogle Scholar
  28. Sonigo P, Alizon M, Staskus K, Klatzmann D, Cole S, Danos O, Retzel E, Tiollais P, Haase A, Wain-Hobson S (1985) Nucleotide sequence of the visna lentivirus: relationship to the AIDS virus. Cell 42:369–382CrossRefPubMedGoogle Scholar
  29. Stephens RM, Casey JW, Rice NR (1986) Equine infectious anemia virusgag andpol genes: relatedness to visna and AIDS virus. Science 231:589–594PubMedGoogle Scholar
  30. Takahata N, Kimura M (1981) A model of evolutionary base substitutions and its application with special reference to rapid change of pseudogenes. Genetics 98:641–657PubMedGoogle Scholar
  31. Temin HM (1974) The cellular and molecular biology of RNA tumor viruses, especially avian leukosis-sarcoma viruses and their relatives. Adv Cancer Res 19:47–104PubMedGoogle Scholar
  32. Van Beveren C, van Straaten F, Galleshaw JA, Verma IM (1981a) Nucleotide sequence of the genome of a murine sarcoma virus Cell 27:97–108CrossRefPubMedGoogle Scholar
  33. Van Beveren C, Galleshaw JA, Jonas V, Berns AJM, Doolittle RF, Donoghue DJ, Verma IM (1981b) Nucleotide sequence and formation of the transforming gene of a mouse sarcoma virus. Nature 289:258–262CrossRefPubMedGoogle Scholar
  34. Varmus HE (1982) Form and function of retroviral proviruses. Science 216:812–820PubMedGoogle Scholar
  35. Wain-Hobson S, Sonigo P, Danos O, Cole S, Alizon M (1985a) Nucleotide sequence of the AIDS virus, LAV. Cell 40:9–17CrossRefPubMedGoogle Scholar
  36. Wain-Hobson S, Alizon M, Montagnier L (1985b) Relationship of AIDS to other retroviruses. Nature 313:743CrossRefGoogle Scholar

Copyright information

© Springer-Verlag New York Inc 1987

Authors and Affiliations

  • Shozo Yokoyama
    • 1
  • Takashi Gojobori
    • 2
  1. 1.Department of PsychiatryWashington University School of MedicineSt. LouisUSA
  2. 2.National Institute of GeneticsMishima, Shizuoka-kenJapan

Personalised recommendations