Predicting HIV-1 coreceptor usage with sequence analysis

AIDS Reviews

Volumn 5, Issue 2, 2003, Pages 104-112

  Jensen, Mark A ^a   Van't Wout, Angélique B ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

Envelope; HIV coreceptor; HIV phenotype; Pathogenesis

Indexed keywords

AMINO ACID; ANTIRETROVIRUS AGENT; CHEMOKINE RECEPTOR CCR4; CHEMOKINE RECEPTOR CCR5; HUMAN IMMUNODEFICIENCY VIRUS 1 CORECEPTOR; NUCLEOSIDE ANALOG; UNCLASSIFIED DRUG; VIRUS RECEPTOR;

AMINO ACID ANALYSIS; BIOINFORMATICS; GENETIC VARIABILITY; GENOTYPE PHENOTYPE CORRELATION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MOLECULAR EVOLUTION; NONHUMAN; PATHOGENESIS; PHENOTYPE; PREDICTION; REVIEW; SCORING SYSTEM; SEQUENCE ANALYSIS; VIRUS ENVELOPE; VIRUS MUTATION;

COMPUTATIONAL BIOLOGY; GENOTYPE; HIV INFECTIONS; HIV-1; HUMANS; PHENOTYPE; RECEPTORS, HIV;

EID: 0038637409     PISSN: 11396121     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (85)

1. Koot M, Vos A, Keet R, et al. HIV-1 biological phenotype in long-term infected individuals evaluated with an MT-2 cocultivation assay. AIDS 1992;6:49-54.
2. Collman R, Hassan N, Walker R, et al. Infection of monocyte-derived macrophages with HIV-1. Monocyte-tropic and lymphocyte-tropic strains of HIV-1 show distinctive patterns of replication in a panel of cell types. J Exp Med 1989;170:1149-63.
3. Fenyö E, Albert J, Åsjö B. Replicative capacity, cytopathic effect and cell tropism of HIV. AIDS 1989;3(Suppl. 1):5-12.
4. Tersmette M, De Goede R, Al B, et al. Differential syncytium-inducing capacity of HIV isolates: Frequent detection of syncytium-inducing isolates in patients with AIDS and AIDS-related complex. J Virol 1988;62:2026-32.
5. Schuitemaker H, Kootstra N, De Goede R, et al. Monocytotropic HIV-1 variants detectable in all stages of HIV-1 infection lack T-cell line tropism and syncytium-inducing ability in primary T-cell culture. J Virol 1991;65:356-63.
6. Roos M, Lange J, De Goede R, et al. Viral phenotype and immune response in primary HIV type 1 infection. J Infect Dis 1992;165:427-32.
7. Keet I, Krijnen P, Koot M, et al. Predictors of rapid progression to AIDS in HIV-1 seroconverters. AIDS 1993;7:51-7.
8. Shankarappa R, Margolick J, Gange S, et al. Consistent viral evolutionary changes associated with the progression of HIV type 1 infection. J Virol 1999;73:10489-502.
9. Koot M, Keet I, Vos A, et al. Prognostic value of HIV-1 syncytium-inducing phenotype for rate of CD4+ cell depletion and progression to AIDS. Ann Intern Med 1993;118:681-8.
10. Richman D, Bozzette S. The impact of the syncytium-inducing phenotype of HIV on disease progression. J Infect Dis 1994;169:968-74.
11. Bozzette S, McCutchan J, Spector S, et al. A cross-sectional comparison of persons with syncytium- and non-synchtium-inducing HIV. J Infect Dis 1993;168:1374-9.
12. Feng Y, Broder C, Kennedy P, Berger E. HIV-1 entry cofactor: Functional cDNA cloning of a seven-transmembrane, G protein-coupled receptor. Science 1996;272:872-7.
13. Deng H, Liu R, Ellmeier W, et al. Identification of a major co-receptor for primary isolates of HIV-1. Nature 1996;381:661-6.
14. Alkhatib G, Combadiere C, Broder C, et al. CC CKR5: A RANTES, MIP-1α, MIP-1β Receptor as a fusion cofactor for macrophage-tropic HIV-1. Science 1996;272:1955-8.
15. Dragic T, Litwin V, Allaway G, et al. HIV-1 entry into CD4+ cells is mediated by the chemokine receptor CC- CKR-5. Nature 1996;381:667-73.
16. Björndal A, Deng H, Jansson M, et al. Co-receptor usage of primary HIV type 1 isolates varies according to biological phenotype. J Virol 1997;71:7478-87.
17. Connor R, Sheridan K, Ceradini D, et al. Change in coreceptor use correlates with disease progression in HIV-1-infected individuals. J Exp Med 1997,185:621-8.
18. Scarlatti G, Tresoldi E, Björndal A, et al. In vivo evolution of HIV-1 coreceptor usage and sensitivity to chemokine-mediated suppression. Nat Med 1997;3:1259-65.
19. Zhang L, He T, Huang Y, et al. Chemokine coreceptor usage by diverse primary isolates of HIV type 1. J Virol 1998;72:9307-12.
20. Choe H, Farzan M, Sun Y, et al. The beta-chemokine receptors CCR3 and CCR5 facilitate infection by primary HIV-1 isolates. Cell 1996;85:1135-48.
21. Doranz B, Rucker J, Yi Y, et al. A dual-tropic primary HIV-1 isolate that uses fusin and the beta-chemokine receptors CKR-5, CKR-3, and CKR-2b as fusion cofactors. Cell 1996;85:1149-58.
22. Zhang L, Huang Y, He T, et al. HIV-1 subtype and second-receptor use. Nature 1996;383:768.
23. Simmons G, Wilkinson D, Reeves J, et al. Primary, syncytium-inducing HIV-1 isolates are dual-tropic and most can use either Lestr or CCR5 as coreceptors for virus entry. J Virol 1996;70:8355-60.
24. Berger E, Doms R, Fenyö E, et al. A new classification for HIV-1. Nature 1998;391:240.
25. Oberlin E, Amara A, Bachelerie F, et al. The CXC chemokine SDF-1 is the ligand for LESTR/fusin and prevents infection by T-cell-line-adapted HIV-1. Nature 1996;382:833-5.
26. Bleul C, Wu L, Hoxie J, et al. The HIV coreceptors CXCR4 and CCR5 are differentially expressed and regulated on human T lymphocytes. Proc Natl Acad Sci USA 1997;94:1925-30.
27. Berkowitz R, Beckerman K, Schall T, McCune J. CXCR4 and CCR5 expression delineates targets for HIV-1 disruption of T cell differentiation. J Immunol 1998;161:3702-10.
28. Rosu-Myles M, Gallacher L, Murdoch B, et al. The human hematopoietic stem cell compartment is heterogenous for CXCR4 expression. Proc Natl Acad Sci USA 2000; 97: 14626-31.
29. Taylor J, Kimbrell K, Scoggins R, et al. Expression and function of chemokine receptors on human thymocytes: Implications for infection by HIV type 1. J Virol 2001;75:8752-60.
30. Wu L, Paxton W, Kassam N, et al. CCR5 levels and expression pattern correlate with infectivity by macrophage-tropic HIV-1, in vitro. J Exp Med 1997;185:1681-91.
31. Blaak H, Van't Wout A, Brouwer M, et al. In vivo HIV-1 infection of CD45RA(+)CD4(+) T cells is established primarily by syncytium-inducing variants and correlates with the rate of CD4(+) T cell decline. Proc Natl Acad Sci USA 2000;97:1269-74.
32. Ostrowski M, Chun T, Justement S, et al. Both memory and CD45RA+/CD62L+ naive CD4(+) T cells are infected in HIV type 1-infected individuals. J Virol 1999;73:6430-5.
33. Dimitrov D, Norwood D, Stantchev T, et al. A mechanism of resistance to HIV-1 entry: Inefficient interactions of CXCR4 with CD4 and gp120 in macrophages. Virology 1999;259:1-6.
34. Lapham C, Zaitseva M, Lee S, et al. Fusion of monocytes and macrophages with HIV-1 correlates with biochemical properties of CXCR4 and CCR5. Nat Med 1999;5:303-8.
35. Platt E, Madani N, Kozak S, Kabat D. Infectious properties of HIV type 1 mutants with distinct affinities for the CD4 receptor. J Virol 1997;71:883-90.
36. Kozak S, Platt E, Madani N, et al. CD4, CXCR-4, and CCR-5 dependencies for infections by primary patient and laboratory-adapted isolates of HIV type 1. J Virol 1997;71:873-82.
37. Tokunaga K, Greenberg M, Morse M, et al. Molecular basis for cell tropism of CXCR4-dependent HIV type 1 isolates. J Virol 2001;75:6776-85.
38. Kabat D, Kozak S, Wehrly K, Chesebro B. Differences in CD4 dependence for infectivity of laboratory-adapted and primary patient isolates of HIV type 1. J Virol 1994;68:2570-7.
39. Groenink M, Andeweg A, Fouchier R, et al. Phenotype-associated env gene variation among eight related HIV type 1 clones: Evidence for in vivo recombination and determinants of cytotropism outside the V3 domain. J Virol 1992;66:6175-80.
40. O'Brien W, Koyanagi Y, Namazie A, et al. HIV-1 tropism for mononuclear phagocytes can be determined by regions of gp120 outside the CD4-binding domain. Nature 1990;348:69-73.
41. Shioda T, Levy J, Cheng-Mayer C. Macrophage and T cell-line tropisms of HIV-1 are determined by specific regions of the envelope gp120 gene. Nature 1991;349:167-9.
42. Chesebro B, Nishio J, Perryman S, et al. Identification of HIV envelope gene sequences influencing viral entry into CD4-positive Hela cells. T-leukemic cells and macrophages. J Virol 1991;65:5782.
43. Shioda T, Levy J, Cheng-Mayer C. Small amino acid changes in the V3 hypervariable region of gp120 can affect the T-cell-line and macrophage tropism of HIV type 1. Proc Natl Acad Sci USA 1992;89:9434-8.
44. Fouchier R, Groenink M, Kootstra N, et al. Phenotype-associated sequence variation in the third variable domain (V3) of the HIV type 1 gp120 molecule. J Virol 1992;66:3183-7.
45. Groenink M, Fouchier R, Broersen S, et al. Relation of phenotype evolution of HIV-1 to envelope V2 configuration. Science 1993;260:1513-6.
46. Hwang S, Boyle T, Kim-Lyerly H, Cullen B. Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1. Science 1991;253:71-4.
47. De Jong JJ, Goudsmit J, Keulen W, et al. HIV type 1 clones chimeric for the envelope V3 domain differ in syncytium formation and replication capacity. J Virol 1992;66:757-65.
48. Chesebro B, Wehrly K, Nishio J, Perryman S. Macrophage-tropic HIV isolates from different patients exhibit unusual V3 envelope sequence homogeneity in comparison with T-cell-tropic isolates: Definition of critical amino acids involved in cell tropism. J Virol 1992;66:6547-54.
49. Hoffman T, Stephens E, Narayan O, Doms R. HIV type 1 envelope determinants for use of the CCR2b, CCR3, STRL33, and APJ coreceptors. Proc Natl Acad Sci USA 1998;95:11360-5.
50. Lee M, Heaton J, Cho M. Identification of determinants of interaction between CXCR4 and gp120 of a dual-tropic HIV-1DH12 isolate. Virology 1999;257:290-6.
51. Smyth R, Yi Y, Singh A, Collman R. Determinants of entry cofactor utilization and tropism in a dual tropic HIV type 1 primary isolate. J Virol 1998;72:4478-84.
52. Ohagen A, Ghosh S, He J, et al. Apoptosis induced by infection of primary brain cultures with diverse HIV type 1 isolates: Evidence for a role of the envelope. J Virol 1999;73:897-906.
53. De Jong JJ, De Ronde A, Keulen W, et al. 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.
54. Stamatatos L, Wiskerchen M, Cheng-Mayer C. Effect of major deletions in the V1 and V2 loops of a macrophage-tropic HIV type 1 isolate on viral envelope structure, cell entry, and replication. AIDS Res Hum Retroviruses 1998;14:1129-39.
55. Carrillo A, Ratner L. Cooperative effects of the HIV type 1 envelope variable loops V1 and V3 in mediating infectivity for T cells. J Virol 1996;70:1310-6.
56. Schuitemaker H, Fouchier R, Broersen S, et al. Envelope V2 configuration and HIV-1 phenotype: Clarification. Science 1995;268:115.
57. Este J, Cabrera C, Blanco J, et al. Shift of clinical HIV type 1 isolates from X4 to R5 and prevention of emergence of the syncytium-inducing phenotype by blockade of CXCR4. J Virol 1999;73:5577-85.
58. Schneider T, Stephens R. Sequence logos: A new way to display consensus sequences. Nucleic Acids Res 1990;18:6097-100.
59. Yamaguchi Y, Gojobori T. Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts. Proc Natl Acad Sci USA 1997;94:1264-9.
60. Korber B, MacInnes K, Smith R, Myers G. Mutational trends in V3 loop protein sequences observed in different genetic lineages of HIV type 1. J Virol 1994;68:6730-44.
61. Bickel P, Cosman P, Olshen R, et al. Covariability of V3 loop amino acids. AIDS Res Human Retroviruses 1996;12:1401-11.
62. Milich L, Margolin B, Swanstrom R. V3 loop of the HIV type 1 Env protein: Interpreting sequence variability. J Virol 1993;67:5623-34.
63. Milich L, Margolin B, Swanstrom R. Patterns of amino acid variability in NSI-like and SI-like V3 sequences and a linked change in the CD4-binding domain of the HIV-1 Env protein. Virology 1997;239:108-18.
64. Hoffman N, Seillier-Moiseiwitsch F, Ahn J, et al. Variability in the HIV type 1 gp120 Env protein linked to phenotype-associated changes in the V3 loop. J Virol 2002;76:3852-64.
65. Briggs D, Tuttle D, Sleasman J, Goodenow M. Envelope V3 amino acid sequence predicts HIV-1 phenotype (co-receptor usage and tropism for macrophages). AIDS 2000;14:2937-9.
66. Resch W, Hoffman N, Swanstrom R. Improved success of phenotype prediction of the HIV type 1 from envelope variable loop 3 sequence using neural networks. Virology 2001;288:51-62.
67. Pillai S, Good B, Richman D, Corbeil J. A new perspective on V3 phenotype prediction. AIDS Res Hum Retroviruses 2003;19:145-9.
68. Gribskov M, McLachlan AD, Eisenberg D. Profile analysis: Detection of distantly related proteins. Proc Natl Acad Sci USA 1987;84:4355-8.
69. Henikoff S, Wallace J, Brown J. Finding protein similarities with nucleotide sequence databases. Methods Enzymol 1990;183:111-32.
70. Van Rij R, Blaak H, Visser J, et al. Differential coreceptor expression allows for independent evolution of non-syncytium-inducing and syncytium-inducing HIV-1. J Clin Invest 2000;106:1039-52.
71. Yi Y, Isaacs S, Williams D, et al. Role of CXCR4 in cell-cell fusion and infection of monocyte-derived macrophages by primary HIV-1 strains: Two distinct mechanisms of HIV-1 dual tropism. J Virol 1999;73:7117-25.
72. Paxton WA, Martin SR, Tse D, et al. Relative resistance to HIV-1 infection of CD4 lymphocytes from persons who remain uninfected despite multiple high-risk sexual exposure. Nature Medicine 1996;2:412-7.
73. Liu R, Paxton W, Choe S, et al. Homozygous defect in HIV-1 coreceptor accounts for resistance of some multiply-exposed individuals to HIV-1 infection. Cell 1996;86:367-77.
74. Dean M, Carrington M, Winkler C, et al. Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Science 1996;273:1856-62.
75. Sheppard H, Celum C, Michael N, et al. HIV-1 infection in individuals with the CCR5-Delta/Delta32 genotype: Acquisition of syncytium-inducing virus at seroconversion. J Acquir Immune Defic Syndr 2002;29:307-13.
76. Iversen A, Christiansen C, Attermann J, et al. Limited protective effect of the CCR5Delta32/CCR5Delta32 genotype on HIV infection incidence in a cohort of patients with hemophilia and selection for genotypic X4 virus. J Infect Dis 2003;187:215-25.
77. Michael N, Nelson J, Kewal Ramani V, et al. Exclusive and persistent use of the entry coreceptor CXCR4 by HIV type 1 from a subject homozygous for CCR5 delta32. J Virol 1998;72:6040-7.
78. Gorry P, Zhang C, Wu S, et al. Persistence of dual-tropic HIV-1 in an individual homozygous for the CCR5 Delta 32 allele. Lancet 2002;359:1832-4.
79. Van't Wout A, Blaak H, Ran L, et al. Evolution of syncytium-inducing and non-syncytium-inducing biological virus clones in relation to replication kinetics during the course of HIV type 1 infection. J Virol 1998;72:5099-107.
80. Mosier D, Picchio G, Gulizia R, et al. Highly potent RANTES analogues either prevent CCR5-using HIV type 1 infection in vivo or rapidly select for CXCR4-using variants. J Virol 1999;73:3544-50.
81. Trkola A, Kuhmann S, Strizki J, et al. HIV-1 escape from a small molecule, CCR5-specific entry inhibitor does not involve CXCR4 use. Proc Natl Acad Sci USA 2002;99:395-400.
82. Schols D, Este J, Cabrera C, De Clercq E. T-cell-line-tropic HIV type 1 that is made resistant to stromal cell-derived factor 1alpha contains mutations in the envelope gp120 but does not show a switch in coreceptor use. J Virol 1998;72:4032-7.
83. Van't Wout A, Ran L, De Jong M, et al. Selective inhibition of syncytium-inducing and nonsyncytium-inducing HIV-1 variants in individuals receiving didanosine or zidovudine, respectively. J Clin Invest 1997;100:2325-32.
84. Philpott S, Weiser B, Anastos K, et al. Preferential suppression of CXCR4-specific strains of HIV-1 by antiviral therapy. J Clin Invest 2001;107:431-8.
85. Derdeyn C, Decker J, Sfakianos J, et al. Sensitivity of HIV type 1 to the fusion inhibitor T-20 is modulated by coreceptor specificity defined by the V3 loop of gp120. J Virol 2000;74:8358-67.