Human immunodeficiency virus type 1 DNA sequences genetically damaged by hypermutation are often abundant in patient peripheral blood mononuclear cells and may be generated during near-simultaneous infection and activation of CD4+ T cells

Journal of Virology

Volumn 75, Issue 17, 2001, Pages 7973-7986

  Janini, M ^a   Rogers, M ^a   Birx, D R ^a   McCutchan, F E ^a  

^a HENRY M JACKSON FOUNDATION FOR THE ADVANCEMENT OF MILITARY MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE; PHYTOHEMAGGLUTININ; PROTEINASE;

AGAR GEL ELECTROPHORESIS; ARTICLE; DNA SEQUENCE; GENE AMPLIFICATION; GENE MUTATION; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR CLONING; MONONUCLEAR CELL; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; STOP CODON; T LYMPHOCYTE ACTIVATION;

BASE SEQUENCE; CD4-POSITIVE T-LYMPHOCYTES; CELLS, CULTURED; HIV INFECTIONS; HIV PROTEASE; HIV-1; HUMANS; LEUKOCYTES, MONONUCLEAR; LYMPHOCYTE ACTIVATION; MOLECULAR SEQUENCE DATA; MUTATION; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 0034878971     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.75.17.7973-7986.2001     Document Type: Article

References (72)

1. DNA sequence preferences of several AT-selective minor groove binding ligands
2. Specificity and mechanism of error-prone replication by human immunodeficiency virus-1 reverse transcriptase
3. Cell cycle-dependent metabolism of pyrimidine deoxynucleoside triphosphates in CEM cells
4. A highly defective HIV-1 group O provirus: Evidence for the role of local sequence determinants in G→A hypermutation during negative-strand viral DNA synthesis
5. Deoxyribonucleoside 5′-triphosphate pool fluctuations during the mammalian cell cycle
6. Drug resistance patterns, genetic subtypes, clinical features, and risk factors in military personnel with HIV-1 seroconversion
7. Nucleotide composition as a driving force in the evolution of retroviruses
8. Biased (A→I) hypermutation of animal RNA virus genomes
9. Biased hypermutation and other genetic changes in defective measles viruses in human brain infections
10. Purine and pyrimidine metabolism in human T lymphocytes. Regulation of deoxyribonucleotide metabolism
11. Evolution of human immunodeficiency virus type 1 nef and long terminal repeat sequences over 4 years in vivo and in vitro
12. The quasispecies (extremely heterogeneous) nature of viral RNA genome populations: Biological relevance-a review
13. 'Touchdown' PCR to circumvent spurious priming during gene amplification
14. Rates of spontaneous mutation among RNA viruses
15. The hypercycle. A principle of natural self-organization. A. Emergence of the hypercycle
16. Functional and biological properties of an avian variant long terminal repeat containing multiple A-to-G conversions in the U3 sequence
17. PHYLIP - Phylogeny inference package
18. A new type of G→A hypermutation affecting human immunodeficiency virus
19. Human infection by genetically diverse SIVSM-related HIV-2 in West Africa
20. Low levels of deoxynucleotides in peripheral blood lymphocytes: A strategy to inhibit human immunodeficiency virus type 1 replication
21. HIV-1 isolates are rapidly evolving quasispecies: Evidence for viral mixtures and preferred nucleotide substitutions
22. Naturally occurring hepatitis B virus genomes bearing the hallmarks of retroviral G→A hypermutation
23. Modification of retroviral RNA by double-stranded RNA adenosine deaminase
24. High and low annealing temperatures increase both specificity and yield in touchdown and stepdown PCR
25. HIV type 1 V3 serotyping of Tanzanian samples: Probable reasons for mismatching with genetic subtyping
26. RNA virus populations as quasispecies
27. Mutation frequencies at defined single codon sites in vesicular stomatitis virus and poliovirus can be increased only slightly by chemical mutagenesis
28. Identification of single and dual infections with distinct subtypes of human immunodeficiency virus type 1 by using restriction fragment length polymorphism analysis
29. Fidelity of HIV-1 reverse transcriptase copying RNA in vitro
30. The genetic fate of molecularly cloned simian immunodeficiency virus in experimentally infected macaques
31. The antiretrovirus drug 3′-azido-3′-deoxythymidine increases the retrovirus mutation rate
32. Deoxyribonucleoside triphosphate pool imbalances in vivo are associated with an increased retroviral mutation rate
33. Retroviral mutation rates and A-to-G hypermutations during different stages of retroviral replication
34. Biological asymmetries and the fidelity of eukaryotic DNA replication
35. Modulation of mutagenesis by deoxyribonucleotide levels
36. Deoxyribonucleoside triphosphate levels: A critical factor in the maintenance of genetic stability
37. Analysis of genetic heterogeneity within the type strain of satellite tobacco mosaic virus reveals variants and a strong bias for G to A substitution mutations
38. Clinical, immunologic, and serologic findings in men at risk for acquired immunodeficiency syndrome
39. Molecular characterization of human immunodeficiency virus type 1 cloned directly from uncultured human brain tissue: Identification of replication-competent and defective viral genomes
40. Analysis of human immunodeficiency virus type 1 gp160 sequences from a patient with HIV dementia: Evidence for monocyte trafficking into brain
41. Antibiotic induced electrophoretic mobility shifts of DNA restriction fragments
42. The mutation rate of human immunodeficiency virus type 1 is influenced by the vpr gene
43. Reverse transcriptase and substrate dependence of the RNA hypermutagenesis reaction
44. Hypermutagenesis of RNA using human immunodeficiency virus type 1 reverse transcriptase and biased dNTP concentrations
45. DNA precursor asymmetries, replication fidelity, and variable genome evolution
46. The molecular basis of mutations induced by deoxyribonucleoside triphosphate pool imbalances in mammalian cells
47. High resolution analysis of HIV-1 quasispecies in the brain
48. Polyethylene glycol derivatives of base and sequence specific DNA ligands: DNA interaction and application for base specific separation of DNA fragments by gel electrophoresis
49. Vesicular stomatitis virus defective interfering particles can contain extensive genomic sequence rearrangements and base substitutions
50. 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
51. Extension of mismatched 3′ termini of DNA is a major determinant of the infidelity of human immunodeficiency virus type 1 reverse transcriptase
52. The surface envelope protein gene region of equine infectious anemia virus is not an important determinant of tropism in vitro
53. Identification of mixed HIV-1/HIV-2 infections in Brazil by polymerase chain reactioin
54. The accuracy of reverse transcriptase from HIV-1
55. Detecting hypermutations in viral sequences with an emphasis on G→A hypermutation
56. Using mismatched primer-template pairs in touchdown PCR
57. Construction and biological characterization of infectious molecular clones of HIV-1 subtypes B and E (CRF01-AE) generated by the polymerase chain reaction
58. Recovery of virtually full-length HIV-1 provirus of diverse subtypes from primary virus cultures using the polymerase chain reaction
59. Effect of hydroxyurea and 5-fluorodeoxyuridine on deoxyribonucleoside triphosphate pools early in phytohemagglutinin-stimulated human lymphocytes
60. Hypermutagenic PCR involving all four transitions and a sizeable proportion of transversions
61. Selection, recombination, and G→A hypermutation of human immunodeficiency virus type 1 genomes
62. G→A hypermutation of the human immunodeficiency virus type 1 genome: Evidence for dCTP pool imbalance during reverse transcription
63. HIV genetic variation is directed and restricted by DNA precursor availability
64. Retroviral G to A hypermutation
65. Erratic G→A hypermutation within a complete caprine arthritis-encephalitis virus (CAEV) provirus
66. A simple and rapid electrophoresis method to detect sequence variation in PCR-amplified DNA fragments
67. Sexual practices and risk of infection by the human immunodeficiency virus
68. Unusual distribution of mutations associated with serial bottleneck passages of human immunodeficiency virus type 1
69. The role of the cell cycle in HIV-1 infection
70. HIV-1 entry into quiescent primary lymphocytes: Molecular analysis reveals a labile, latent viral structure
71. Incompletely reverse-transcribed human immunodeficiency virus type 1 genomes in quiescent cells can function as intermediates in the retroviral life cycle
72. Compositional bimodality and evolution of retroviral genomes