Transition between stochastic evolution and deterministic evolution in the presence of selection: General theory and application to virology

Microbiology and Molecular Biology Reviews

Volumn 65, Issue 1, 2001, Pages 151-185

  Rouzine, I M ^a   Rodrigo, A ^a   Coffin, J M ^a  

^a TUFTS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; CORRELATION FUNCTION; EVOLUTION; GENE DELETION; GENETIC SELECTION; HAPLOIDY; HUMAN IMMUNODEFICIENCY VIRUS; MUTATION RATE; NONHUMAN; POPULATION GENETICS; PROBABILITY; REVERTANT; REVIEW; STEADY STATE; STOCHASTIC MODEL;

EVOLUTION; GENES, VIRAL; HIV; HUMANS; MARKOV CHAINS; MATHEMATICS; MODELS, BIOLOGICAL; POLYMORPHISM, GENETIC; SELECTION (GENETICS); SELECTION BIAS; STOCHASTIC PROCESSES; VIRUSES;

HUMAN IMMUNODEFICIENCY VIRUS; MARTES PENNANTI;

EID: 0035102156     PISSN: 10922172     EISSN: None     Source Type: Journal    
DOI: 10.1128/MMBR.65.1.151-185.2001     Document Type: Review

References (86)

1. 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
2. Causes of HIV diversity
3. Envelope sequence variation, neutralizing antibodies, and primate lentivirus persistence
4. Selection of genetic variants of simian immunodeficiency virus in persistently infected rhesus monkeys
5. Fitness of RNA virus decreased by Muller's ratchet
6. The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations
7. Sequence variation: Looking for effects of genetic linkage
8. Molecular determinants of the V3 loop of human immunodeficiency virus type 1 glycoprotein gpl20 responsible for controlling cell tropism
9. Evolution of zidovudine resistance-associated genotypes in human immunodeficiency virus type 1-infected patients
10. In vivo emergence of HIV-1 variants resistant to multiple protease inhibitors
11. Human immunodeficiency virus type 1 evolution in vivo tracked by DNA heteroduplex mobility assays
12. Muller's ratchet and flu virus
13. Rapid fitness losses in mammalian RNA virus clones due to Muller's ratchet
14. Sequence space and quasispecies distribution
15. Multiple molecular pathways for fitness recovery of an RNA virus debilitated by operation of Muller's ratchet
16. The evolutionary advantage of recombination
17. On the dominance ratio
18. The distribution of gene ratios for rare mutations
19. Phenotype-associated env gene variation among eight related human immunodeficiency virus type 1 clones: Evidence for in vivo recombination and determinants of cytotropism outside the V3 domain
20. Population biology of HIV-1 infection: Viral and CD4 + T cell demographics and dynamics in lymphatic tissues
21. Quantitative image analysis of HIV-1 infection in lymphoid tissue
22. A mathematical theory of natural and artificial selection
23. A mathematical theory of natural and artificial selection. V. Selection and mutation
24. Rapid turnover of plasma virions and CD4 lymphocytes in HIV infection
25. RNA virus populations as quasispecies
26. Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient
27. A statistical test for detecting geographic subdivision
28. On some stochastic models in genetics
29. V3 sequences of paired HIV-1 isolates from blood and cerebrospinal fluid cluster according to host and show variation related to m clinical stage of disease
30. Process leading to quasi-fixation of genes in natural populations due to random fluctuations of selection intensities
31. Solution of a process of random genetic drift with a continuous model
32. Stochastic processes and distribution of gene frequencies under natural selection
33. On the probability of fixation of mutant genes in a population
34. Diffusion models in population genetics
35. The neutral theory of molecular evolution and the world view of the neutralists
36. The average number of generations until fixation of a mutant gene in a finite population
37. The coalescent
38. On the genealogy of large populations
39. Ueber die analitischen Methoden in der Wahrscheinlichkeitrechnung
40. Ancestral processes with selection
41. Independent variation and positive selection in env V1 and V2 domains within maternal-infant strains of human immunodeficiency virus type 1 in vivo
42. In vivo sequence diversity of the protease of human immunodeficiency virus type 1: Presence of protease inhibitor-resistant variants in untreated subjects
43. Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population
44. Divergent patterns of progression to AIDS after infection from the same source: Human immunodeficiency virus type 1 evolution and antiviral responses
45. Characterization of genetic variation and 3′-azido-3′-deoxythymi-dine-resistance mutations of human immunodeficiency virus by the RNase A mismatch cleavage method
46. Intrahost human immunodeficiency virus type 1 evolution is related to length of the immunocompetent period
47. Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase
48. Characterization of HIV isolates arising after prolonged zidovu-dine therapy
49. What use is sex?
50. A general theory of the distribution of gene frequencies. I. Overlapping generations. II. Non-overlapping generations
51. Some genetic aspects of sex
52. Genetic distance between populations
53. The genealogy of samples in models with selection
54. Sequence constraints and recognition by CTL of an HLA-B27-restricted HIV-1 gag epitope
55. The effect of recombination on background selection
56. Large-population passages of vesicular stomatitis virus in interferon-treated cells select variants of only limited resistance
57. Extreme fitness differences in mammalian and insect hosts after continuous replication of vesicular stomatitis virus in sandfly cells
58. Size of genetic bottlenecks leading to virus fitness loss is determined by mean initial population fitness
59. Evolution in bacteria: Evidence for a universal substitution rate in cellular genomes
60. HIV-1 dynamics in vivo: Virion clearance rate, infected cell life span, and viral generation time
61. Transmittance fluctuations in randomly non-uniform barriers and incoherent mesoscopics
62. Tracking members of the simian immunodeficiency virus delta B670 quasispecies population in vivo at single-cell resolution
63. Coalescent approaches to HIV population genetics
64. Coalescent estimates of HIV-1 generation time in vivo
65. Linkage disequilibrium test implies a large effective population number for HIV in vivo
66. Search for the mechanism of genetic variation in the pro gene of human immunodeficiency virus
67. Recovery of virtually full-length HIV-1 provirus of diverse subtypes from primary virus cultures using the polymerase chain reaction
68. Natural selection on the gag, pol, and env genes of human immunodeficiency virus 1 (HIV-1)
69. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection
70. Structural requirements for class I MHC molecule-mediated antigen presentation and cytotoxic T cell recognition of an immunodominant determinant of the human immunodeficiency virus envelope protein
71. Drift and conservatism in RNA virus evolution: Are they adapting or merely changing?
72. Some theoretical aspects of diffusion theory in population genetics
73. On the number of segregating sites in genetical models without recombination
74. Viral dynamics in human immunodeficiency virus type 1 infection
75. Evolution of sequences encoding the principal neutralization epitope of human immunodeficiency virus 1 is host dependent, rapid, and continuous
76. Naturally occurring mutations within HIV-1 V3 genomic RNA leads to antigenic variation dependent on a single amino acid substitution
77. Evolution in Mendelian populations
78. The differential equation of the distribution of gene frequencies
79. Tempo and mode in evolution: A critical review
80. Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts
81. Intrapatient sequence variation of the gag gene of human immunodeficiency virus type 1 plasma virions
82. Rapid clearance of simian immunodeficiency virus particles from plasma of rhesus macaques
83. Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection