Development of an HIV-1 reference panel of subtype B envelope clones isolated from the plasma of recently infected individuals

Journal of Acquired Immune Deficiency Syndromes

Volumn 46, Issue 1, 2007, Pages 1-11

  Schweighardt, Becky ^a   Liu, Yang ^a   Huang, Wei ^a   Chappey, Colombe ^a   Lie, Yolanda S ^a   Petropoulos, Christos J ^a   Wrin, Terri ^a  

^a MONOGRAM BIOSCIENCES   (United States)

Author keywords

HIV vaccine evaluation; HIV 1 envelope; Neutralizing antibodies

Indexed keywords

ANTIGEN; HUMAN IMMUNODEFICIENCY VIRUS VACCINE;

ANTIBODY RESPONSE; ARTICLE; CLONE; CONTROLLED STUDY; DISEASE TRANSMISSION; EMBRYO; GENETIC DISTANCE; GENETIC VARIABILITY; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMA; PRIORITY JOURNAL; VIRUS ENVELOPE; VIRUS STRAIN;

GENE PRODUCTS, ENV; HIV INFECTIONS; HIV-1; HUMANS; NEUTRALIZATION TESTS; PHYLOGENY; VARIATION (GENETICS);

EID: 34848864584     PISSN: 15254135     EISSN: None     Source Type: Journal    
DOI: 10.1097/QAI.0b013e318074eb5a     Document Type: Article

References (74)

1. Mascola JR, Lewis MG, Stiegler G, et al. Protection of Macaques against pathogenic simian/human immunodeficiency virus 89.6PD by passive transfer of neutralizing antibodies. J Virol. 1999;73:4009-4018.
2. Mascola JR, Stiegler G, VanCott TC, et al. Protection of macaques against vaginal transmission of a pathogenic HIV-1/SIV chimeric virus by passive infusion of neutralizing antibodies. Nat Med. 2000;6:207-210.
3. Okamoto Y, Eda Y, Ogura A, et al. In SCID-hu mice, passive transfer of a humanized antibody prevents infection and atrophic change of medulla in human thymic implant due to intravenous inoculation of primary HIV-1 isolate. J Immunol. 1998;160:69-76.
4. Parren PW, Marx PA, Hessell AJ, et al. Antibody protects macaques against vaginal challenge with a pathogenic R5 simian/human immunodeficiency virus at serum levels giving complete neutralization in vitro. J Virol. 2001;75:8340-8347.
5. Baba TW, Liska V, Hofmann-Lehmann R, et al. Human neutralizing monoclonal antibodies of the IgG1 subtype protect against mucosal simian-human immunodeficiency virus infection. Nat Med. 2000;6:200-206.
6. Ferrantelli F, Rasmussen RA, Buckley KA, et al. Complete protection of neonatal rhesus macaques against oral exposure to pathogenic simianhuman immunodeficiency virus by human anti-HIV monoclonal antibodies. J Infect Dis. 2004;189:2167-2173.
7. Hofmann-Lehmann R, Vlasak J, Rasmussen RA, et al. Postnatal pre- and postexposure passive immunization strategies: protection of neonatal macaques against oral simian-human immunodeficiency virus challenge. J Med Primatol. 2002;31:109-119.
8. Veazey RS, Shattock RJ, Pope M, et al. Prevention of virus transmission to macaque monkeys by a vaginally applied monoclonal antibody to HIV-1 gp120. Nat Med. 2003;9:343-346.
9. Shibata R, Igarashi T, Haigwood N, et al. Neutralizing antibody directed against the HIV-1 envelope glycoprotein can completely block HIV-1/SIV chimeric virus infections of macaque monkeys. Nat Med. 1999;5:204-210.
10. Nishimura Y, Igarashi T, Haigwood NL, et al. Transfer of neutralizing IgG to macaques 6 h but not 24 h after SHIV infection confers sterilizing protection: implications for HIV-1 vaccine development. Proc Natl Acad Sci USA. 2003;100:15131-15136.
11. Burton DR. Antibodies, viruses and vaccines. Nat Rev Immunol. 2002;2:706-713.
12. Burton DR, Saphire EO, Parren PW. A model for neutralization of viruses based on antibody coating of the virion surface. Curr Top Microbiol Immunol. 2001;260:109-143.
13. Xiao Y, Dong X, Chen YH. Neutralizing antibodies mechanism of neutralization and protective activity against HIV-1. Immunol Res. 2002;25:193-200.
14. Yang X, Kurteva S, Ren X, et al. Stoichiometry of envelope glycoprotein trimers in the entry of human immunodeficiency virus type 1. J Virol. 2005;79:12132-12147.
15. Koch M, Pancera M, Kwong PD, et al. Structure-based, targeted deglycosylation of HIV-1 gp120 and effects on neutralization sensitivity and antibody recognition. Virology. 2003;313:387-400.
16. Wyatt R, Kwong PD, Desjardins E, et al. The antigenic structure of the HIV gp120 envelope glycoprotein. Nature. 1998;393:705-711.
17. Kwong PD, Wyatt R, Robinson J, et al. Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature. 1998;393:648-659.
18. Gauduin MC, Parren PW, Weir R, et al. Passive immunization with a human monoclonal antibody protects hu-PBL-SCID mice against challenge by primary isolates of HIV-1. Nat Med. 1997;3:1389-1393.
19. Safrit JT, Fung MS, Andrews CA, et al. hu-PBL-SCID mice can be protected from HIV-1 infection by passive transfer of monoclonal antibody to the principal neutralizing determinant of envelope gp120. AIDS. 1993;7:15-21.
20. Trkola A, Kuster H, Rusert P, et al. Delay of HIV-1 rebound after cessation of antiretroviral therapy through passive transfer of human neutralizing antibodies. Nat Med. 2005;11:615-622.
21. Mascola JR. Passive transfer studies to elucidate the role of antibodymediated protection against HIV-1. Vaccine. 2002;20:1922-1925.
22. Xu W, Hofmann-Lehmann R, McClure HM, et al. Passive immunization with human neutralizing monoclonal antibodies: correlates of protective immunity against HIV. Vaccine. 2002;20:1956-1960.
23. Moore JP, Burton DR. Urgently needed: a filter for the HIV-1 vaccine pipeline. Nat Med. 2004;10:769-771.
24. Mascola JR, D'Souza P, Gilbert P, et al. Recommendations for the design and use of standard virus panels to assess neutralizing antibody responses elicited by candidate human immunodeficiency virus type 1 vaccines. J Virol. 2005;79:10103-10107.
25. Richman DD, Wrin T, Little SJ, et al. Rapid evolution of the neutralizing antibody response to HIV type 1 infection. Proc Natl Acad Sci USA. 2003;100:4144-4149.
26. Deeks SG, Schweighardt B, Wrin T, et al. Neutralizing antibody responses against autologous and heterologous viruses in acute versus chronic human immunodeficiency virus (HIV) infection: evidence for a constraint on the ability of HIV to completely evade neutralizing antibody responses. J Virol. 2006;80:6155-6164.
27. Frost SD, Wrin T, Smith DM, et al. Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection. Proc Natl Acad Sci USA. 2005;102:18514-18519.
28. Sullivan N, Sun Y, Li J, et al. Replicative function and neutralization sensitivity of envelope glycoproteins from primary and T-cell line-passaged human immunodeficiency virus type 1 isolates. J Virol. 1995;69:4413-4422.
29. Sawyer LS, Wrin MT, Crawford-Miksza L, et al. Neutralization sensitivity of human immunodeficiency virus type 1 is determined in part by the cell in which the virus is propagated. J Virol. 1994;68:1342-1349.
30. Moore JP, Burkly LC, Connor RI, et al. Adaptation of two primary human immunodeficiency virus type 1 isolates to growth in transformed T cell lines correlates with alterations in the responses of their envelope glycoproteins to soluble CD4. AIDS Res Hum Retroviruses. 1993;9:529-539.
31. Beaumont T, Quakkelaar E, van Nuenen A, et al. Increased sensitivity to CD4 binding site-directed neutralization following in vitro propagation on primary lymphocytes of a neutralization-resistant human immunodeficiency virus IIIB strain isolated from an accidentally infected laboratory worker. J Virol. 2004;78:5651-5657.
32. Pugach P, Kuhmann SE, Taylor J, et al. The prolonged culture of human immunodeficiency virus type 1 in primary lymphocytes increases its sensitivity to neutralization by soluble CD4. Virology. 2004;321:8-22.
33. Quakkelaar ED, Beaumont T, van Nuenen AC, et al. T cell line passage can select for pre-existing neutralization-sensitive variants from the quasispecies of primary human immunodeficiency virus type-1 isolates. Virology. 2007;359:92-104.
34. Petropoulos CJ, Parkin NT, Limoli KL, et al. A novel phenotypic drug susceptibility assay for human immunodeficiency virus type 1. Antimicrob Agents Chemother. 2000;44:920-928.
35. Blish CA, Nedellec R, Mandaliya K, et al. HIV-1 subtype A envelope variants from early in infection have variable sensitivity to neutralization and to inhibitors of viral entry. AIDS. 2007;21:693-702.
36. Brown BK, Darden JM, Tovanabutra S, et al. Biologic and genetic characterization of a panel of 60 human immunodeficiency virus type 1 isolates, representing clades A, B, C, D, CRF01_AE, and CRF02_AG, for the development and assessment of candidate vaccines. J Virol. 2005;79:6089-6101.
37. Gao F, Robertson DL, Carruthers CD, et al. A comprehensive panel of near-full-length clones and reference sequences for non-subtype B isolates of human immunodeficiency virus type 1. J Virol. 1998;72:5680-5698.
38. Li M, Gao F, Mascola JR, et al. Human immunodeficiency virus type 1 env clones from acute and early subtype B infections for standardized assessments of vaccine-elicited neutralizing antibodies. J Virol. 2005;79:10108-10125.
39. Li M, Salazar-Gonzalez JF, Derdeyn CA, et al. Genetic and neutralization properties of subtype C human immunodeficiency virus type 1 molecular env clones from acute and early heterosexually acquired infections in Southern Africa. J Virol. 2006;80:11776-11790.
40. Liu Y, Wrin T, Chappey C, et al. Recombination in the HIV-1 envelope gene is a common occurrence: evidence from subjects infected with diverse viral populations. Presented at: HIV Vaccines Keystone Symposia; 2006; Keystone.
41. Grant RM, McConnel J, Marcus J, et al. High frequency of apparent HIV-1 superinfection in a seroconverter cohort. Presented at: 12th Conference on Retroviruses and Opportunistic Infections; 2005; Boston.
42. Moore JP, Kitchen SG, Pugach P, et al. The CCR5 and CXCR4 coreceptors - central to understanding the transmission and pathogenesis of human immunodeficiency virus type 1 infection. AIDS Res Hum Retroviruses. 2004;20:111-126.
43. Connor RI, Sheridan KE, Ceradini D, et al. Change in coreceptor use correlates with disease progression in HIV-1-infected individuals. J Exp Med. 1997;185:621-628.
44. Hecht FM, Busch MP, Rawal B, et al. Use of laboratory tests and clinical symptoms for identification of primary HIV infection. AIDS. 2002;16:1119-1129.
45. Janssen RS, Satten GA, Stramer SL, et al. New testing strategy to detect early HIV-1 infection for use in incidence estimates and for clinical and prevention purposes. JAMA. 1998;280:42-48.
46. Deeks SG, Martin JN, Sinclair E, et al. Strong cell-mediated immune responses are associated with the maintenance of low-level viremia in antiretroviral-treated individuals with drug-resistant human immunodeficiency virus type 1. J Infect Dis. 2004;189:312-321.
47. Hunt PW, Martin JN, Sinclair E, et al. T cell activation is associated with lower CD4+ T cell gains in human immunodeficiency virus-infected patients with sustained viral suppression during antiretroviral therapy. J Infect Dis. 2003;187:1534-1543.
48. Allaway GP, Davis-Bruno KL, Beaudry GA, et al. Expression and characterization of CD4-IgG2, a novel heterotetramer that neutralizes primary HIV type 1 isolates. AIDS Res Hum Retroviruses. 1995;11:533-539.
49. Nagashima KA, Thompson DA, Rosenfield SI, et al. Human immunodeficiency virus type 1 entry inhibitors PRO 542 and T-20 are potently synergistic in blocking virus-cell and cell-cell fusion. J Infect Dis. 2001;183:1121-1125.
50. Jacobson JM, Israel RJ, Lowy I, et al. Treatment of advanced human immunodeficiency virus type 1 disease with the viral entry inhibitor PRO 542. Antimicrob Agents Chemother. 2004;48:423-429.
51. Deleted in proof.
52. Burton DR, Barbas CF 3rd, Persson MA, et al. A large array of human monoclonal antibodies to type 1 human immunodeficiency virus from combinatorial libraries of asymptomatic seropositive individuals. Proc Natl Acad Sci USA. 1991;88:10134-10137.
53. Burton DR, Pyati J, Koduri R, et al. Efficient neutralization of primary isolates of HIV-1 by a recombinant human monoclonal antibody. Science. 1994;266:1024-1027.
54. Roben P, Moore JP, Thali M, et al. Recognition properties of a panel of human recombinant Fab fragments to the CD4 binding site of gp120 that show differing abilities to neutralize human immunodeficiency virus type 1. J Virol. 1994;68:4821-4828.
55. Buchacher A, Predl R, Strutzenberger K, et al. Generation of human monoclonal antibodies against HIV-1 proteins; electrofusion and Epstein-Barr virus transformation for peripheral blood lymphocyte immortalization. AIDS Res Hum Retroviruses. 1994;10:359-369.
56. Zwick MB, Labrijn AF, Wang M, et al. Broadly neutralizing antibodies targeted to the membrane-proximal external region of human immunodeficiency virus type 1 glycoprotein gp41. J Virol. 2001;75:10892-10905.
57. Stiegler G, Kunert R, Purtscher M, et al. A potent cross-clade neutralizing human monoclonal antibody against a novel epitope on gp41 of human immunodeficiency virus type 1. AIDS Res Hum Retroviruses. 2001;17:1757-1765.
58. Muster T, Steindl F, Purtscher M, et al. A conserved neutralizing epitope on gp41 of human immunodeficiency virus type 1. J Virol. 1993;67:6642-6647.
59. Parker CE, Deterding LJ, Hager-Braun C, et al. Fine definition of the epitope on the gp41 glycoprotein of human immunodeficiency virus type 1 for the neutralizing monoclonal antibody 2F5. J Virol. 2001;75:10906-10911.
60. Purtscher M, Trkola A, Grassauer A, et al. Restricted antigenic variability of the epitope recognized by the neutralizing gp41 antibody 2F5. AIDS. 1996;10:587-593.
61. Kunert R, Ruker F, Katinger H. Molecular characterization of five neutralizing anti-HIV type 1 antibodies: identification of nonconventional D segments in the human monoclonal antibodies 2G12 and 2F5. AIDS Res Hum Retroviruses. 1998;14:1115-1128.
62. Trkola A, Purtscher M, Muster T, et al. Human monoclonal antibody 2G12 defines a distinctive neutralization epitope on the gp120 glycoprotein of human immunodeficiency virus type 1. J Virol. 1996;70:1100-1108.
63. Calarese DA, Lee HK, Huang CY, et al. Dissection of the carbohydrate specificity of the broadly neutralizing anti-HIV-1 antibody 2G12. Proc Natl Acad Sci USA. 2005;102:13372-13377.
64. Scanlan CN, Pantophlet R, Wormald MR, et al. The broadly neutralizing anti-human immunodeficiency virus type 1 antibody 2G12 recognizes a cluster of alpha1!2 mannose residues on the outer face of gp120. J Virol. 2002;76:7306-7321.
65. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22:4673-4680.
66. Kumar S, Tamura K, Nei M. MEGA3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform. 2004;5:150-163.
67. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution Int J Org Evolution. 1985;39:783-791.
68. Whitcomb JM, Huang W, Fransen S, et al. Development and characterization of a novel single-cycle recombinant-virus assay to determine human immunodeficiency virus type 1 coreceptor tropism. Antimicrob Agents Chemother. 2007;51:566-575.
69. Brandt SM, Mariani R, Holland AU, et al. Association of chemokinemediated block to HIVentry with coreceptor internalization. J Biol Chem. 2002;277:17291-17299.
70. Sanders RW, Venturi M, Schiffner L, et al. The mannose-dependent epitope for neutralizing antibody 2G12 on human immunodeficiency virus type 1 glycoprotein gp120. J Virol. 2002;76:7293-7305.
71. Michael NL, Nelson JA, Kewalramani VN, et al. Exclusive and persistent use of the entry coreceptor CXCR4 by human immunodeficiency virus type 1 from a subject homozygous for CCR5 delta32. J Virol. 1998;72:6040-6047.
72. Sheppard HW, Celum C, Michael NL, et al. HIV-1 infection in individuals with the CCR5-Delta32/Delta32 genotype: acquisition of syncytiuminducing virus at seroconversion. J Acquir Immune Defic Syndr. 2002;29:307-313.
73. Theodorou I, Meyer L, Magierowska M, et al. HIV-1 infection in an individual homozygous for CCR5 delta 32. Seroco Study Group. Lancet. 1997;349:1219-1220.
74. O'Brien TR, Winkler C, Dean M, et al. HIV-1 infection in a man homozygous for CCR5 delta 32. Lancet. 1997;349:1219.