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J Virol. Aug 1995; 69(8): 5087–5094.
PMCID: PMC189326

Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase.

Abstract

The level of genetic variation of human immunodeficiency virus type 1 (HIV-1), a member of the lentivirus genus of the Retroviridae family, is high relative to that of retroviruses in some other genera. The high error rates of purified HIV-1 reverse transcriptase in cell-free systems suggest an explanation for this high genetic variation. To test whether the in vivo rate of mutation during reverse transcription of HIV-1 is as high as predicted by cell-free studies, and therefore higher than that rates of mutation of retroviruses in other genera, we developed an in vivo assay for detecting forward mutations in HIV-1, using the lacZ alpha peptide gene as a reporter for mutations. This system allows the rates and types of mutations that occur during a single cycle of replication to be studied. We found that the forward mutation rate for HIV-1 was 3.4 x 10(-5) mutations per bp per cycle. Base substitution mutations predominated; G-to-A transition mutations were the most common base substitution. The in vivo mutation rates for HIV-1 are three and seven times higher than those previously reported for two other retroviruses, spleen necrosis virus and bovine leukemia virus, respectively. In contrast, our calculated in vivo mutation rate for HIV-1 is about 20-fold lower than the error rate of purified HIV-1 reverse transcriptase, with the same target sequence. This finding indicates that HIV-1 reverse transcription in vivo is not as error prone as predicted from the fidelity of purified reverse transcriptase in cell-free studies. Our data suggest that the fidelity of purified HIV-1 reverse transcriptase may not accurately reflect the level of genetic variation in a natural infection.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Alizon M, Wain-Hobson S, Montagnier L, Sonigo P. Genetic variability of the AIDS virus: nucleotide sequence analysis of two isolates from African patients. Cell. 1986 Jul 4;46(1):63–74. [PubMed]
  • Bakhanashvili M, Hizi A. The fidelity of the reverse transcriptases of human immunodeficiency viruses and murine leukemia virus, exhibited by the mispair extension frequencies, is sequence dependent and enzyme related. FEBS Lett. 1993 Mar 15;319(1-2):201–205. [PubMed]
  • Balfe P, Simmonds P, Ludlam CA, Bishop JO, Brown AJ. 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. J Virol. 1990 Dec;64(12):6221–6233. [PMC free article] [PubMed]
  • Baltimore D. RNA-dependent DNA polymerase in virions of RNA tumour viruses. Nature. 1970 Jun 27;226(5252):1209–1211. [PubMed]
  • Bartolomé B, Jubete Y, Martínez E, de la Cruz F. Construction and properties of a family of pACYC184-derived cloning vectors compatible with pBR322 and its derivatives. Gene. 1991 Jun 15;102(1):75–78. [PubMed]
  • Bebenek K, Abbotts J, Roberts JD, Wilson SH, Kunkel TA. Specificity and mechanism of error-prone replication by human immunodeficiency virus-1 reverse transcriptase. J Biol Chem. 1989 Oct 5;264(28):16948–16956. [PubMed]
  • Bebenek K, Abbotts J, Wilson SH, Kunkel TA. Error-prone polymerization by HIV-1 reverse transcriptase. Contribution of template-primer misalignment, miscoding, and termination probability to mutational hot spots. J Biol Chem. 1993 May 15;268(14):10324–10334. [PubMed]
  • Boyer JC, Bebenek K, Kunkel TA. Unequal human immunodeficiency virus type 1 reverse transcriptase error rates with RNA and DNA templates. Proc Natl Acad Sci U S A. 1992 Aug 1;89(15):6919–6923. [PMC free article] [PubMed]
  • Buchschacher GL, Jr, Panganiban AT. Human immunodeficiency virus vectors for inducible expression of foreign genes. J Virol. 1992 May;66(5):2731–2739. [PMC free article] [PubMed]
  • Burns DP, Temin HM. High rates of frameshift mutations within homo-oligomeric runs during a single cycle of retroviral replication. J Virol. 1994 Jul;68(7):4196–4203. [PMC free article] [PubMed]
  • Cheng-Mayer C, Shioda T, Levy JA. Host range, replicative, and cytopathic properties of human immunodeficiency virus type 1 are determined by very few amino acid changes in tat and gp120. J Virol. 1991 Dec;65(12):6931–6941. [PMC free article] [PubMed]
  • Coffin JM. Genetic diversity and evolution of retroviruses. Curr Top Microbiol Immunol. 1992;176:143–164. [PubMed]
  • Coffin JM. HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science. 1995 Jan 27;267(5197):483–489. [PubMed]
  • Dougherty JP, Temin HM. High mutation rate of a spleen necrosis virus-based retrovirus vector. Mol Cell Biol. 1986 Dec;6(12):4387–4395. [PMC free article] [PubMed]
  • Dougherty JP, Temin HM. Determination of the rate of base-pair substitution and insertion mutations in retrovirus replication. J Virol. 1988 Aug;62(8):2817–2822. [PMC free article] [PubMed]
  • Dube DK, Sherman MP, Saksena NK, Bryz-Gornia V, Mendelson J, Love J, Arnold CB, Spicer T, Dube S, Glaser JB, et al. Genetic heterogeneity in human T-cell leukemia/lymphoma virus type II. J Virol. 1993 Mar;67(3):1175–1184. [PMC free article] [PubMed]
  • Fitzgibbon JE, Mazar S, Dubin DT. A new type of G-->A hypermutation affecting human immunodeficiency virus. AIDS Res Hum Retroviruses. 1993 Sep;9(9):833–838. [PubMed]
  • Hahn BH, Shaw GM, Taylor ME, Redfield RR, Markham PD, Salahuddin SZ, Wong-Staal F, Gallo RC, Parks ES, Parks WP. Genetic variation in HTLV-III/LAV over time in patients with AIDS or at risk for AIDS. Science. 1986 Jun 20;232(4757):1548–1553. [PubMed]
  • 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 Jan 12;373(6510):123–126. [PubMed]
  • Holland JJ, De La Torre JC, Steinhauer DA. RNA virus populations as quasispecies. Curr Top Microbiol Immunol. 1992;176:1–20. [PubMed]
  • Hu WS, Temin HM. Genetic consequences of packaging two RNA genomes in one retroviral particle: pseudodiploidy and high rate of genetic recombination. Proc Natl Acad Sci U S A. 1990 Feb;87(4):1556–1560. [PMC free article] [PubMed]
  • Hu WS, Temin HM. Retroviral recombination and reverse transcription. Science. 1990 Nov 30;250(4985):1227–1233. [PubMed]
  • Hübner A, Kruhoffer M, Grosse F, Krauss G. Fidelity of human immunodeficiency virus type I reverse transcriptase in copying natural RNA. J Mol Biol. 1992 Feb 5;223(3):595–600. [PubMed]
  • Ji JP, Loeb LA. Fidelity of HIV-1 reverse transcriptase copying RNA in vitro. Biochemistry. 1992 Feb 4;31(4):954–958. [PubMed]
  • Katz RA, Skalka AM. Generation of diversity in retroviruses. Annu Rev Genet. 1990;24:409–445. [PubMed]
  • Kawai S, Nishizawa M. New procedure for DNA transfection with polycation and dimethyl sulfoxide. Mol Cell Biol. 1984 Jun;4(6):1172–1174. [PMC free article] [PubMed]
  • Kunkel TA. Misalignment-mediated DNA synthesis errors. Biochemistry. 1990 Sep 4;29(35):8003–8011. [PubMed]
  • Kunkel TA, Alexander PS. The base substitution fidelity of eucaryotic DNA polymerases. Mispairing frequencies, site preferences, insertion preferences, and base substitution by dislocation. J Biol Chem. 1986 Jan 5;261(1):160–166. [PubMed]
  • Landau NR, Littman DR. Packaging system for rapid production of murine leukemia virus vectors with variable tropism. J Virol. 1992 Aug;66(8):5110–5113. [PMC free article] [PubMed]
  • Levy JA. Pathogenesis of human immunodeficiency virus infection. Microbiol Rev. 1993 Mar;57(1):183–289. [PMC free article] [PubMed]
  • Mansky LM, Temin HM. Lower mutation rate of bovine leukemia virus relative to that of spleen necrosis virus. J Virol. 1994 Jan;68(1):494–499. [PMC free article] [PubMed]
  • Nowak M. HIV mutation rate. Nature. 1990 Oct 11;347(6293):522–522. [PubMed]
  • Pathak VK, Temin HM. 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. Proc Natl Acad Sci U S A. 1990 Aug;87(16):6019–6023. [PMC free article] [PubMed]
  • Pathak VK, Temin HM. 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. Proc Natl Acad Sci U S A. 1990 Aug;87(16):6024–6028. [PMC free article] [PubMed]
  • Pathak VK, Temin HM. 5-Azacytidine and RNA secondary structure increase the retrovirus mutation rate. J Virol. 1992 May;66(5):3093–3100. [PMC free article] [PubMed]
  • Pulsinelli GA, Temin HM. Characterization of large deletions occurring during a single round of retrovirus vector replication: novel deletion mechanism involving errors in strand transfer. J Virol. 1991 Sep;65(9):4786–4797. [PMC free article] [PubMed]
  • Ratner L, Philpott T, Trowbridge DB. Nucleotide sequence analysis of isolates of human T-lymphotropic virus type 1 of diverse geographical origins. AIDS Res Hum Retroviruses. 1991 Nov;7(11):923–941. [PubMed]
  • Ricchetti M, Buc H. Reverse transcriptases and genomic variability: the accuracy of DNA replication is enzyme specific and sequence dependent. EMBO J. 1990 May;9(5):1583–1593. [PMC free article] [PubMed]
  • Roberts JD, Bebenek K, Kunkel TA. The accuracy of reverse transcriptase from HIV-1. Science. 1988 Nov 25;242(4882):1171–1173. [PubMed]
  • Smith AJ, Cho MI, Hammarskjöld ML, Rekosh D. Human immunodeficiency virus type 1 Pr55gag and Pr160gag-pol expressed from a simian virus 40 late replacement vector are efficiently processed and assembled into viruslike particles. J Virol. 1990 Jun;64(6):2743–2750. [PMC free article] [PubMed]
  • Starcich BR, Hahn BH, Shaw GM, McNeely PD, Modrow S, Wolf H, Parks ES, Parks WP, Josephs SF, Gallo RC, et al. Identification and characterization of conserved and variable regions in the envelope gene of HTLV-III/LAV, the retrovirus of AIDS. Cell. 1986 Jun 6;45(5):637–648. [PubMed]
  • Streisinger G, Okada Y, Emrich J, Newton J, Tsugita A, Terzaghi E, Inouye M. Frameshift mutations and the genetic code. This paper is dedicated to Professor Theodosius Dobzhansky on the occasion of his 66th birthday. Cold Spring Harb Symp Quant Biol. 1966;31:77–84. [PubMed]
  • Streisinger G, Owen J. Mechanisms of spontaneous and induced frameshift mutation in bacteriophage T4. Genetics. 1985 Apr;109(4):633–659. [PMC free article] [PubMed]
  • TEMIN HM. Mixed infection with two types of Rous sarcoma virus. Virology. 1961 Feb;13:158–163. [PubMed]
  • Temin HM. Studies on carcinogenesis by avian sarcoma viruses. 8. Glycolysis and cell multiplication. Int J Cancer. 1968 Mar 15;3(2):273–282. [PubMed]
  • Temin HM. Retrovirus variation and reverse transcription: abnormal strand transfers result in retrovirus genetic variation. Proc Natl Acad Sci U S A. 1993 Aug 1;90(15):6900–6903. [PMC free article] [PubMed]
  • Temin HM, Mizutani S. RNA-dependent DNA polymerase in virions of Rous sarcoma virus. Nature. 1970 Jun 27;226(5252):1211–1213. [PubMed]
  • Varela-Echavarría A, Garvey N, Preston BD, Dougherty JP. Comparison of Moloney murine leukemia virus mutation rate with the fidelity of its reverse transcriptase in vitro. J Biol Chem. 1992 Dec 5;267(34):24681–24688. [PubMed]
  • Vartanian JP, Meyerhans A, Asjö B, Wain-Hobson S. Selection, recombination, and G----A hypermutation of human immunodeficiency virus type 1 genomes. J Virol. 1991 Apr;65(4):1779–1788. [PMC free article] [PubMed]
  • Wei X, Ghosh SK, Taylor ME, Johnson VA, Emini EA, Deutsch P, Lifson JD, Bonhoeffer S, Nowak MA, Hahn BH, et al. Viral dynamics in human immunodeficiency virus type 1 infection. Nature. 1995 Jan 12;373(6510):117–122. [PubMed]
  • Willems L, Thienpont E, Kerkhofs P, Burny A, Mammerickx M, Kettmann R. Bovine leukemia virus, an animal model for the study of intrastrain variability. J Virol. 1993 Feb;67(2):1086–1089. [PMC free article] [PubMed]
  • Yu H, Goodman MF. Comparison of HIV-1 and avian myeloblastosis virus reverse transcriptase fidelity on RNA and DNA templates. J Biol Chem. 1992 May 25;267(15):10888–10896. [PubMed]
  • Zhang J, Temin HM. Rate and mechanism of nonhomologous recombination during a single cycle of retroviral replication. Science. 1993 Jan 8;259(5092):234–238. [PubMed]

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