Replicative Homeostasis: A fundamental mechanism mediating selective viral replication and escape mutation

Virology Journal

Volumn 2, Issue , 2005, Pages

  Sallie, Richard ^a  

^a NONE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; RNA POLYMERASE;

AUTOREGULATION; BIOLOGY; EVOLUTION; GENE EXPRESSION; HOMEOSTASIS; KINETICS; MUTATION RATE; NONHUMAN; REVIEW; VIRUS GENOME; VIRUS INFECTION; VIRUS MUTATION; VIRUS REPLICATION;

EID: 15744396368     PISSN: 1743422X     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-2-10     Document Type: Review

References (86)

1. Abdelhamed AM, Kelley CM, Miller TG, Furman PA, Isom HC: Rebound of hepatitis B virus replication in HepG2 cells after cessation of antiviral treatment. J Virol 2002, 76:8148-60.
2. Ahlquist P, Dasgupta R, Kaesberg P: Nucleotide sequence of the brome mosaic virus genome and its implications for viral replication. J Mol Biol 1984, 172:369-83.
3. Ahmad N, Venkatesan S: Nef protein of HIV-1 is a transcriptional repressor of HIV-1 LTR. Science 1988, 241:1481-5.
4. Bassett SE, Guerra B, Brasky K, Miskovsky E, Houghton M, Klimpel GR, Lanford RE: Protective immune response to hepatitis C virus in chimpanzees rechallenged following clearance of primary infection. Hepatology 2001, 33:1479-87.
5. Bertoletti A, Ferrari C: Kinetics of the immune response during HBV and HCV infection. Hepatology 2003, 38:4-13.
6. Bock CT, Tillmann HL, Torresi J, Klempnauer J, Locarnini S, Manns MP, Trautwein C: Selection of hepatitis B virus polymerase mutants with enhanced replication by lamivudine treatment after liver transplantation. Gastroenterology 2002, 122:264-73.
7. Cao Y, Qin L, Zhang L, Safrit J, Ho DD: Virologic and immunologic characterization of long-term survivors of human immunodeficiency virus type 1 infection. N Engl J Med 1995, 332:201-8.
8. Carman WF, Zanetti AR, Karayiannis P, Waters J, Manzillo G, Tanzi E, Zuckerman AJ, Thomas HC: Vaccine-induced escape mutant of hepatitis B virus. Lancet 1990, 336:325-9.
9. Chen M, Shi C, Kalia V, Tencza SB, Montelaro RC, Gupta P: HIV gp120 V(1)/V(2) and C(2)-V(3) domains glycoprotein compatibility is required for viral replication. Virus Res 2001, 79:91-101.
10. Chung RT, He W, Saquib A, Contreras AM, Xavier RJ, Chawla A, Wang TC, Schmidt EV: Hepatitis C virus replication is directly inhibited by IFN-alpha in a full-length binary expression system. Proc Natl Acad Sci U S A 2001, 98:9847-52.
11. Coffin JM: HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science 1995, 267:483-9.
12. Daar ES, Moudgil T, Meyer RD, Ho DD: Transient high levels of viremia in patients with primary human immunodeficiency virus type 1 infection. N Engl J Med 1991, 324:961-4.
13. De Jong JJ, De Ronde A, Keulen W, Tersmette M, Goudsmit J: Minimal requirements for the human immunodeficiency virus type 1 V3 domain to support the syncytium-inducing phenotype: analysis by single amino acid substitution. J Virol 1992, 66:6777-80.
14. De Jong JJ, Goudsmit J, Keulen W, Klaver B, Krone W, Tersmette M, de Ronde A: Human immunodeficiency virus type 1 clones chimeric for the envelope V3 domain differ in syncytium formation and replication capacity. J Virol 1992, 66:757-65.
15. DeStefano JJ: Interaction of human immunodeficiency virus nucleocapsid protein with a structure mimicking a replication intermediate. Effects on stability, reverse transcriptase binding, and strand transfer. J Biol Chem 1996, 271:16350-6.
16. Drake JW, Holland JJ: Mutation rates among RNA viruses. Proc Natl Acad Sci U S A 1999, 96:13910-3.
17. Duarte E, Clarke D, Moya A, Domingo E, Holland J: Rapid fitness losses in mammalian RNA virus clones due to Muller's ratchet. Proc Natl Acad Sci U S A 1992, 89:6015-9.
18. Eigen M: Viral quasispecies. Sci Am 1993, 269:42-9.
19. Enomoto N, Sakuma I, Asahina Y, Kurosaki M, Murakami T, Yamamoto C, Ogura Y, Izumi N, Marumo F, Sato C: Mutations in the nonstructural protein 5A gene and response to interferon in patients with chronic hepatitis C virus 1b infection. N Engl J Med 1996, 334:77-81.
20. Erie DA, Hajiseyedjavadi O, Young MC, von Hippel PH: Multiple RNA polymerase conformations and GreA: control of the fidelity of transcription. Science 1993, 262:867-73.
21. Fackler OT, d'Aloja P, Baur AS, Federico M, Peterlin BM: Nef from human immunodeficiency virus type 1(F12) inhibits viral production and infectivity. J Virol 2001, 75:6601-8.
22. Farci P, Alter HJ, Govindarajan S, Wong DC, Engle R, Lesniewski RR, Mushahwar IK, Desai SM, Miller RH, Ogata N, et al.: Lack of protective immunity against reinfection with hepatitis C virus. Science 1992, 258:135-40.
23. Fust G: Enhancing antibodies in HIV infection. Parasitology 1997, 115(Suppl):S127-40.
24. Girn J, Kavoosi M, Chantler J: Enhancement of coxsackievirus B3 infection by antibody to a different coxsackievirus strain. J Gen Virol 2002, 83:351-8.
25. Guidotti LG, Rochford R, Chung J, Shapiro M, Purcell R, Chisari FV: Viral clearance without destruction of infected cells during acute HBV infection. Science 1999, 284:825-9.
26. Guzman MG, Kouri G, Halstead SB: Do escape mutants explain rapid increases in dengue case-fatality rates within epidemics? Lancet 2000, 355:1902-3.
27. Haldane J: The Causes of Evolution. Princeton University Press, New Jersey; 1932.
28. Hedges SB, Chen H, Kumar S, Wang DY, Thompson AS, Watanabe H: A genomic timescale for the origin of eukaryotes. BMC Evol Biol 2001, 1:4.
29. Ho DD, Neumann AU, Perelson AS, Chen W, Leonard JM, Markowitz M: Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature 1995, 373:123-6.
30. Jacobo-Molina A, Arnold E: HIV reverse transcriptase structure-function relationships. Biochemistry 1991, 30:6351-6.
31. Jeon C, Agarwal K: Fidelity of RNA polymerase II transcription controlled by elongation factor TFIIS. Proc Natl Acad Sci U S A 1996, 93:13677-82.
32. Kao JH, Chen PJ, Lai MY, Chen DS: Superinfection of heterologous hepatitis C virus in a patient with chronic type C hepatitis. Gastroenterology 1993, 105:583-7.
33. Kao JH, Chen PJ, Wang JT, Yang PM, Lai MY, Wang TH, Chen DS: Superinfection by homotypic virus in hepatitis C virus carriers: studies on patients with post-transfusion hepatitis. J Med Virol 1996, 50:303-8.
34. Kiho Y, Nishiguchi M: Unique nature of an attenuated strain of tobacco mosaic virus: autoregulation. Microbiol Immunol 1984, 28:589-99.
35. Kirchhoff F, Mori K, Desrosiers RC: The "V3" domain is a determinant of simian immunodeficiency virus cell tropism. J Virol 1994, 68:3682-92.
36. Kirchhoff F, Morrison HG, Murray MG, Rennert P, Desrosiers RC: SIVmac expressing hybrid envelope proteins containing HIV-1 V3 and/or C4 sequences is not competent for replication. AIDS Res Hum Retroviruses 1994, 10:309-13.
37. Kohmoto M, Miyazawa T, Tomonaga K, Kawaguchi Y, Mori T, Tohya Y, Kai C, Mikami T: Comparison of biological properties of feline immunodeficiency virus isolates using recombinant chimeric viruses. J Gen Virol 1994, 75(Pt 8):1935-42.
38. Kolber MA, Gabr AH, De La Rosa A, Glock JA, Jayaweera D, Miller N, Dickinson GM: Genotypic analysis of plasma HIV-1 RNA after influenza vaccination of patients with previously undetectable viral loads. Aids 2002, 16:537-42.
39. Kuwata T, Shioda T, Igarashi T, Ido E, Ibuki K, Enose Y, Stahl-Hennig C, Hunsmann G, Miura T, Hayami M: Chimeric viruses between SIVmac and various HIV-1 isolates have biological properties that are similar to those of the parental HIV-1. Aids 1996, 10:1331-7.
40. Lazaro E, Escarmis C, Perez-Mercader J, Manrubia SC, Domingo E: Resistance of virus to extinction on bottleneck passages: study of a decaying and fluctuating pattern of fitness loss. Proc Natl Acad Sci U S A 2003, 100:10830-5.
41. Lok AS, Lai CL, Wu PC, Leung EK, Lam TS: Spontaneous hepatitis B e antigen to antibody seroconversion and reversion in Chinese patients with chronic hepatitis B virus infection. Gastroenterology 1987, 92:1839-43.
42. Maga G, Frouin I, Spadari S, Hubscher U: Replication protein A as a "fidelity clamp" for DNA polymerase alpha. J Biol Chem 2001, 276:18235-42.
43. Mahaney K, Tedeschi V, Maertens G, Di Bisceglie AM, Vergalla J, Hoofnagle JH, Sallie R: Genotypic analysis of hepatitis C virus in American patients. Hepatology 1994, 20:1405-11.
44. Manzin A, Candela M, Solforosi L, Gabrielli A, Clementi M: Dynamics of hepatitis C viremia after plasma exchange. J Hepatol 1999, 31:389-93.
45. Marrone A, Sallie R: Genetic heterogeneity of hepatitis C virus. The clinical significance of genotypes and quasispecies behavior. Clin Lab Med 1996, 16:429-49.
46. McCright IJ, Tsunoda I, Whitby FG, Fujinami RS: Theiler's viruses with mutations in loop I of VP1 lead to altered tropism and pathogenesis. J Virol 1999, 73:2814-24.
47. Melegari M, Scaglioni PP, Wands JR: Hepatitis B virus mutants associated with 3TC and famciclovir administration are replication defective. Hepatology 1998, 27:628-33.
48. Michalak TI, Pasquinelli C, Guilhot S, Chisari FV: Hepatitis B virus persistence after recovery from acute viral hepatitis. J Clin Invest 1994, 93:230-9.
49. Miller MD, Warmerdam MT, Gaston I, Greene WC, Feinberg MB: The human immunodeficiency virus-1 nef gene product: a positive factor for viral infection and replication in primary lymphocytes and macrophages. J Exp Med 1994, 179:101-13.
50. Moss WJ, Ryon JJ, Monze M, Cutts F, Quinn TC, Griffin DE: Suppression of human immunodeficiency virus replication during acute measles. J Infect Dis 2002, 185:1035-42.
51. Mustafa F, Richmond JF, Fernandez-Larsson R, Lu S, Fredriksson R, Fenyo EM, O'Connell M, Johnson E, Weng J, Santoro JC, Robinson HL: HIV-1 Env glycoproteins from two series of primary isolates: replication phenotype and immunogenicity. Virology 1997, 229:269-78.
52. Neumann AU, Lam NP, Dahari H, Gretch DR, Wiley TE, Layden TJ, Perelson AS: Hepatitis C viral dynamics in vivo and the antiviral efficacy of interferon-alpha therapy. Science 1998, 282:103-7.
53. Nevens F, Main J, Honkoop P, Tyrrell DL, Barber J, Sullivan MT, Fevery J, De Man RA, Thomas HC: Lamivudine therapy for chronic hepatitis B: a six-month randomized dose-ranging study. Gastroenterology 1997, 113:1258-63.
54. Nowak MA, May RM, Phillips RE, Rowland-Jones S, Lalloo DG, McAdam S, Klenerman P, Koppe B, Sigmund K, Bangham CR, et al.: Antigenic oscillations and shifting immunodominance in HIV-1 infections. Nature 1995, 375:606-11.
55. Oehlenschlager F, Eigen M: 30 years later - a new approach to Sol Spiegelman's and Leslie Orgel's in vitro evolutionary studies. Dedicated to Leslie Orgel on the occasion of his 70th birthday. Orig Life Evol Biosph 1997, 27:437-57.
56. Ostrowski MA, Krakauer DC, Li Y, Justement SJ, Learn G, Ehler LA, Stanley SK, Nowak M, Fauci AS: Effect of immune activation on the dynamics of human immunodeficiency virus replication and on the distribution of viral quasispecies. J Virol 1998, 72:7772-84.
57. Perelson AS, Neumann AU, Markowitz M, Leonard JM, Ho DD: HIV-1 dynamics in vivo: virion clearance rate, infected cell lifespan, and viral generation time. Science 1996, 271:1582-6.
58. Piatak M Jr, Saag MS, Yang LC, Clark SJ, Kappes JC, Luk KC, Hahn BH, Shaw GM, Lifson JD: High levels of HIV-1 in plasma during all stages of infection determined by competitive PCR. Science 1993, 259:1749-54.
59. Poaty-Mavoungou V, Toure FS, Tevi-Benissan C, Mavoungou E: Enhancement of natural killer cell activation and antibody-dependent cellular cytotoxicity by interferon-alpha and interleukin-12 in vaginal mucosae Sivmac251-infected Macaca fascicularis. Viral Immunol 2002, 15:197-212.
60. Pol S: Immunotherapy of chronic hepatitis B by anti HBV vaccine. Biomed Pharmacother 1995, 49:105-9.
61. Preston BD, Poiesz BJ, Loeb LA: Fidelity of HIV-1 reverse transcriptase. Science 1988, 242:1168-71.
62. Prince AM, Brotman B, Lee DH, Ren L, Moore BS, Scheffel JW: Significance of the anti-E2 response in self-limited and chronic hepatitis C virus infections in chimpanzees and in humans. J Infect Dis 1999, 180:987-91.
63. Pruett TL, McGory R: Hepatitis B immune globulin: the US experience. Clin Transplant 2000, 14(Suppl 2):7-13.
64. Quesada-Rolander M, Makitalo B, Thorstensson R, Zhang YJ, Castanos-Velez E, Biberfeld G, Putkonen P: Protection against mucosal SIVsm challenge in macaques infected with a chimeric SIV that expresses HIV type 1 envelope. AIDS Res Hum Retroviruses 1996, 12:993-9.
65. Ribeiro RM, Layden-Almer J, Powers KA, Layden TJ, Perelson AS: Dynamics of alanine aminotransferase during hepatitis C virus treatment. Hepatology 2003, 38:509-17.
66. Sakai A, Claire MS, Faulk K, Govindarajan S, Emerson SU, Purcell RH, Bukh J: The p7 polypeptide of hepatitis C virus is critical for infectivity and contains functionally important genotype-specific sequences. Proc Natl Acad Sci U S A 2003, 100:11646-51.
67. Sakuma I, Enomoto N, Kurosaki M, Marumo F, Sato C: Selection of hepatitis C virus quasispecies during interferon treatment. Arch Virol 1996, 141:1921-32.
68. Sallie R: Hepatitis C: IIb (IV) or not IIb (IV) that is the question. Hepatology 1995, 22:671-4.
69. Sallie R: Transcriptional homeostasis: a mechanism of protein quality control. Med Hypotheses 2004, 63:232-4.
70. Sanchez-Palomino S, Rojas JM, Martinez MA, Fenyo EM, Najera R, Domingo E, Lopez-Galindez C: Dilute passage promotes expression of genetic and phenotypic variants of human immunodeficiency virus type 1 in cell culture. J Virol 1993, 67:2938-43.
71. Shibata R, Siemon C, Czajak SC, Desrosiers RC, Martin MA: Live, attenuated simian immunodeficiency virus vaccines elicit potent resistance against a challenge with a human immunodeficiency virus type 1 chimeric virus. J Virol 1997, 71:8141-8.
72. Shields PL, Owsianka A, Carman WF, Boxall E, Hubscher SG, Shaw J, O'Donnell K, Elias E, Mutimer DJ: Selection of hepatitis B surface "escape" mutants during passive immune prophylaxis following liver transplantation: potential impact of genetic changes on polymerase protein function. Gut 1999, 45:306-9.
73. Simmonds P, Holmes EC, Cha TA, Chan SW, McOmish F, Irvine B, Beall E, Yap PL, Kolberg J, Urdea MS: Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region. J Gen Virol 1993, 74(Pt 11):2391-9.
74. Simmonds P, McOmish F, Yap PL, Chan SW, Lin CK, Dusheiko G, Saeed AA, Holmes EC: Sequence variability in the 5′ non-coding region of hepatitis C virus: identification of a new virus type and restrictions on sequence diversity. J Gen Virol 1993, 74(Pt 4):661-8.
75. Steffy KR, Wong-Staal F: Transdominant inhibition of wild-type human immunodeficiency virus type 2 replication by an envelope deletion mutant. J Virol 1993, 67:1854-9.
76. Steinhauer DA, Domingo E, Holland JJ: Lack of evidence for proof-reading mechanisms associated with an RNA virus polymerase. Gene 1992, 122:281-8.
77. Su L, Kaneshima H, Bonyhadi ML, Lee R, Auten J, Wolf A, Du B, Rabin L, Hahn BH, Terwilliger E, McCune JM: Identification of HIV-1 determinants for replication in vivo. Virology 1997, 227:45-52.
78. Takada A, Watanabe S, Okazaki K, Kida H, Kawaoka Y: Infectivity-enhancing antibodies to Ebola virus glycoprotein. J Virol 2001, 75:2324-30.
79. Talbot SJ, Goodman S, Bates SR, Fishwick CW, Stockley PG: Use of synthetic oligoribonucleotides to probe RNA-protein interactions in the MS2 translational operator complex. Nucleic Acids Res 1990, 18:3521-8.
80. Tonegawa S: Somatic generation of antibody diversity. Nature 1983, 302:575-81.
81. Torresi J, Earnest-Silveira L, Civitico G, Walters TE, Lewin SR, Fyfe J, Locarnini SA, Manns M, Trautwein C, Bock TC: Restoration of replication phenotype of lamivudine-resistant hepatitis B virus mutants by compensatory changes in the "fingers" subdomain of the viral polymerase selected as a consequence of mutations in the overlapping S gene. Virology 2002, 299:88-99.
82. Tran A, Kremsdorf D, Capel F, Housset C, Dauguet C, Petit MA, Brechot C: Emergence of and takeover by hepatitis B virus (HBV) with rearrangements in the pre-S/S and pre-C/C genes during chronic HBV infection. J Virol 1991, 65:3566-74.
83. Voss G, Manson K, Montefiori D, Watkins DI, Heeney J, Wyand M, Cohen J, Bruck C: Prevention of disease induced by a partially heterologous AIDS virus in rhesus monkeys by using an adjuvanted multicomponent protein vaccine. J Virol 2003, 77:1049-58.
84. Wallace MJ, Smith DW, Broom AK, Mackenzie JS, Hall RA, Shellam GR, McMinn PC: Antibody-dependent enhancement of Murray Valley encephalitis virus virulence in mice. J Gen Virol 2003, 84:1723-8.
85. Watt G, Kantipong P, Jongsakul K: Decrease in human immunodeficiency virus type 1 load during acute dengue fever. Clin Infect Dis 2003, 36:1067-9.
86. Witherell GW, Uhlenbeck OC: Specific RNA binding by Q beta coat protein. Biochemistry 1989, 28:71-6.