references - shodhgangashodhganga.inflibnet.ac.in/bitstream/10603/2237/15/15_references.pdf · phd...

References

PhD Thesis (2008) Kalpana Agnihotri

National AIDS Research Institute, Pune 17

References

1. Abrahamyan LG, Mkrtchyan SR, Binley J, Lu M, Melikyan GB, Cohen FS: The

cytoplasmic tail slows the folding of human immunodeficiency virus type 1

Env from a late prebundle configuration into the six-helix bundle. J Virol 2005,

79(1):106-115.

2. Adams O, Schaal H, Scheid A: Natural variation in the amino acid sequence

around the HIV type 1 glycoprotein 160 cleavage site and its effect on

cleavability, subunit association, and membrane fusion. AIDS Res Hum

Retroviruses 2000, 16(13):1235-1245.

3. Agnihotri KD, Tripathy SP, Jere AP, Kale SM, Paranjape RS: Molecular analysis

of gp41 sequences of HIV type 1 subtype C from India. J Acquir Immune Defic

Syndr 2006, 41(3):345-351.

4. Agwale SM, Robbins KE, Odama L, Saekhou A, Zeh C, Edubio A, Njoku OM,

Sani-Gwarzo N, Gboun MF, Gao F et al: Development of an env gp41-based

heteroduplex mobility assay for rapid human immunodeficiency virus type 1

subtyping. J Clin Microbiol 2001, 39(6):2110-2114.

5. Amara RR, Robinson HL: A new generation of HIV vaccines. Trends Mol Med

2002, 8(10):489-495.

6. Amara RR, Smith JM, Staprans SI, Montefiori DC, Villinger F, Altman JD, O'Neil

SP, Kozyr NL, Xu Y, Wyatt LS et al: Critical role for Env as well as Gag-Pol in

control of a simian-human immunodeficiency virus 89.6P challenge by a DNA

prime/recombinant modified vaccinia virus Ankara vaccine. J Virol 2002,

76(12):6138-6146.

7. Ashkenazi A, Dixit VM: Death receptors: signaling and modulation. Science

1998, 281(5381):1305-1308.

8. Asjo B, Morfeldt-Manson L, Albert J, Biberfeld G, Karlsson A, Lidman K, Fenyo

EM: Replicative capacity of human immunodeficiency virus from patients

with varying severity of HIV infection. Lancet 1986, 2(8508):660-662.


National AIDS Research Institute, Pune Page 218

9. Back NK, Smit L, De Jong JJ, Keulen W, Schutten M, Goudsmit J, Tersmette M:

An N-glycan within the human immunodeficiency virus type 1 gp120 V3 loop

affects virus neutralization. Virology 1994, 199(2):431-438.

10. Barnett SW, Rajasekar S, Legg H, Doe B, Fuller DH, Haynes JR, Walker CM,

Steimer KS: Vaccination with HIV-1 gp120 DNA induces immune responses

that are boosted by a recombinant gp120 protein subunit. Vaccine 1997,

15(8):869-873.

11. Barouch DH, Letvin NL: DNA vaccination for HIV-1 and SIV. Intervirology 2000,

43(4-6):282-287.

12. Barouch DH, Santra S, Schmitz JE, Kuroda MJ, Fu TM, Wagner W, Bilska M,

Craiu A, Zheng XX, Krivulka GR et al: Control of viremia and prevention of

clinical AIDS in rhesus monkeys by cytokine-augmented DNA vaccination.

Science 2000, 290(5491):486-492.

13. Barre-Sinoussi F, Chermann JC, Rey F, Nugeyre MT, Chamaret S, Gruest J,

Dauguet C, Axler-Blin C, Vezinet-Brun F, Rouzioux C et al: Isolation of a T-

lymphotropic retrovirus from a patient at risk for acquired immune deficiency

syndrome (AIDS). Science 1983, 220(4599):868-871.

14. Baskar PV, Ray SC, Rao R, Quinn TC, Hildreth JE, Bollinger RC: Presence in

India of HIV type 1 similar to North American strains. AIDS Res Hum

Retroviruses 1994, 10(8):1039-1041.

15. Batra M, Tien PC, Shafer RW, Contag CH, Katzenstein DA: HIV type 1 envelope

subtype C sequences from recent seroconverters in Zimbabwe. AIDS Res Hum

Retroviruses 2000, 16(10):973-979.

16. Beddows S, Schulke N, Kirschner M, Barnes K, Franti M, Michael E, Ketas T,

Sanders RW, Maddon PJ, Olson WC et al: Evaluating the immunogenicity of a

disulfide-stabilized, cleaved, trimeric form of the envelope glycoprotein

complex of human immunodeficiency virus type 1. J Virol 2005, 79(14):8812-

8827.

17. Belshe RB, Gorse GJ, Mulligan MJ, Evans TG, Keefer MC, Excler JL, Duliege AM,

Tartaglia J, Cox WI, McNamara J et al: Induction of immune responses to HIV-1



by canarypox virus (ALVAC) HIV-1 and gp120 SF-2 recombinant vaccines in

uninfected volunteers. NIAID AIDS Vaccine Evaluation Group. AIDS 1998,

12(18):2407-2415.

18. Berger EA, Murphy PM, Farber JM: Chemokine receptors as HIV-1 coreceptors:

roles in viral entry, tropism, and disease. Annu Rev Immunol 1999, 17:657-700.

19. Berlioz-Torrent C, Shacklett BL, Erdtmann L, Delamarre L, Bouchaert I, Sonigo P,

Dokhelar MC, Benarous R: Interactions of the cytoplasmic domains of human

and simian retroviral transmembrane proteins with components of the clathrin

adaptor complexes modulate intracellular and cell surface expression of

envelope glycoproteins. J Virol 1999, 73(2):1350-1361.

20. Berman PW, Gregory TJ, Riddle L, Nakamura GR, Champe MA, Porter JP, Wurm

FM, Hershberg RD, Cobb EK, Eichberg JW: Protection of chimpanzees from

infection by HIV-1 after vaccination with recombinant glycoprotein gp120 but

not gp160. Nature 1990, 345(6276):622-625.

21. Bernstein HB, Tucker SP, Hunter E, Schutzbach JS, Compans RW: Human

immunodeficiency virus type 1 envelope glycoprotein is modified by O-linked

oligosaccharides. J Virol 1994, 68(1):463-468.

22. Binley J, Moore JP: HIV-cell fusion. The viral mousetrap. Nature 1997,

387(6631):346-348.

23. Binley JM, Wyatt R, Desjardins E, Kwong PD, Hendrickson W, Moore JP,

Sodroski J: Analysis of the interaction of antibodies with a conserved

enzymatically deglycosylated core of the HIV type 1 envelope glycoprotein

120. AIDS Res Hum Retroviruses 1998, 14(3):191-198.

24. Blot G, Janvier K, Le Panse S, Benarous R, Berlioz-Torrent C: Targeting of the

human immunodeficiency virus type 1 envelope to the trans-Golgi network

through binding to TIP47 is required for env incorporation into virions and

infectivity. J Virol 2003, 77(12):6931-6945.

25. Bolmstedt A, Hinkula J, Rowcliffe E, Biller M, Wahren B, Olofsson S: Enhanced

immunogenicity of a human immunodeficiency virus type 1 env DNA vaccine



by manipulating N-glycosylation signals. Effects of elimination of the V3

N306 glycan. Vaccine 2001, 20(3-4):397-405.

26. Bolmstedt A, Sjolander S, Hansen JE, Akerblom L, Hemming A, Hu SL, Morein

B, Olofsson S: Influence of N-linked glycans in V4-V5 region of human

immunodeficiency virus type 1 glycoprotein gp160 on induction of a virus-

neutralizing humoral response. J Acquir Immune Defic Syndr Hum Retrovirol 1996,

12(3):213-220.

27. Broder S, Gallo RC: A pathogenic retrovirus (HTLV-III) linked to AIDS. N Engl

J Med 1984, 311(20):1292-1297.

28. Bruce CB, Akrigg A, Sharpe SA, Hanke T, Wilkinson GW, Cranage MP:

Replication-deficient recombinant adenoviruses expressing the human

immunodeficiency virus Env antigen can induce both humoral and CTL

immune responses in mice. J Gen Virol 1999, 80 ( Pt 10):2621-2628.

29. Bruck C, Thiriart C, Fabry L, Francotte M, Pala P, Van Opstal O, Culp J,

Rosenberg M, De Wilde M, Heidt P et al: HIV-1 envelope-elicited neutralizing

antibody titres correlate with protection and virus load in chimpanzees.

Vaccine 1994, 12(12):1141-1148.

30. Burke B, Derby NR, Kraft Z, Saunders CJ, Dai C, Llewellyn N, Zharkikh I,

Vojtech L, Zhu T, Srivastava IK et al: Viral evolution in macaques coinfected

with CCR5- and CXCR4-tropic SHIVs in the presence or absence of vaccine-

elicited anti-CCR5 SHIV neutralizing antibodies. Virology 2006, 355(2):138-151.

31. Burton DR, Barbas CF, 3rd: Human monoclonal antibodies: recent

achievements. Hosp Pract (Off Ed) 1994, 29(11):111, 114-116, 119 passim.

32. Burton DR, Desrosiers RC, Doms RW, Koff WC, Kwong PD, Moore JP, Nabel GJ,

Sodroski J, Wilson IA, Wyatt RT: HIV vaccine design and the neutralizing

antibody problem. Nat Immunol 2004, 5(3):233-236.

33. Burton DR, Montefiori DC: The antibody response in HIV-1 infection. AIDS

1997, 11 Suppl A:S87-98.

34. Burton DR, Pyati J, Koduri R, Sharp SJ, Thornton GB, Parren PW, Sawyer LS,

Hendry RM, Dunlop N, Nara PL et al: Efficient neutralization of primary



isolates of HIV-1 by a recombinant human monoclonal antibody. Science 1994,

266(5187):1024-1027.

35. Cann AJ, Churcher MJ, Boyd M, O'Brien W, Zhao JQ, Zack J, Chen IS: The region

of the envelope gene of human immunodeficiency virus type 1 responsible for

determination of cell tropism. J Virol 1992, 66(1):305-309.

36. Cao J, Bergeron L, Helseth E, Thali M, Repke H, Sodroski J: Effects of amino acid

changes in the extracellular domain of the human immunodeficiency virus

type 1 gp41 envelope glycoprotein. J Virol 1993, 67(5):2747-2755.

37. Carrillo A, Ratner L: Human immunodeficiency virus type 1 tropism for T-

lymphoid cell lines: role of the V3 loop and C4 envelope determinants. J Virol

1996, 70(2):1301-1309.

38. Casimiro DR, Chen L, Fu TM, Evans RK, Caulfield MJ, Davies ME, Tang A, Chen

M, Huang L, Harris V et al: Comparative immunogenicity in rhesus monkeys of

DNA plasmid, recombinant vaccinia virus, and replication-defective

adenovirus vectors expressing a human immunodeficiency virus type 1 gag

gene. J Virol 2003, 77(11):6305-6313.

39. Casimiro DR, Tang A, Perry HC, Long RS, Chen M, Heidecker GJ, Davies ME,

Freed DC, Persaud NV, Dubey S et al: Vaccine-induced immune responses in

rodents and nonhuman primates by use of a humanized human

immunodeficiency virus type 1 pol gene. J Virol 2002, 76(1):185-194.

40. Cecilia D, Kulkarni SS, Tripathy SP, Gangakhedkar RR, Paranjape RS, Gadkari

DA: Absence of coreceptor switch with disease progression in human

immunodeficiency virus infections in India. Virology 2000, 271(2):253-258.

41. Chackerian B, Rudensey LM, Overbaugh J: Specific N-linked and O-linked

glycosylation modifications in the envelope V1 domain of simian

immunodeficiency virus variants that evolve in the host alter recognition by

neutralizing antibodies. J Virol 1997, 71(10):7719-7727.

42. Chakrabarti BK, Kong WP, Wu BY, Yang ZY, Friborg J, Ling X, King SR,

Montefiori DC, Nabel GJ: Modifications of the human immunodeficiency virus



envelope glycoprotein enhance immunogenicity for genetic immunization. J

Virol 2002, 76(11):5357-5368.

43. Chakrabarti S, Panda S, Chatterjee A, Sarkar S, Manna B, Singh NB, Naik TN,

Detels R, Bhattacharya SK: HIV-1 subtypes in injecting drug users & their non-

injecting wives in Manipur, India. Indian J Med Res 2000, 111:189-194.

44. Chan DC, Fass D, Berger JM, Kim PS: Core structure of gp41 from the HIV

envelope glycoprotein. Cell 1997, 89(2):263-273.

45. Chan DC, Kim PS: HIV entry and its inhibition. Cell 1998, 93(5):681-684.

46. Chanda PK, Natuk RJ, Mason BB, Bhat BM, Greenberg L, Dheer SK, Molnar-

Kimber KL, Mizutani S, Lubeck MD, Davis AR et al: High level expression of the

envelope glycoproteins of the human immunodeficiency virus type I in

presence of rev gene using helper-independent adenovirus type 7

recombinants. Virology 1990, 175(2):535-547.

47. Cheng-Mayer C, Brown A, Harouse J, Luciw PA, Mayer AJ: Selection for

neutralization resistance of the simian/human immunodeficiency virus

SHIVSF33A variant in vivo by virtue of sequence changes in the extracellular

envelope glycoprotein that modify N-linked glycosylation. J Virol 1999,

73(7):5294-5300.

48. Chhaya SU, Shankarkumar U: HLA antigen distribution in Jain population

from Mumbai, Maharashtra, India. Indian J Med Res 2001, 114:25-29.

49. Chohan B, Lang D, Sagar M, Korber B, Lavreys L, Richardson B, Overbaugh J:

Selection for human immunodeficiency virus type 1 envelope glycosylation

variants with shorter V1-V2 loop sequences occurs during transmission of

certain genetic subtypes and may impact viral RNA levels. J Virol 2005,

79(10):6528-6531.

50. Cleveland SM, McLain L, Cheung L, Jones TD, Hollier M, Dimmock NJ: A region

of the C-terminal tail of the gp41 envelope glycoprotein of human

immunodeficiency virus type 1 contains a neutralizing epitope: evidence for

its exposure on the surface of the virion. J Gen Virol 2003, 84(Pt 3):591-602.



51. Coffin J, Haase A, Levy JA, Montagnier L, Oroszlan S, Teich N, Temin H,

Toyoshima K, Varmus H, Vogt P et al: Human immunodeficiency viruses.

Science 1986, 232(4751):697.

52. Coffin J, Haase A, Levy JA, Montagnier L, Oroszlan S, Teich N, Temin H,

Toyoshima K, Varmus H, Vogt P et al: What to call the AIDS virus? Nature 1986,

321(6065):10.

53. Cole KS, Murphey-Corb M, Narayan O, Joag SV, Shaw GM, Montelaro RC:

Common themes of antibody maturation to simian immunodeficiency virus,

simian-human immunodeficiency virus, and human immunodeficiency virus

type 1 infections. J Virol 1998, 72(10):7852-7859.

54. Conley AJ, Kessler JA, 2nd, Boots LJ, Tung JS, Arnold BA, Keller PM, Shaw AR,

Emini EA: Neutralization of divergent human immunodeficiency virus type 1

variants and primary isolates by IAM-41-2F5, an anti-gp41 human monoclonal

antibody. Proc Natl Acad Sci U S A 1994, 91(8):3348-3352.

55. Connor RI, Sheridan KE, Ceradini D, Choe S, Landau NR: Change in coreceptor

use coreceptor use correlates with disease progression in HIV-1--infected

individuals. J Exp Med 1997, 185(4):621-628.

56. Dalgleish AG, Beverley PC, Clapham PR, Crawford DH, Greaves MF, Weiss RA:

The CD4 (T4) antigen is an essential component of the receptor for the AIDS

retrovirus. Nature 1984, 312(5996):763-767.

57. Dash B, McIntosh A, Barrett W, Daniels R: Deletion of a single N-linked

glycosylation site from the transmembrane envelope protein of human

immunodeficiency virus type 1 stops cleavage and transport of gp160

preventing env-mediated fusion. J Gen Virol 1994, 75 ( Pt 6):1389-1397.

58. Davis KC, Horsburgh CR, Jr., Hasiba U, Schocket AL, Kirkpatrick CH: Acquired

immunodeficiency syndrome in a patient with hemophilia. Ann Intern Med

1983, 98(3):284-286.

59. Dedera DA, Gu RL, Ratner L: Role of asparagine-linked glycosylation in

human immunodeficiency virus type 1 transmembrane envelope function.

Virology 1992, 187(1):377-382.



60. Deng H, Liu R, Ellmeier W, Choe S, Unutmaz D, Burkhart M, Di Marzio P,

Marmon S, Sutton RE, Hill CM et al: Identification of a major co-receptor for

primary isolates of HIV-1. Nature 1996, 381(6584):661-666.

61. Derdeyn CA, Decker JM, Bibollet-Ruche F, Mokili JL, Muldoon M, Denham SA,

Heil ML, Kasolo F, Musonda R, Hahn BH et al: Envelope-constrained

neutralization-sensitive HIV-1 after heterosexual transmission. Science 2004,

303(5666):2019-2022.

62. Dewar RL, Natarajan V, Vasudevachari MB, Salzman NP: Synthesis and

processing of human immunodeficiency virus type 1 envelope proteins

encoded by a recombinant human adenovirus. J Virol 1989, 63(1):129-136.

63. Doms RW, Moore JP: HIV-1 membrane fusion: targets of opportunity. J Cell Biol

2000, 151(2):F9-14.

64. Downing R, Pieniazek D, Hu DJ, Biryahwaho B, Fridlund C, Rayfield MA,

Sempala SD, Lal RB: Genetic characterization and phylogenetic analysis of

HIV-1 subtype C from Uganda. AIDS Res Hum Retroviruses 2000, 16(8):815-819.

65. Dragic T, Litwin V, Allaway GP, Martin SR, Huang Y, Nagashima KA, Cayanan

C, Maddon PJ, Koup RA, Moore JP et al: HIV-1 entry into CD4+ cells is

mediated by the chemokine receptor CC-CKR-5. Nature 1996, 381(6584):667-673.

66. Dubay JW, Roberts SJ, Hahn BH, Hunter E: Truncation of the human

immunodeficiency virus type 1 transmembrane glycoprotein cytoplasmic

domain blocks virus infectivity. J Virol 1992, 66(11):6616-6625.

67. Earl PL, Broder CC, Long D, Lee SA, Peterson J, Chakrabarti S, Doms RW, Moss

B: Native oligomeric human immunodeficiency virus type 1 envelope

glycoprotein elicits diverse monoclonal antibody reactivities. J Virol 1994,

68(5):3015-3026.

68. Earl PL, Moss B, Doms RW: Folding, interaction with GRP78-BiP, assembly,

and transport of the human immunodeficiency virus type 1 envelope protein. J

Virol 1991, 65(4):2047-2055.

69. Edwards TG, Hoffman TL, Baribaud F, Wyss S, LaBranche CC, Romano J,

Adkinson J, Sharron M, Hoxie JA, Doms RW: Relationships between CD4



independence, neutralization sensitivity, and exposure of a CD4-induced

epitope in a human immunodeficiency virus type 1 envelope protein. J Virol

2001, 75(11):5230-5239.

70. Edwards TG, Wyss S, Reeves JD, Zolla-Pazner S, Hoxie JA, Doms RW, Baribaud

F: Truncation of the cytoplasmic domain induces exposure of conserved

regions in the ectodomain of human immunodeficiency virus type 1 envelope

protein. J Virol 2002, 76(6):2683-2691.

71. Farzan M, Choe H, Desjardins E, Sun Y, Kuhn J, Cao J, Archambault D,

Kolchinsky P, Koch M, Wyatt R et al: Stabilization of human immunodeficiency

virus type 1 envelope glycoprotein trimers by disulfide bonds introduced into

the gp41 glycoprotein ectodomain. J Virol 1998, 72(9):7620-7625.

72. Fennie C, Lasky LA: Model for intracellular folding of the human

immunodeficiency virus type 1 gp120. J Virol 1989, 63(2):639-646.

73. Fenouillet E, Gluckman JC, Bahraoui E: Role of N-linked glycans of envelope

glycoproteins in infectivity of human immunodeficiency virus type 1. J Virol

1990, 64(6):2841-2848.

74. Fenouillet E, Jones I, Powell B, Schmitt D, Kieny MP, Gluckman JC: Functional

role of the glycan cluster of the human immunodeficiency virus type 1

transmembrane glycoprotein (gp41) ectodomain. J Virol 1993, 67(1):150-160.

75. Flanagan B, Pringle CR, Leppard KN: A recombinant human adenovirus

expressing the simian immunodeficiency virus Gag antigen can induce long-

lived immune responses in mice. J Gen Virol 1997, 78 ( Pt 5):991-997.

76. Freed EO, Martin MA: Virion incorporation of envelope glycoproteins with

long but not short cytoplasmic tails is blocked by specific, single amino acid

substitutions in the human immunodeficiency virus type 1 matrix. J Virol 1995,

69(3):1984-1989.

77. Freed EO, Martin MA: Domains of the human immunodeficiency virus type 1

matrix and gp41 cytoplasmic tail required for envelope incorporation into

virions. J Virol 1996, 70(1):341-351.



78. Furuta RA, Wild CT, Weng Y, Weiss CD: Capture of an early fusion-active

conformation of HIV-1 gp41. Nat Struct Biol 1998, 5(4):276-279.

79. Gabuzda DH, Lever A, Terwilliger E, Sodroski J: Effects of deletions in the

cytoplasmic domain on biological functions of human immunodeficiency

virus type 1 envelope glycoproteins. J Virol 1992, 66(6):3306-3315.

80. Gadkari DA, Moore D, Sheppard HW, Kulkarni SS, Mehendale SM, Bollinger

RC: Transmission of genetically diverse strains of HIV-1 in Pune, India. Indian

J Med Res 1998, 107:1-9.

81. Gallo RC, Salahuddin SZ, Popovic M, Shearer GM, Kaplan M, Haynes BF, Palker

TJ, Redfield R, Oleske J, Safai B et al: Frequent detection and isolation of

cytopathic retroviruses (HTLV-III) from patients with AIDS and at risk for

AIDS. Science 1984, 224(4648):500-503.

82. Gallo SA, Finnegan CM, Viard M, Raviv Y, Dimitrov A, Rawat SS, Puri A, Durell

S, Blumenthal R: The HIV Env-mediated fusion reaction. Biochim Biophys Acta

2003, 1614(1):36-50.

83. Gao F, Bailes E, Robertson DL, Chen Y, Rodenburg CM, Michael SF, Cummins

LB, Arthur LO, Peeters M, Shaw GM et al: Origin of HIV-1 in the chimpanzee

Pan troglodytes troglodytes. Nature 1999, 397(6718):436-441.

84. Gao F, Morrison SG, Robertson DL, Thornton CL, Craig S, Karlsson G, Sodroski

J, Morgado M, Galvao-Castro B, von Briesen H et al: Molecular cloning and

analysis of functional envelope genes from human immunodeficiency virus

type 1 sequence subtypes A through G. The WHO and NIAID Networks for

HIV Isolation and Characterization. J Virol 1996, 70(3):1651-1667.

85. Gao F, Weaver EA, Lu Z, Li Y, Liao HX, Ma B, Alam SM, Scearce RM, Sutherland

LL, Yu JS et al: Antigenicity and immunogenicity of a synthetic human

immunodeficiency virus type 1 group m consensus envelope glycoprotein. J

Virol 2005, 79(2):1154-1163.

86. Garrity RR, Rimmelzwaan G, Minassian A, Tsai WP, Lin G, de Jong JJ, Goudsmit

J, Nara PL: Refocusing neutralizing antibody response by targeted dampening

of an immunodominant epitope. J Immunol 1997, 159(1):279-289.



87. Gaschen B, Taylor J, Yusim K, Foley B, Gao F, Lang D, Novitsky V, Haynes B,

Hahn BH, Bhattacharya T et al: Diversity considerations in HIV-1 vaccine

selection. Science 2002, 296(5577):2354-2360.

88. Girard M, Kieny MP, Pinter A, Barre-Sinoussi F, Nara P, Kolbe H, Kusumi K,

Chaput A, Reinhart T, Muchmore E et al: Immunization of chimpanzees confers

protection against challenge with human immunodeficiency virus. Proc Natl

Acad Sci U S A 1991, 88(2):542-546.

89. Gomez-Roman VR, Florese RH, Peng B, Montefiori DC, Kalyanaraman VS,

Venzon D, Srivastava I, Barnett SW, Robert-Guroff M: An adenovirus-based

HIV subtype B prime/boost vaccine regimen elicits antibodies mediating

broad antibody-dependent cellular cytotoxicity against non-subtype B HIV

strains. J Acquir Immune Defic Syndr 2006, 43(3):270-277.

90. Gottlieb MS, Schroff R, Schanker HM, Weisman JD, Fan PT, Wolf RA, Saxon A:

Pneumocystis carinii pneumonia and mucosal candidiasis in previously

healthy homosexual men: evidence of a new acquired cellular

immunodeficiency. N Engl J Med 1981, 305(24):1425-1431.

91. Graham FL, Prevec L: Methods for construction of adenovirus vectors. Mol

Biotechnol 1995, 3(3):207-220.

92. Gram GJ, Hemming A, Bolmstedt A, Jansson B, Olofsson S, Akerblom L, Nielsen

JO, Hansen JE: Identification of an N-linked glycan in the V1-loop of HIV-1

gp120 influencing neutralization by anti-V3 antibodies and soluble CD4. Arch

Virol 1994, 139(3-4):253-261.

93. Grundner C, Li Y, Louder M, Mascola J, Yang X, Sodroski J, Wyatt R: Analysis of

the neutralizing antibody response elicited in rabbits by repeated inoculation

with trimeric HIV-1 envelope glycoproteins. Virology 2005, 331(1):33-46.

94. Grundner C, Pancera M, Kang JM, Koch M, Sodroski J, Wyatt R: Factors limiting

the immunogenicity of HIV-1 gp120 envelope glycoproteins. Virology 2004,

330(1):233-248.

95. Haggerty S, Dempsey MP, Bukrinsky MI, Guo L, Stevenson M: Posttranslational

modifications within the HIV-1 envelope glycoprotein which restrict virus



assembly and CD4-dependent infection. AIDS Res Hum Retroviruses 1991,

7(6):501-510.

96. Hahn BH, Shaw GM, De Cock KM, Sharp PM: AIDS as a zoonosis: scientific

and public health implications. Science 2000, 287(5453):607-614.

97. Hallenberger S, Tucker SP, Owens RJ, Bernstein HB, Compans RW: Secretion of

a truncated form of the human immunodeficiency virus type 1 envelope

glycoprotein. Virology 1993, 193(1):510-514.

98. Hansen JE, Clausen H, Nielsen C, Teglbjaerg LS, Hansen LL, Nielsen CM,

Dabelsteen E, Mathiesen L, Hakomori SI, Nielsen JO: Inhibition of human

immunodeficiency virus (HIV) infection in vitro by anticarbohydrate

monoclonal antibodies: peripheral glycosylation of HIV envelope glycoprotein

gp120 may be a target for virus neutralization. J Virol 1990, 64(6):2833-2840.

99. Hardy AM, Allen JR, Morgan WM, Curran JW: The incidence rate of acquired

immunodeficiency syndrome in selected populations. Jama 1985, 253(2):215-

220.

100. Hemsley A, Arnheim N, Toney MD, Cortopassi G, Galas DJ: A simple method

for site-directed mutagenesis using the polymerase chain reaction. Nucleic

Acids Res 1989, 17(16):6545-6551.

101. Hernandez LD, Hoffman LR, Wolfsberg TG, White JM: Virus-cell and cell-cell

fusion. Annu Rev Cell Dev Biol 1996, 12:627-661.

102. Hoffman TL, Doms RW: HIV-1 envelope determinants for cell tropism and

chemokine receptor use. Mol Membr Biol 1999, 16(1):57-65.

103. Jere A, Tripathy S, Agnihotri K, Jadhav S, Paranjape R: Genetic analysis of

Indian HIV-1 nef: subtyping, variability and implications. Microbes Infect 2004,

6(3):279-289.

104. Johnson WE, Desrosiers RC: Viral persistance: HIV's strategies of immune

system evasion. Annu Rev Med 2002, 53:499-518.

105. Johnson WE, Sauvron JM, Desrosiers RC: Conserved, N-linked carbohydrates

of human immunodeficiency virus type 1 gp41 are largely dispensable for

viral replication. J Virol 2001, 75(23):11426-11436.



106. Jones DH, McBride BW, Roff MA, Farrar GH: Efficient purification and

rigorous characterisation of a recombinant gp120 for HIV vaccine studies.

Vaccine 1995, 13(11):991-999.

107. Juillard V, Villefroy P, Godfrin D, Pavirani A, Venet A, Guillet JG: Long-term

humoral and cellular immunity induced by a single immunization with

replication-defective adenovirus recombinant vector. Eur J Immunol 1995,

25(12):3467-3473.

108. Kalpana A, Srikanth T, Abhay J, Sushama J, Swarali K, Ramesh P: gp120

sequences from HIV type 1 subtype C early seroconverters in India. AIDS Res

Hum Retroviruses 2004, 20(8):889-894.

109. Kent KA, Robinson J: Antigenic determinants on HIV-1 envelope

glycoproteins: a dickens of a time with oligomer twist. AIDS 1996, 10 Suppl

A:S107-114.

110. Koch M, Pancera M, Kwong PD, Kolchinsky P, Grundner C, Wang L,

Hendrickson WA, Sodroski J, Wyatt R: Structure-based, targeted

deglycosylation of HIV-1 gp120 and effects on neutralization sensitivity and

antibody recognition. Virology 2003, 313(2):387-400.

111. Kolchinsky P, Kiprilov E, Bartley P, Rubinstein R, Sodroski J: Loss of a single

N-linked glycan allows CD4-independent human immunodeficiency virus

type 1 infection by altering the position of the gp120 V1/V2 variable loops. J

Virol 2001, 75(7):3435-3443.

112. Korber B, Muldoon M, Theiler J, Gao F, Gupta R, Lapedes A, Hahn BH,

Wolinsky S, Bhattacharya T: Timing the ancestor of the HIV-1 pandemic

strains. Science 2000, 288(5472):1789-1796.

113. Kornfeld R, Kornfeld S: Assembly of asparagine-linked oligosaccharides.

Annu Rev Biochem 1985, 54:631-664.

114. Kowalski M, Potz J, Basiripour L, Dorfman T, Goh WC, Terwilliger E, Dayton

A, Rosen C, Haseltine W, Sodroski J: Functional regions of the envelope

glycoprotein of human immunodeficiency virus type 1. Science 1987,

237(4820):1351-1355.



115. Kumar S, Tamura K, Jakobsen IB, Nei M: MEGA2: molecular evolutionary

genetics analysis software. Bioinformatics 2001, 17(12):1244-1245.

116. 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(13):1115-1128.

117. Kurle S, Tripathy S, Jadhav S, Agnihotri K, Paranjape R: Full-length gag

sequences of HIV type 1 subtype C recent seroconverters from Pune, India.

AIDS Res Hum Retroviruses 2004, 20(10):1113-1118.

118. Kwong PD, Wyatt R, Majeed S, Robinson J, Sweet RW, Sodroski J, Hendrickson

WA: Structures of HIV-1 gp120 envelope glycoproteins from laboratory-

adapted and primary isolates. Structure 2000, 8(12):1329-1339.

119. Kwong PD, Wyatt R, Robinson J, Sweet RW, Sodroski J, Hendrickson WA:

Structure of an HIV gp120 envelope glycoprotein in complex with the CD4

receptor and a neutralizing human antibody. Nature 1998, 393(6686):648-659.

120. LaBranche CC, Sauter MM, Haggarty BS, Vance PJ, Romano J, Hart TK,

Bugelski PJ, Marsh M, Hoxie JA: A single amino acid change in the cytoplasmic

domain of the simian immunodeficiency virus transmembrane molecule

increases envelope glycoprotein expression on infected cells. J Virol 1995,

69(9):5217-5227.

121. LaCasse RA, Follis KE, Trahey M, Scarborough JD, Littman DR, Nunberg JH:

Fusion-competent vaccines: broad neutralization of primary isolates of HIV.

Science 1999, 283(5400):357-362.

122. Lal RB, Chakrabarti S, Yang C: Impact of genetic diversity of HIV-1 on

diagnosis, antiretroviral therapy & vaccine development. Indian J Med Res 2005,

121(4):287-314.

123. Land A, Braakman I: Folding of the human immunodeficiency virus type 1

envelope glycoprotein in the endoplasmic reticulum. Biochimie 2001, 83(8):783-

790.



124. LaRosa GJ, Weinhold K, Profy AT, Langlois AJ, Dreesman GR, Boswell RN,

Shadduck P, Bolognesi DP, Matthews TJ, Emini EA et al: Conserved sequence

and structural elements in the HIV-1 principal neutralizing determinant:

further clarifications. Science 1991, 253(5024):1146.

125. Lasky LA, Nakamura G, Smith DH, Fennie C, Shimasaki C, Patzer E, Berman P,

Gregory T, Capon DJ: Delineation of a region of the human immunodeficiency

virus type 1 gp120 glycoprotein critical for interaction with the CD4 receptor.

Cell 1987, 50(6):975-985.

126. Learn GH, Muthui D, Brodie SJ, Zhu T, Diem K, Mullins JI, Corey L: Virus

population homogenization following acute human immunodeficiency virus

type 1 infection. J Virol 2002, 76(23):11953-11959.

127. Lee WR, Syu WJ, Du B, Matsuda M, Tan S, Wolf A, Essex M, Lee TH:

Nonrandom distribution of gp120 N-linked glycosylation sites important for

infectivity of human immunodeficiency virus type 1. Proc Natl Acad Sci U S A

1992, 89(6):2213-2217.

128. Lee WR, Yu XF, Syu WJ, Essex M, Lee TH: Mutational analysis of conserved

N-linked glycosylation sites of human immunodeficiency virus type 1 gp41. J

Virol 1992, 66(3):1799-1803.

129. Leonard CK, Spellman MW, Riddle L, Harris RJ, Thomas JN, Gregory TJ:

Assignment of intrachain disulfide bonds and characterization of potential

glycosylation sites of the type 1 recombinant human immunodeficiency virus

envelope glycoprotein (gp120) expressed in Chinese hamster ovary cells. J Biol

Chem 1990, 265(18):10373-10382.

130. Levy JA, Shimabukuro J: Recovery of AIDS-associated retroviruses from

patients with AIDS or AIDS-related conditions and from clinically healthy

individuals. J Infect Dis 1985, 152(4):734-738.

131. Li B, Decker JM, Johnson RW, Bibollet-Ruche F, Wei X, Mulenga J, Allen S,

Hunter E, Hahn BH, Shaw GM et al: Evidence for potent autologous

neutralizing antibody titers and compact envelopes in early infection with

subtype C human immunodeficiency virus type 1. J Virol 2006, 80(11):5211-5218.



132. Li Y, Cleveland B, Klots I, Travis B, Richardson BA, Anderson D, Montefiori D,

Polacino P, Hu SL: Removal of a single N-linked glycan in human

immunodeficiency virus type 1 gp120 results in an enhanced ability to induce

neutralizing antibody responses. J Virol 2008, 82(2):638-651.

133. Li Y, Luo L, Rasool N, Kang CY: Glycosylation is necessary for the correct

folding of human immunodeficiency virus gp120 in CD4 binding. J Virol 1993,

67(1):584-588.

134. Lian Y, Srivastava I, Gomez-Roman VR, Zur Megede J, Sun Y, Kan E, Hilt S,

Engelbrecht S, Himathongkham S, Luciw PA et al: Evaluation of envelope

vaccines derived from the South African subtype C human immunodeficiency

virus type 1 TV1 strain. J Virol 2005, 79(21):13338-13349.

135. Liang X, Casimiro DR, Schleif WA, Wang F, Davies ME, Zhang ZQ, Fu TM,

Finnefrock AC, Handt L, Citron MP et al: Vectored Gag and Env but not Tat

show efficacy against simian-human immunodeficiency virus 89.6P challenge

in Mamu-A*01-negative rhesus monkeys. J Virol 2005, 79(19):12321-12331.

136. Liu MA: The immunologist's grail: vaccines that generate cellular immunity.

Proc Natl Acad Sci U S A 1997, 94(20):10496-10498.

137. Liu R, Paxton WA, Choe S, Ceradini D, Martin SR, Horuk R, MacDonald ME,

Stuhlmann H, Koup RA, Landau NR: Homozygous defect in HIV-1 coreceptor

accounts for resistance of some multiply-exposed individuals to HIV-1

infection. Cell 1996, 86(3):367-377.

138. Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG,

Ingersoll R, Sheppard HW, Ray SC: Full-length human immunodeficiency virus

type 1 genomes from subtype C-infected seroconverters in India, with

evidence of intersubtype recombination. J Virol 1999, 73(1):152-160.

139. Lu M, Kim PS: A trimeric structural subdomain of the HIV-1 transmembrane

glycoprotein. J Biomol Struct Dyn 1997, 15(3):465-471.

140. Lubeck MD, Natuk RJ, Chengalvala M, Chanda PK, Murthy KK, Murthy S,

Mizutani S, Lee SG, Wade MS, Bhat BM et al: Immunogenicity of recombinant

adenovirus-human immunodeficiency virus vaccines in chimpanzees



following intranasal administration. AIDS Res Hum Retroviruses 1994,

10(11):1443-1449.

141. Ly A, Stamatatos L: V2 loop glycosylation of the human immunodeficiency

virus type 1 SF162 envelope facilitates interaction of this protein with CD4 and

CCR5 receptors and protects the virus from neutralization by anti-V3 loop and

anti-CD4 binding site antibodies. J Virol 2000, 74(15):6769-6776.

142. Maerz AL, Center RJ, Kemp BE, Kobe B, Poumbourios P: Functional

implications of the human T-lymphotropic virus type 1 transmembrane

glycoprotein helical hairpin structure. J Virol 2000, 74(14):6614-6621.

143. Maerz AL, Drummer HE, Wilson KA, Poumbourios P: Functional analysis of

the disulfide-bonded loop/chain reversal region of human immunodeficiency

virus type 1 gp41 reveals a critical role in gp120-gp41 association. J Virol 2001,

75(14):6635-6644.

144. Maitra A, Singh B, Banu S, Deshpande A, Robbins K, Kalish ML, Broor S, Seth

P: Subtypes of HIV type 1 circulating in India: partial envelope sequences.


145. Malkevitch NV, Patterson LJ, Aldrich MK, Wu Y, Venzon D, Florese RH,

Kalyanaraman VS, Pal R, Lee EM, Zhao J et al: Durable protection of rhesus

macaques immunized with a replicating adenovirus-SIV multigene

prime/protein boost vaccine regimen against a second SIVmac251 rectal

challenge: role of SIV-specific CD8+ T cell responses. Virology 2006, 353(1):83-

98.

146. Mandal D, Jana S, Bhattacharya SK, Chakrabarti S: HIV type 1 subtypes

circulating in eastern and northeastern regions of India. AIDS Res Hum

Retroviruses 2002, 18(16):1219-1227.

147. Mascola JR, Sambor A, Beaudry K, Santra S, Welcher B, Louder MK, Vancott

TC, Huang Y, Chakrabarti BK, Kong WP et al: Neutralizing antibodies elicited

by immunization of monkeys with DNA plasmids and recombinant

adenoviral vectors expressing human immunodeficiency virus type 1 proteins.

J Virol 2005, 79(2):771-779.



148. Mascola JR, Snyder SW, Weislow OS, Belay SM, Belshe RB, Schwartz DH,

Clements ML, Dolin R, Graham BS, Gorse GJ et al: Immunization with envelope

subunit vaccine products elicits neutralizing antibodies against laboratory-

adapted but not primary isolates of human immunodeficiency virus type 1.

The National Institute of Allergy and Infectious Diseases AIDS Vaccine

Evaluation Group. J Infect Dis 1996, 173(2):340-348.

149. McCaffrey RA, Saunders C, Hensel M, Stamatatos L: N-linked glycosylation of

the V3 loop and the immunologically silent face of gp120 protects human

immunodeficiency virus type 1 SF162 from neutralization by anti-gp120 and

anti-gp41 antibodies. J Virol 2004, 78(7):3279-3295.

150. McClure P, Curran R, Boneham S, Ball JK: A polymerase chain reaction

method for the amplification of full-length envelope genes of HIV-1 from

DNA samples containing single molecules of HIV-1 provirus. J Virol Methods

2000, 88(1):73-80.

151. McDougal JS, Nicholson JK, Cross GD, Cort SP, Kennedy MS, Mawle AC:

Binding of the human retrovirus HTLV-III/LAV/ARV/HIV to the CD4 (T4)

molecule: conformation dependence, epitope mapping, antibody inhibition,

and potential for idiotypic mimicry. J Immunol 1986, 137(9):2937-2944.

152. McMichael AJ, Hanke T: HIV vaccines 1983-2003. Nat Med 2003, 9(7):874-880.

153. Mehra NK, Jaini R, Rajalingam R, Balamurugan A, Kaur G: Molecular

diversity of HLA-A*02 in Asian Indians: predominance of A*0211. Tissue

Antigens 2001, 57(6):502-507.

154. Micoli KJ, Pan G, Wu Y, Williams JP, Cook WJ, McDonald JM: Requirement of

calmodulin binding by HIV-1 gp160 for enhanced FAS-mediated apoptosis. J

Biol Chem 2000, 275(2):1233-1240.

155. Montefiori DC, Pantaleo G, Fink LM, Zhou JT, Zhou JY, Bilska M, Miralles GD,

Fauci AS: Neutralizing and infection-enhancing antibody responses to human

immunodeficiency virus type 1 in long-term nonprogressors. J Infect Dis 1996,

173(1):60-67.



156. Moog C, Fleury HJ, Pellegrin I, Kirn A, Aubertin AM: Autologous and

heterologous neutralizing antibody responses following initial seroconversion

in human immunodeficiency virus type 1-infected individuals. J Virol 1997,

71(5):3734-3741.

157. Moore JP, Cao Y, Qing L, Sattentau QJ, Pyati J, Koduri R, Robinson J, Barbas

CF, 3rd, Burton DR, Ho DD: Primary isolates of human immunodeficiency

virus type 1 are relatively resistant to neutralization by monoclonal antibodies

to gp120, and their neutralization is not predicted by studies with monomeric

gp120. J Virol 1995, 69(1):101-109.

158. Moore JP, Ho DD: HIV-1 neutralization: the consequences of viral adaptation

to growth on transformed T cells. AIDS 1995, 9 Suppl A:S117-136.

159. Murakami T, Freed EO: The long cytoplasmic tail of gp41 is required in a cell

type-dependent manner for HIV-1 envelope glycoprotein incorporation into

virions. Proc Natl Acad Sci U S A 2000, 97(1):343-348.

160. Muster T, Guinea R, Trkola A, Purtscher M, Klima A, Steindl F, Palese P,

Katinger H: Cross-neutralizing activity against divergent human

immunodeficiency virus type 1 isolates induced by the gp41 sequence

ELDKWAS. J Virol 1994, 68(6):4031-4034.

161. Muster T, Steindl F, Purtscher M, Trkola A, Klima A, Himmler G, Ruker F,

Katinger H: A conserved neutralizing epitope on gp41 of human

immunodeficiency virus type 1. J Virol 1993, 67(11):6642-6647.

162. Nakayama EE, Shioda T, Tatsumi M, Xin X, Yu D, Ohgimoto S, Kato A, Sakai

Y, Ohnishi Y, Nagai Y: Importance of the N-glycan in the V3 loop of HIV-1

envelope protein for CXCR-4- but not CCR-5-dependent fusion. FEBS Lett 1998,

426(3):367-372.

163. Nara PL, Garrity RR, Goudsmit J: Neutralization of HIV-1: a paradox of

humoral proportions. Faseb J 1991, 5(10):2437-2455.

164. Natuk RJ, Chanda PK, Lubeck MD, Davis AR, Wilhelm J, Hjorth R, Wade MS,

Bhat BM, Mizutani S, Lee S et al: Adenovirus-human immunodeficiency virus



(HIV) envelope recombinant vaccines elicit high-titered HIV-neutralizing

antibodies in the dog model. Proc Natl Acad Sci U S A 1992, 89(16):7777-7781.

165. Natuk RJ, Lubeck MD, Chanda PK, Chengalvala M, Wade MS, Murthy SC,

Wilhelm J, Vernon SK, Dheer SK, Mizutani S et al: Immunogenicity of

recombinant human adenovirus-human immunodeficiency virus vaccines in

chimpanzees. AIDS Res Hum Retroviruses 1993, 9(5):395-404.

166. Novitsky V, Cao H, Rybak N, Gilbert P, McLane MF, Gaolekwe S, Peter T,

Thior I, Ndung'u T, Marlink R et al: Magnitude and frequency of cytotoxic T-

lymphocyte responses: identification of immunodominant regions of human

immunodeficiency virus type 1 subtype C. J Virol 2002, 76(20):10155-10168.

167. Novitsky V, Smith UR, Gilbert P, McLane MF, Chigwedere P, Williamson C,

Ndung'u T, Klein I, Chang SY, Peter T et al: Human immunodeficiency virus

type 1 subtype C molecular phylogeny: consensus sequence for an AIDS

vaccine design? J Virol 2002, 76(11):5435-5451.

168. Novitsky VA, Montano MA, McLane MF, Renjifo B, Vannberg F, Foley BT,

Ndung'u TP, Rahman M, Makhema MJ, Marlink R et al: Molecular cloning and

phylogenetic analysis of human immunodeficiency virus type 1 subtype C: a

set of 23 full-length clones from Botswana. J Virol 1999, 73(5):4427-4432.

169. Oberlin E, Amara A, Bachelerie F, Bessia C, Virelizier JL, Arenzana-Seisdedos

F, Schwartz O, Heard JM, Clark-Lewis I, Legler DF 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(6594):833-835.

170. Ogert RA, Lee MK, Ross W, Buckler-White A, Martin MA, Cho MW: N-linked

glycosylation sites adjacent to and within the V1/V2 and the V3 loops of

dualtropic human immunodeficiency virus type 1 isolate DH12 gp120 affect

coreceptor usage and cellular tropism. J Virol 2001, 75(13):5998-6006.

171. Ohagen A, Devitt A, Kunstman KJ, Gorry PR, Rose PP, Korber B, Taylor J, Levy

R, Murphy RL, Wolinsky SM et al: Genetic and functional analysis of full-

length human immunodeficiency virus type 1 env genes derived from brain

and blood of patients with AIDS. J Virol 2003, 77(22):12336-12345.



172. Oldstone MB, Tishon A, Lewicki H, Dyson HJ, Feher VA, Assa-Munt N, Wright

PE: Mapping the anatomy of the immunodominant domain of the human

immunodeficiency virus gp41 transmembrane protein: peptide conformation

analysis using monoclonal antibodies and proton nuclear magnetic resonance

spectroscopy. J Virol 1991, 65(4):1727-1734.

173. Olshevsky U, Helseth E, Furman C, Li J, Haseltine W, Sodroski J: Identification

of individual human immunodeficiency virus type 1 gp120 amino acids

important for CD4 receptor binding. J Virol 1990, 64(12):5701-5707.

174. Ourmanov I, Brown CR, Moss B, Carroll M, Wyatt L, Pletneva L, Goldstein S,

Venzon D, Hirsch VM: Comparative efficacy of recombinant modified vaccinia

virus Ankara expressing simian immunodeficiency virus (SIV) Gag-Pol and/or

Env in macaques challenged with pathogenic SIV. J Virol 2000, 74(6):2740-2751.

175. Pan Z, Radding W, Zhou T, Hunter E, Mountz J, McDonald JM: Role of

calmodulin in HIV-potentiated Fas-mediated apoptosis. Am J Pathol 1996,

149(3):903-910.

176. Paranjape RS, Gadkari DA, Lubaki M, Quinn TC, Bollinger RC: Cross-reactive

HIV-1-specific CTL in recent seroconverters from Pune, India. Indian J Med Res

1998, 108:35-41.

177. Parker KC, Bednarek MA, Coligan JE: Scheme for ranking potential HLA-A2

binding peptides based on independent binding of individual peptide side-

chains. J Immunol 1994, 152(1):163-175.

178. Parren PW, Burton DR, Sattentau QJ: HIV-1 antibody--debris or virion? Nat

Med 1997, 3(4):366-367.

179. Parren PW, Gauduin MC, Koup RA, Poignard P, Fisicaro P, Burton DR,

Sattentau QJ: Relevance of the antibody response against human

immunodeficiency virus type 1 envelope to vaccine design. Immunol Lett 1997,

57(1-3):105-112.

180. Parren PW, Gauduin MC, Koup RA, Poignard P, Sattentau QJ, Fisicaro P,

Burton DR: Erratum to "Relevance of the antibody response against human


National AIDS Research Institute, Pune 8

immunodeficiency virus type 1 envelope to vaccine design". Immunol Lett 1997,

58(2):125-132.

181. Parren PW, Moore JP, Burton DR, Sattentau QJ: The neutralizing antibody

response to HIV-1: viral evasion and escape from humoral immunity. Aids

1999, 13 Suppl A:S137-162.

182. Pastore C, Nedellec R, Ramos A, Pontow S, Ratner L, Mosier DE: Human

immunodeficiency virus type 1 coreceptor switching: V1/V2 gain-of-fitness

mutations compensate for V3 loss-of-fitness mutations. J Virol 2006, 80(2):750-

758.

183. Patterson LJ, Malkevitch N, Venzon D, Pinczewski J, Gomez-Roman VR, Wang

L, Kalyanaraman VS, Markham PD, Robey FA, Robert-Guroff M: Protection

against mucosal simian immunodeficiency virus SIV(mac251) challenge by

using replicating adenovirus-SIV multigene vaccine priming and subunit

boosting. J Virol 2004, 78(5):2212-2221.

184. Peng B, Wang LR, Gomez-Roman VR, Davis-Warren A, Montefiori DC,

Kalyanaraman VS, Venzon D, Zhao J, Kan E, Rowell TJ et al: Replicating rather

than nonreplicating adenovirus-human immunodeficiency virus recombinant

vaccines are better at eliciting potent cellular immunity and priming high-titer

antibodies. J Virol 2005, 79(16):10200-10209.

185. Perrin C, Fenouillet E, Jones IM: Role of gp41 glycosylation sites in the

biological activity of human immunodeficiency virus type 1 envelope

glycoprotein. Virology 1998, 242(2):338-345.

186. Piller SC, Dubay JW, Derdeyn CA, Hunter E: Mutational analysis of conserved

domains within the cytoplasmic tail of gp41 from human immunodeficiency

virus type 1: effects on glycoprotein incorporation and infectivity. J Virol 2000,

74(24):11717-11723.

187. Pinter A, Honnen WJ: O-linked glycosylation of retroviral envelope gene

products. J Virol 1988, 62(3):1016-1021.

188. Poon B, Hsu JF, Gudeman V, Chen IS, Grovit-Ferbas K: Formaldehyde-treated,

heat-inactivated virions with increased human immunodeficiency virus type 1



env can be used to induce high-titer neutralizing antibody responses. J Virol

2005, 79(16):10210-10217.

189. Poumbourios P, Wilson KA, Center RJ, El Ahmar W, Kemp BE: Human

immunodeficiency virus type 1 envelope glycoprotein oligomerization

requires the gp41 amphipathic alpha-helical/leucine zipper-like sequence. J

Virol 1997, 71(3):2041-2049.

190. Purtscher M, Trkola A, Grassauer A, Schulz PM, Klima A, Dopper S, Gruber G,

Buchacher A, Muster T, Katinger H: Restricted antigenic variability of the

epitope recognized by the neutralizing gp41 antibody 2F5. Aids 1996, 10(6):587-

593.

191. Quinones-Kochs MI, Buonocore L, Rose JK: Role of N-linked glycans in a

human immunodeficiency virus envelope glycoprotein: effects on protein

function and the neutralizing antibody response. J Virol 2002, 76(9):4199-4211.

192. Rao Z, Belyaev AS, Fry E, Roy P, Jones IM, Stuart DI: Crystal structure of SIV

matrix antigen and implications for virus assembly. Nature 1995, 378(6558):743-

747.

193. Reitter JN, Means RE, Desrosiers RC: A role for carbohydrates in immune

evasion in AIDS. Nat Med 1998, 4(6):679-684.

194. Rimsky LT, Shugars DC, Matthews TJ: Determinants of human

immunodeficiency virus type 1 resistance to gp41-derived inhibitory peptides.

J Virol 1998, 72(2):986-993.

195. Ritola K, Pilcher CD, Fiscus SA, Hoffman NG, Nelson JA, Kitrinos KM, Hicks

CB, Eron JJ, Jr., Swanstrom R: Multiple V1/V2 env variants are frequently

present during primary infection with human immunodeficiency virus type 1.

J Virol 2004, 78(20):11208-11218.

196. Rizzuto C, Sodroski J: Fine definition of a conserved CCR5-binding region on

the human immunodeficiency virus type 1 glycoprotein 120. AIDS Res Hum

Retroviruses 2000, 16(8):741-749.



197. Rizzuto CD, Wyatt R, Hernandez-Ramos N, Sun Y, Kwong PD, Hendrickson

WA, Sodroski J: A conserved HIV gp120 glycoprotein structure involved in

chemokine receptor binding. Science 1998, 280(5371):1949-1953.

198. Rodenburg CM, Li Y, Trask SA, Chen Y, Decker J, Robertson DL, Kalish ML,

Shaw GM, Allen S, Hahn BH et al: Near full-length clones and reference

sequences for subtype C isolates of HIV type 1 from three different continents.


199. Rose NF, Marx PA, Luckay A, Nixon DF, Moretto WJ, Donahoe SM, Montefiori

D, Roberts A, Buonocore L, Rose JK: An effective AIDS vaccine based on live

attenuated vesicular stomatitis virus recombinants. Cell 2001, 106(5):539-549.

200. Ross TM, Cullen BR: The ability of HIV type 1 to use CCR-3 as a coreceptor is

controlled by envelope V1/V2 sequences acting in conjunction with a CCR-5

tropic V3 loop. Proc Natl Acad Sci U S A 1998, 95(13):7682-7686.

201. Rousso I, Mixon MB, Chen BK, Kim PS: Palmitoylation of the HIV-1 envelope

glycoprotein is critical for viral infectivity. Proc Natl Acad Sci U S A 2000,

97(25):13523-13525.

202. Rudd PM, Dwek RA: Glycosylation: heterogeneity and the 3D structure of

proteins. Crit Rev Biochem Mol Biol 1997, 32(1):1-100.

203. Saitou N, Nei M: The neighbor-joining method: a new method for

reconstructing phylogenetic trees. Mol Biol Evol 1987, 4(4):406-425.

204. Santra S, Seaman MS, Xu L, Barouch DH, Lord CI, Lifton MA, Gorgone DA,

Beaudry KR, Svehla K, Welcher B et al: Replication-defective adenovirus

serotype 5 vectors elicit durable cellular and humoral immune responses in

nonhuman primates. J Virol 2005, 79(10):6516-6522.

205. Sattentau QJ, Zolla-Pazner S, Poignard P: Epitope exposure on functional,

oligomeric HIV-1 gp41 molecules. Virology 1995, 206(1):713-717.

206. Scanlan CN, Pantophlet R, Wormald MR, Ollmann Saphire E, Stanfield R,

Wilson IA, Katinger H, Dwek RA, Rudd PM, Burton DR: 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(14):7306-7321.

207. Schonning K, Jansson B, Olofsson S, Nielsen JO, Hansen JS: Resistance to V3-

directed neutralization caused by an N-linked oligosaccharide depends on the

quaternary structure of the HIV-1 envelope oligomer. Virology 1996, 218(1):134-

140.

208. Schuitemaker H, Koot M, Kootstra NA, Dercksen MW, de Goede RE, van

Steenwijk RP, Lange JM, Schattenkerk JK, Miedema F, Tersmette M: Biological

phenotype of human immunodeficiency virus type 1 clones at different stages

of infection: progression of disease is associated with a shift from

monocytotropic to T-cell-tropic virus population. J Virol 1992, 66(3):1354-1360.

209. Schuitemaker H, Kootstra NA, de Goede RE, de Wolf F, Miedema F, Tersmette

M: Monocytotropic human immunodeficiency virus type 1 (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(1):356-363.

210. Schwartz S, Felber BK, Fenyo EM, Pavlakis GN: Rapidly and slowly

replicating human immunodeficiency virus type 1 isolates can be

distinguished according to target-cell tropism in T-cell and monocyte cell

lines. Proc Natl Acad Sci U S A 1989, 86(18):7200-7203.

211. Shankarappa R, Chatterjee R, Learn GH, Neogi D, Ding M, Roy P, Ghosh A,

Kingsley L, Harrison L, Mullins JI et al: Human immunodeficiency virus type 1

env sequences from Calcutta in eastern India: identification of features that

distinguish subtype C sequences in India from other subtype C sequences. J

Virol 2001, 75(21):10479-10487.

212. Shankarappa R, Margolick JB, Gange SJ, Rodrigo AG, Upchurch D, Farzadegan

H, Gupta P, Rinaldo CR, Learn GH, He X et al: Consistent viral evolutionary

changes associated with the progression of human immunodeficiency virus

type 1 infection. J Virol 1999, 73(12):10489-10502.

213. Shankarkumar U: HLA matching and problems related to cadaveric renal

transplantation in India. Indian J Med Sci 2001, 55(8):417-420.



214. Shankarkumar U, Ghosh K, Mohanty D: HLA B27 polymorphism in Western

India. Tissue Antigens 2002, 60(1):98-101.

215. Shioda T, Levy JA, 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(6305):167-169.

216. Shiver JW, Fu TM, Chen L, Casimiro DR, Davies ME, Evans RK, Zhang ZQ,

Simon AJ, Trigona WL, Dubey SA et al: Replication-incompetent adenoviral

vaccine vector elicits effective anti-immunodeficiency-virus immunity. Nature

2002, 415(6869):331-335.

217. Spies CP, Ritter GD, Jr., Mulligan MJ, Compans RW: Truncation of the

cytoplasmic domain of the simian immunodeficiency virus envelope

glycoprotein alters the conformation of the external domain. J Virol 1994,

68(2):585-591.

218. Srinivas SK, Srinivas RV, Anantharamaiah GM, Compans RW, Segrest JP:

Cytosolic domain of the human immunodeficiency virus envelope

glycoproteins binds to calmodulin and inhibits calmodulin-regulated proteins.

J Biol Chem 1993, 268(30):22895-22899.

219. Staropoli I, Chanel C, Girard M, Altmeyer R: Processing, stability, and

receptor binding properties of oligomeric envelope glycoprotein from a

primary HIV-1 isolate. J Biol Chem 2000, 275(45):35137-35145.

220. Su J, Palm A, Wu Y, Sandin S, Hoglund S, Vahlne A: Deletion of the GPG

motif in the HIV type 1 V3 loop does not abrogate infection in all cells. AIDS

Res Hum Retroviruses 2000, 16(1):37-48.

221. Subramanian VS, Damodaran C: Distribution of HLA antigens in Sadhu

Chetty of Tamil Nadu, south India. Anthropol Anz 1995, 53(3):221-230.

222. Subramanian VS, Selvaraj P, Narayanan PR, Prabhakar R, Damodaran C:

Distribution of HLA (class I and class II) antigens in the native Dravidian

Hindus of Tamil Nadu, south India. Gene Geogr 1995, 9(1):15-24.

223. Tan K, Liu J, Wang J, Shen S, Lu M: Atomic structure of a thermostable

subdomain of HIV-1 gp41. Proc Natl Acad Sci U S A 1997, 94(23):12303-12308.



224. Tencza SB, Mietzner TA, Montelaro RC: Calmodulin-binding function of LLP

segments from the HIV type 1 transmembrane protein is conserved among

natural sequence variants. AIDS Res Hum Retroviruses 1997, 13(3):263-269.

225. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The

CLUSTAL_X windows interface: flexible strategies for multiple sequence

alignment aided by quality analysis tools. Nucleic Acids Res 1997, 25(24):4876-

4882.

226. Tripathy S, Renjifo B, Wang WK, McLane MF, Bollinger R, Rodrigues J,

Osterman J, Tripathy S, Essex M: Envelope glycoprotein 120 sequences of

primary HIV type 1 isolates from Pune and New Delhi, India. AIDS Res Hum

Retroviruses 1996, 12(12):1199-1202.

227. Tripathy SP, Kulkarni SS, Jadhav SD, Agnihotri KD, Jere AJ, Kurle SN,

Bhattacharya SK, Singh K, Tripathy SP, Paranjape RS: Subtype B and subtype C

HIV type 1 recombinants in the northeastern state of Manipur, India. AIDS Res

Hum Retroviruses 2005, 21(2):152-157.

228. Trivedi VD, Cheng SF, Wu CW, Karthikeyan R, Chen CJ, Chang DK: The

LLSGIV stretch of the N-terminal region of HIV-1 gp41 is critical for binding

to a model peptide, T20. Protein Eng 2003, 16(4):311-317.

229. Uppal SS, Verma S, Dhot PS: Normal values of CD4 and CD8 lymphocyte

subsets in healthy indian adults and the effects of sex, age, ethnicity, and

smoking. Cytometry B Clin Cytom 2003, 52(1):32-36.

230. VanCott TC, Mascola JR, Loomis-Price LD, Sinangil F, Zitomersky N, McNeil J,

Robb ML, Birx DL, Barnett S: Cross-subtype neutralizing antibodies induced in

baboons by a subtype E gp120 immunogen based on an R5 primary human

immunodeficiency virus type 1 envelope. J Virol 1999, 73(6):4640-4650.

231. Vinner L, Wee EG, Patel S, Corbet S, Gao GP, Nielsen C, Wilson JM, Ertl HC,

Hanke T, Fomsgaard A: Immunogenicity in Mamu-A*01 rhesus macaques of a

CCR5-tropic human immunodeficiency virus type 1 envelope from the

primary isolate (Bx08) after synthetic DNA prime and recombinant adenovirus

5 boost. J Gen Virol 2003, 84(Pt 1):203-213.



232. Wang B, Spira TJ, Owen S, Lal RB, Saksena NK: HIV-1 strains from a cohort of

American subjects reveal the presence of a V2 region extension unique to slow

progressors and non-progressors. Aids 2000, 14(3):213-223.

233. Wang S, Arthos J, Lawrence JM, Van Ryk D, Mboudjeka I, Shen S, Chou TH,

Montefiori DC, Lu S: Enhanced immunogenicity of gp120 protein when

combined with recombinant DNA priming to generate antibodies that

neutralize the JR-FL primary isolate of human immunodeficiency virus type 1.

J Virol 2005, 79(12):7933-7937.

234. Wei X, Decker JM, Wang S, Hui H, Kappes JC, Wu X, Salazar-Gonzalez JF,

Salazar MG, Kilby JM, Saag MS et al: Antibody neutralization and escape by

HIV-1. Nature 2003, 422(6929):307-312.

235. Weissenhorn W, Dessen A, Harrison SC, Skehel JJ, Wiley DC: Atomic structure

of the ectodomain from HIV-1 gp41. Nature 1997, 387(6631):426-430.

236. Weissenhorn W, Wharton SA, Calder LJ, Earl PL, Moss B, Aliprandis E, Skehel

JJ, Wiley DC: The ectodomain of HIV-1 env subunit gp41 forms a soluble,

alpha-helical, rod-like oligomer in the absence of gp120 and the N-terminal

fusion peptide. EMBO J 1996, 15(7):1507-1514.

237. Willey RL, Rutledge RA, Dias S, Folks T, Theodore T, Buckler CE, Martin MA:

Identification of conserved and divergent domains within the envelope gene

of the acquired immunodeficiency syndrome retrovirus. Proc Natl Acad Sci U S

A 1986, 83(14):5038-5042.

238. Witvrouw M, Fikkert V, Hantson A, Pannecouque C, O'Keefe B R, McMahon J,

Stamatatos L, de Clercq E, Bolmstedt A: Resistance of human

immunodeficiency virus type 1 to the high-mannose binding agents

cyanovirin N and concanavalin A. J Virol 2005, 79(12):7777-7784.

239. Woods RJ, Edge CJ, Dwek RA: Protein surface oligosaccharides and protein

function. Nat Struct Biol 1994, 1(8):499-501.

240. Wyatt R, Kwong PD, Desjardins E, Sweet RW, Robinson J, Hendrickson WA,

Sodroski JG: The antigenic structure of the HIV gp120 envelope glycoprotein.

Nature 1998, 393(6686):705-711.



241. Wyatt R, Sodroski J: The HIV-1 envelope glycoproteins: fusogens, antigens,

and immunogens. Science 1998, 280(5371):1884-1888.

242. Wyma DJ, Kotov A, Aiken C: Evidence for a stable interaction of gp41 with

Pr55(Gag) in immature human immunodeficiency virus type 1 particles. J Virol

2000, 74(20):9381-9387.

243. Xiang ZQ, Yang Y, Wilson JM, Ertl HC: A replication-defective human

adenovirus recombinant serves as a highly efficacious vaccine carrier. Virology

1996, 219(1):220-227.

244. Yang X, Farzan M, Wyatt R, Sodroski J: Characterization of stable, soluble

trimers containing complete ectodomains of human immunodeficiency virus

type 1 envelope glycoproteins. J Virol 2000, 74(12):5716-5725.

245. Ye L, Bu Z, Vzorov A, Taylor D, Compans RW, Yang C: Surface stability and

immunogenicity of the human immunodeficiency virus envelope

glycoprotein: role of the cytoplasmic domain. J Virol 2004, 78(24):13409-13419.

246. Zwart G, Back NK, Ramautarsing C, Valk M, van der Hoek L, Goudsmit J:

Frequent and early HIV-1MN neutralizing capacity in sera from Dutch HIV-1

seroconverters is related to antibody reactivity to peptides from the gp120 V3

domain. AIDS Res Hum Retroviruses 1994, 10(3):245-251.

247. Zwick MB, Labrijn AF, Wang M, Spenlehauer C, Saphire EO, Binley JM, Moore

JP, Stiegler G, Katinger H, Burton DR et al: Broadly neutralizing antibodies

targeted to the membrane-proximal external region of human

immunodeficiency virus type 1 glycoprotein gp41. J Virol 2001, 75(22):10892-

10905.

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