Retrovirus mutation rates and their role in genetic variation

References

1. Alevy M. C., Vogt P. K. 1978; Ts pol mutants of avian sarcoma viruses: mapping and demonstration of single cycle recombinants. Virology 87:21–33
   [Google Scholar]
2. Anderson J. A., Bowman E. H., Hu W. -S. 1988a; Retroviral recombination rates do not increase linearly with marker distance and are limited by the size of the recombining subpopulation. Journal of Virology 72:1195–1202
   [Google Scholar]
3. Anderson J. A., Teufel R. J., Yin P. D., Hu W. -S. 1988b; Correlated template-switching events during minus-strand DNA synthesis: a mechanism for high negative interference during retroviral recombination. Journal of Virology 72:1186–1194
   [Google Scholar]
4. Balfe P, Simmonds P, Ludlam C. A., Bishop J. O., Brown A. J. L. 1990; Concurrent evolution of human immunodeficiency virus type 1 in patients infected from the same source: rate of sequence change and low frequency of inactivating mutations. Journal of Virology 64:6221–6233
   [Google Scholar]
5. Bebenek K, Kunkel T. A. 1993; The fidelity of retroviral reverse transcriptases. In Reverse Transcriptase pp 85–102 Skalka A. M, Goff S. P. Edited by Plainview, NY: Cold Spring Harbor Laboratory Press;
   [Google Scholar]
6. Blair D. G. 1977; Genetic recombination between avian leukosis and sarcoma viruses. Experimental variables and the frequencies of recombination. Virology 77:534–544
   [Google Scholar]
7. Bonhoeffer S, Coffin J. M., Nowak M. A. 1997a; Human immunodeficiency virus drug therapy and virus load. Journal of Virology 71:3275–3278
   [Google Scholar]
8. Bonhoeffer S, May R. M., Shaw G. M., Nowak M. A. 1997b; Virus dynamics and drug therapy. roceedings of the National Academy of Sciences, USA 94:6971–6923
   [Google Scholar]
9. Boucher C. A., O’Sullivan E., Mulder J. W., Ramautarsing C., Kellam P., Darby G., Lange J. M., Goudsmit J., Larder B. A. 1992; Ordered appearance of zidovudine resistance mutations during treatment of 18 human immunodeficiency virus-positive subjects. Journal of Infectious Diseases 165:105–110
   [Google Scholar]
10. Bouhamdan M., Benichou S., Rey F., Navarro J. -M, Agostini I., Spire B., Camonis J., Slupphaug G., Vigne R., Benarous R., Sire J. 1996; Human immunodeficiency virus type 1 Vpr protein binds to the uracil DNA glycosylase DNA repair enzyme. Journal of Virology 70:697–704
    [Google Scholar]
11. Boyer J. C., Bebenek K., Kunkel T. A. 1992; Unequal human immunodeficiency virus type 1 reverse transcriptase error rates with RNA and DNA templates. Proceedings of the National Academy of Sciences, USA 89:6919–6923
    [Google Scholar]
12. Burns D. P., Desrosiers R. C. 1991; Selection of genetic variants of simian immunodeficiency virus in persistently infected rhesus monkeys. Journal of Virology 65:1843–1854
    [Google Scholar]
13. Cleland A., Watson H. G., Robertson P., Ludlam C. A., Brown A. J. 1996; Evolution of zidovudine resistance-associated genotypes in human immunodeficiency virus type 1-infected patients. Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology 12:6–18
    [Google Scholar]
14. Coffin J. M. 1979; Structure, replication, and recombination of retrovirus genomes : some unifying hypotheses. Journal ofGeneral Virology 42:1–26
    [Google Scholar]
15. Coffin J. 1992; Genetic diversity and evolution of retroviruses. Current Topics in Microbiology and Immunology 176:143–164
    [Google Scholar]
16. Coffin J. 1995; HIV population dynamics in vivo : implications for genetic variation, pathogenesis, and therapy. Science 267:483–489
    [Google Scholar]
17. Coffin J. M. 1996; Retroviridae : the viruses and their replication. In Fields Virology, 3rd edn. pp 1767–1847 Fields B. N., Knipe D. M., Howley P. M. Edited by Philadelphia: Lippincott-Raven;
    [Google Scholar]
18. Coffin J. M., Tsichlis P. N., Barker C. S. 1980; Variation in avian retrovirus genomes. Annals of the New York Academy of Sciences 354:410–425
    [Google Scholar]
19. Cohen E. A., Dehni G., Sodroski J. G., Haseltine W. A. 1990; Human immunodeficiency virus vpr product is a virion-associated regulatory protein. Journal of Virology 64:3097–3099
    [Google Scholar]
20. Domingo E., Martinez-Salas E., Sobrino F., delaTorre J. C., Portela A., Ortin J., Lopez-Galindez C., Perez-Brena P., Villanueva N., Najera R., VandePol S., Steinhauer D., DePolo N., Holland J. 1985; The quasispecies (extremely heterogeneous) nature of viral RNA genome populations : biological relevance - a review. Gene1–8
    [Google Scholar]
21. Dougherty J. P., Temin H. M. 1988; Determination of the rate of base-pair substitution and insertion mutation in retrovirus replication. Journal of Virology 62:2817–2822
    [Google Scholar]
22. Duran-Reynals F. 1942; The reciprocal infection of ducks and chickens with tumor-inducing viruses. Cancer Research 2:343–369
    [Google Scholar]
23. Hahn B. H., Shaw G. M., Taylor M. E., Redfield R. R., Markham P. D., Salahuddin S. Z., Wong-Staal F., Gallo R. C., Parks E. S., Parks W. P. 1986; TLV-III/LAV over time inpatients with AIDS or at risk for AIDS. Science 232:1548–1553
    [Google Scholar]
24. He J., Choe S., Walker R., DiMarzio P., Morgan D. O., Landau N. R. 1995; Human immunodeficiency virus type 1 viral protein R (Vpr) arrests cells in the G₂ phase of the cell cycle by inhibiting p34^cdc2activity. Journal of Virology 69:6705–6711
    [Google Scholar]
25. Heinzinger N. K., Bukrinsky M. I., Haggerty S. A., Ragland A. M., Kewalramani V., Lee M. -A., Gendelman H. E., Ratner L., Stevenson M., Emerman M. 1994; The Vpr protein of human immunodeficiency virus type 1 influences nuclear localization of viral nucleic acids in nondividing host cells. Proceedings of the National Academy of Sciences USA 91:7311–7315
    [Google Scholar]
26. Holmes E. C., Zhang L. Q., Simmonds P., Ludlam C. A., LeighBrown A. J. 1992; Convergent and divergent sequence evolution in the surface envelope glycoprotein of HIV-1 within a single infected patient. Proceedings of the National Academy of Sciences USA 89:4835–4839
    [Google Scholar]
27. Hu W. -S., Temin H. M. 1990a; Genetic consequences of packaging two RNA genomes in one retroviral particle : pseudodiploidy and high rate of genetic recombination. Proceedings of the National Academy of Sciences, USA 87:1556–1560
    [Google Scholar]
28. Hu W. -S, Temin H. M. 1990b; Retroviral recombination and reverse transcription. Science 250:1227–1233
    [Google Scholar]
29. Hu W.-S, Bowman E. H., Delviks K. A., Pathak V. K. 1997; Homologous recombination occurs in a distinct retroviral subpopulation and exhibits high negative interference. Journal of Virology 71:6028–6036
    [Google Scholar]
30. Hunter E. 1978; The mechanism for genetic recombination in the avian retroviruses. Current Topics in Microbiology and Immunology 79:295–309
    [Google Scholar]
31. Johnson P. R., Hamm T. E., Goldstein S., Kitov S., Hirsch V. M. 1990; The genetic fate of molecularly cloned simian immunodeficiency virus in experimentally infected macaques. Virology 185:217–228
    [Google Scholar]
32. Jones J. S., Allan R. W., Temin H. M. 1994; One retroviral RNA is sufficient for synthesis of viral DNA. Journal of Virology 68:207–216
    [Google Scholar]
33. Jowett J. B. M., Planelles V., Poon B., Shah N. P., Chen M. -L, Chen I. S. Y. 1995; The human immunodeficiency virus type 1 vpr gene arrests infected T cells in the G₂ + M phase of the cell cycle. Journal of Virology 69:6304–6313
    [Google Scholar]
34. Kawai S., Hanafusa H. 1972; Genetic recombination with avian tumor viruses. Virology 49:37–44
    [Google Scholar]
35. Kim T., Mudry R. A., Rexrode C. A., Pathak V. K. 1996; Retroviral mutation rates and A-to-G hypermutations during different stages of retroviral replication. Journal of Virology 70:7594–7602
    [Google Scholar]
36. Kondo E., Mammano F., Cohen E. A., Gottlinger H. G. 1995; The p6^gag domain of human immunodeficiency virus type 1 is sufficient for the incorporation of Vpr into heterologous viral particles. Journal of Virology 69:2759–2764
    [Google Scholar]
37. Leider J. M., Palese P., Smith F. I. 1988; Determination of the mutation rate of a retrovirus. Journal of Virology 62:3084–3091
    [Google Scholar]
38. Leigh Brown A. J. 1997; Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population. Proceedings of the National Academy of Sciences, USA 94:1862–1865
    [Google Scholar]
39. Leigh Brown A. J., Richman D. D. 1997 HIV-1: gambling on the evolution of drug resistance? Nature Medicine 3:268–271
    [Google Scholar]
40. Linial M., Brown S. 1979; High-frequency recombination within the gag gene of Rous sarcoma virus. Journal of Virology 31:257–260
    [Google Scholar]
41. Lu Y. -L, Spearman P., Ratner L. 1993; Human immunodeficiency virus type 1 viral protein R localization in infected cells and virions. Journal of Virology 67:6542–6550
    [Google Scholar]
42. Lu Y. -L., Bennett R. P., Wills J. W., Gorelick R., Ratner L. 1995; A leucine triplet repeat sequence (LXX)₄ in p6^9a9 is important for Vpr incorporation into human immunodeficiency virus type 1 particles. Journal of Virology 69:6873–6879
    [Google Scholar]
43. Lukashov V. V., Kuiken C. L., Goudsmit J. 1995; Intrahost human immunodeficiency virus type 1 evolution is related to length of the immunocompetent period. Journal of Virology 69:6911–6916
    [Google Scholar]
44. Mansky L. M. 1996a; Forward mutation rate of human immuno-deficiency virus type 1 in a T-lymphoid cell line. AIDS Research and Human Retroviruses 12:307–314
    [Google Scholar]
45. Mansky L. M. 1996b; The mutation rate of human immunodeficiency virus type 1 is influenced by the vpr gene. Virology 222:391–400
    [Google Scholar]
46. Mansky L. M. 1997; Accessory replication proteins and reverse transcription accuracy:implications for retroviral genetic diversity. Trends in Genetics 13:134–136
    [Google Scholar]
47. Mansky L. M., Temin H. M. 1994; Lower mutation rate of bovine leukemia virus relative to that of spleen necrosis virus. Journal of Virology 68:494–499
    [Google Scholar]
48. Mansky L. M., Temin H. M. 1995; Lower in vivo mutation rate of human immunodeficiency virus type 1 than predicted from the fidelity of purified reverse transcriptase. Journal of Virology 69:5087–5094
    [Google Scholar]
49. Martinez M. A., Vartanian J.-P, Wain-Hobson S. 1994; Hypermutagenesis of RNA using human immunodeficiency virus type 1 and biased dNTP concentrations. Proceedings of the National Academy of Sciences, USA 91:11787–11791
    [Google Scholar]
50. Monk R. J., Malik F. G., Stokesberry D., Evans L. H. 1992; Direct determination of the point mutation rate of a murine retrovirus. Journal of Virology 66:3683–3689
    [Google Scholar]
51. Nowak M. 1990; HIV mutation rate. Nature 347:522
    [Google Scholar]
52. Nowak M. A. 1995; AIDS pathogenesis: from models to viral dynamics in patients. Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology 10: Suppl S1–S5
    [Google Scholar]
53. Nowak M. A., Anderson R. M., Boerlijst M. C., Bonhoeffer S., May R. M. 1996; HIV-1 evolution and disease progression. Science 274:1008–1009
    [Google Scholar]
54. Nowak M. A., Anderson R. M., McLean A. R., Wolfs T. F. W., Goudsmit J., May R. M. 1991; Antigenic diversity thresholds and the development of AIDS. Science 254:963–969
    [Google Scholar]
55. O’Rear J. J., Mizutani S., Hoffman G., Flandt M., Temin H. M. 1980; Infectious and noninfectious recombinant clones of the provirus of SNV differ in cellular DNA and are apparently the same in viral DNA. Cell423–430
    [Google Scholar]
56. Overbaugh J., Rudensey L. M., Papenhausen M. D., Benveniste R. E., Morton W. R. 1991; Variation in simian immunodeficiency virus env is confined to V1 and V4 during progression to simian AIDS. Journal of Virology 65:7025–7031
    [Google Scholar]
57. Pathak V. K., Temin H. M. 1990a; Broad spectrum of in vivo forward mutations, hypermutations, and mutational hotspots in a retroviral shuttle vector after a single replication cycle : substitutions, frameshifts, and hypermutations. Proceedings of the National Academy of Sciences, USA 87:6019–6023
    [Google Scholar]
58. Pathak V. K., Temin H. M. 1990b; Broad spectrum of in vivo forward mutations, hypermutations, and mutational hotspots in a retroviral shuttle vector after a single replication cycle : deletions and deletions with insertions. Proceedings of the National Academy of Sciences, USA 87:6024–6028
    [Google Scholar]
59. Paxton W., Connor R. I., Landau N. R. 1993; Incorporation of Vpr into human immunodeficiency virus type 1 virions : requirement for the p6 region of gag and mutational analysis. Journal of Virology 67:7229–7237
    [Google Scholar]
60. Planelles V., Bachelerie F., Jowett J. B., Haislip A., Xie Y., Banooni P., Masuda T., Chen I. S. Y. 1995; Fate of the human immunodeficiency type 1 provirus in infected cells : a role for vpr . Journal of Virology 69:5883–5889
    [Google Scholar]
61. Refaeli Y., Levy D. N., Weiner D. B. 1995; The glucocorticoid receptor type II complex is a target of the HIV-1 vpr gene product. Proceedings of the National Academy of Sciences, USA 92:3621–3625
    [Google Scholar]
62. Rogel M. E., Wu L. I., Emerman M. 1995; The human immunodeficiency virus type 1 vpr gene prevents cell proliferation during chronic infection. Journal of Virology 69:882–888
    [Google Scholar]
63. Rous P., Murphy J. B. 1913; Variations in a chicken sarcoma caused by a filterable agent. Journal of Experimental Medicine 17:219–231
    [Google Scholar]
64. Seibert S. A., Howell C. Y., Hughes M. K., Hughes A. L. 1995; Natural selection on the gag, pol and env genes of HIV-1. Molecular Biology and Evolution 12:803–813
    [Google Scholar]
65. Simmonds P., Balfe P., Ludlam C. A., Bishop J. O., Leigh Brown A. J. 1990; Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1. Journal of Virology 64:5840–5850
    [Google Scholar]
66. Skalka A. M., Boone L., Junghans R., Luk D. 1982; Genetic recombination in avian retroviruses. Journal of Cellular Biochemistry 19:293–304
    [Google Scholar]
67. Temin H. M. 1960; The control of cellular morphology in embryonic cells infected with Rous sarcoma virus in vitro . Virology 10:182–197
    [Google Scholar]
68. Temin H. M. 1989 Is HIV unique or merely different? Journal of Acquired Immune Deficiency Syndromes 2:1–9
    [Google Scholar]
69. Temin H. M. 1993; Retrovirus variation and reverse transcription: abnormal strand transfers result in retrovirus genetic variation. Proceedings of the National Academy of Sciences USA 90:6900–6903
    [Google Scholar]
70. Temin H. M., Rubin H. 1958; Characteristics of an assay for Rous sarcoma virus and Rous sarcoma cells in tissue culture. Virology 6:669–688
    [Google Scholar]
71. Varela-Echavarria A., Garvey N., Preston B. D., Dougherty J. D. 1990; Comparison of Moloney murine leukemia virus mutation rate with the fidelity of its reverse transcriptase in vitro. Journal of Biological Chemistry 267:24681–24688
    [Google Scholar]
72. Vartanian J. -P., Meyerhans A., Asjo B., Wain-Hobson S. 1991; Selection, recombination, and G to A hypermutation of human immunodeficiency virus type 1 genomes. Journal of Virology 65:1779–1788
    [Google Scholar]
73. Vartanian J. -P., Plikat U., Henry M., Mahieux R., Guillemot L., Meyerhans A., Wain-Hobson S. 1997; HIV genetic variation is directed and restricted by DNA precursor availability. Journal ofMolecular Biology 270:139–151
    [Google Scholar]
74. Vogt P. K. 1971; Genetically stable reassortment of markers during mixed infection with avian tumor viruses. Virology 46:947–952
    [Google Scholar]
75. Wain-Hobson S. 1996; Running the gamut of retroviral mutation. Trends in Microbiology 4:135–141
    [Google Scholar]
76. Wainberg M. A., Drosopoulos W. C., Salomon H., Hsu M., Borkow G., Parniak M. A., Gu Z., Song Q., Manne J., Islam S., Castriota G., Prasad V. R. 1996; Enhanced fidelity of 3TC-selected mutant HIV- 1 reverse transcriptase. Science 2 71:1282–1285
    [Google Scholar]
77. Weiss R., Teich N., Varmus H., Coffin J. 1985 RNA Tumor Viruses, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
78. Willems L., Thienpont E., Kerkhofs P., Burny A., Mammerickx M., Kettmann R. 1993; Bovine leukemia virus, an animal model for the study of intrastrain variability. Journal of Virology 67:1086–1089
    [Google Scholar]
79. Wolinsky S. M., Korber B. T. M., Neumann A. U., Daniels M., Kuntsman K. J., Whetsell A. J., Furtado M. R., Cao Y., Ho D. D., Safrit J. T., Koup R. A. 1996; Adaptive the natural course of infection. Science 272:537–542
    [Google Scholar]
80. Wright S. 1969; Evolution and the genetics of populations. In The Theory of Gene Frequencies pp Chicago: University of Chicago Press;512
    [Google Scholar]
81. Wyke J. A., Beamand J. A. 1979; Genetic recombination in Rous sarcoma virus : the genesis of recombinants and lack of evidence for linkage between pol, env and src genes in three factor crosses. Journal of General Virology 43:349–364
    [Google Scholar]
82. Zhang J., Temin H. M. 1993; Rate and mechanisms of nonhomologous recombination during a single cycle of retroviral replication. Science 259:234–238
    [Google Scholar]
83. Zhao L. -J., Mukherjee S., Narayan O. 1994; Biochemical mechanism of HIV-1 Vpr function. Journal of Biological Chemistry 269:15577–15582
    [Google Scholar]