CHAPTER 4 Conclusions 132 !
4.6 Final Remarks 138 !
In conclusion, antibody responses specific to the Env glycoprotein of SIV, HIV, and other primate lentiviruses exert a potent, inhibitory, and selective pressure on viral populations in virus-infected hosts. The long co-evolutionary history between PLVs and their primate hosts has selected several features on the Env gp120 monomer and Env trimer that function in immune evasion from constant antibody responses, including a two-receptor system, glycosylation and variable loops that shield conservative receptor binding regions in gp120. Despite these features antibodies still evolve in the host that can penetrate these defenses requiring the need for sequence variation that evades antibody through
escape at sites of antibody epitopes. However, escape, like any other sequence mutation, comes with an associated fitness difference. Here we helped to uncover some of the earliest events in env sequence variation using the SIV/macaque model, finding that changes cluster in variable loops 1 and 4, evolve in a fashion indicative of natural selection, and found a subset of these adaptations had no associated replicative fitness cost. Understanding that antibody escape must evolve from a homogenous population that is present during acute infection due to the genetic bottleneck during transmission highlights the need to understand early sequence dynamics. It is becoming well accepted that Env-binding nonneutralizing antibodies are protective, though not completely, in HIV-infected individuals and SIV-infected macaques. As these nonneutralizing antibodies potentially possess alternate effector functions such as ADCC it is similarly important to test Env adaptations for escape from antibodies with alternative effector functions. Here, we found that individual Env adaptations do not confer escape to ADCC, suggesting that escape in vivo likely requires multiple adaptations in a single variant to confer complete escape. Thus, the use of SGA, as we applied deep sequencing, on longitudinal samples using the SIV/macaque model might further inform the connection among adaptations such as those in V1 and V4 that potentially function together to provide escape. Understanding which changes are linked will help to inform therapeutic efforts to design Env-based immunogens, which are at the core of a safe and effective vaccine against HIV-1.
References
1. Desrosiers, R., Nonhuman Lentiviruses, in Fields Virology, D.M. Knipe and P.M. Howley, Editors. 2013, Lippincott Williams & Williams: Philadelphia.
2. Freed, E.O. and M.A. Martin, HIVs and Their Replication, in Fields Virology, D.M. Knipe and P.M. Howley, Editors. 2013, Lippincott Williams & Williams: Philadelphia.
3. Sharp, P.M. and B.H. Hahn, Origins of HIV and the AIDS pandemic. Cold Spring Harb Perspect Med, 2011. 1(1): p. a006841.
4. Fauci, A.S., et al., Immunopathogenic mechanisms of HIV infection. Ann Intern Med, 1996. 124(7): p. 654-63.
5. Koup, R.A., et al., Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency virus type 1 syndrome. J Virol, 1994. 68(7): p. 4650-5.
6. Bacchetti, P. and A.R. Moss, Incubation period of AIDS in San Francisco. Nature, 1989.
338(6212): p. 251-3.
7. Bailey, N.T., A revised assessment of the HIV/AIDS incubation period, assuming a very short early period of high infectivity and using only San Francisco public health data on prevalence and incidence. Stat Med, 1997. 16(21): p. 2447-58.
8. Coffin, J.M., HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science, 1995. 267(5197): p. 483-9.
9. Buchacz, K., et al., AIDS-defining opportunistic illnesses in US patients, 1994-2007: a cohort study. AIDS, 2010. 24(10): p. 1549-59.
10. Boshoff, C. and R. Weiss, AIDS-related malignancies. Nat Rev Cancer, 2002. 2(5): p. 373-82.
11. Arts, E.J. and D.J. Hazuda, HIV-1 antiretroviral drug therapy. Cold Spring Harb Perspect Med, 2012. 2(4): p. a007161.
12. Llibre, J.M. and B. Clotet, Once-daily single-tablet regimens: a long and winding road to excellence in antiretroviral treatment. AIDS Rev, 2012. 14(3): p. 168-78.
13. Deeks, E.D., Emtricitabine/rilpivirine/tenofovir disoproxil fumarate single-tablet regimen: a review of its use in HIV infection. Drugs, 2014. 74(17): p. 2079-95.
14. Wong, J.K., et al., Recovery of replication-competent HIV despite prolonged suppression of plasma viremia. Science, 1997. 278(5341): p. 1291-5.
15. Chun, T.W., et al., Presence of an inducible HIV-1 latent reservoir during highly active antiretroviral therapy. Proc Natl Acad Sci U S A, 1997. 94(24): p. 13193-7.
16. Finzi, D., et al., Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy. Science, 1997. 278(5341): p. 1295-300.
17. Chun, T.W., et al., Relationship between pre-existing viral reservoirs and the re-
emergence of plasma viremia after discontinuation of highly active anti-retroviral therapy.
Nat Med, 2000. 6(7): p. 757-61.
18. Ruelas, D.S. and W.C. Greene, An integrated overview of HIV-1 latency. Cell, 2013.
155(3): p. 519-29.
19. Gottlieb, G.J., et al., A preliminary communication on extensively disseminated Kaposi's sarcoma in young homosexual men. Am J Dermatopathol, 1981. 3(2): p. 111-4.
20. Gottlieb, M.S., et al., 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): p. 1425-31.
21. Gottlieb, M.S., Pneumocystis pneumonia--Los Angeles. 1981. Am J Public Health, 2006.
96(6): p. 980-1; discussion 982-3.
22. Gallo, R.C., et al., Frequent detection and isolation of cytopathic retroviruses (HTLV-III) from patients with AIDS and at risk for AIDS. Science, 1984. 224(4648): p. 500-3.
23. Barre-Sinoussi, F., et al., Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Science, 1983. 220(4599): p. 868-71.
24. Organization, W.H. HIV/AIDS. Global Health Observatory (GHO) data 2015 [cited 2015 December 28th 2015]; Available from: http://www.who.int/gho/hiv/en/.
26. Daniel, M.D., et al., Isolation of T-cell tropic HTLV-III-like retrovirus from macaques.
Science, 1985. 228(4704): p. 1201-4.
27. Clavel, F., et al., Isolation of a new human retrovirus from West African patients with AIDS. Science, 1986. 233(4761): p. 343-6.
28. Hirsch, V.M., et al., An African primate lentivirus (SIVsm) closely related to HIV-2.
Nature, 1989. 339(6223): p. 389-92.
29. Huet, T., et al., Genetic organization of a chimpanzee lentivirus related to HIV-1. Nature, 1990. 345(6273): p. 356-9.
30. Van Heuverswyn, F., et al., Human immunodeficiency viruses: SIV infection in wild gorillas. Nature, 2006. 444(7116): p. 164.
31. Jin, M.J., et al., Infection of a yellow baboon with simian immunodeficiency virus from African green monkeys: evidence for cross-species transmission in the wild. J Virol, 1994. 68(12): p. 8454-60.
32. Jin, M.J., et al., Mosaic genome structure of simian immunodeficiency virus from west African green monkeys. EMBO J, 1994. 13(12): p. 2935-47.
33. Bibollet-Ruche, F., et al., Simian immunodeficiency virus infection in a patas monkey (Erythrocebus patas): evidence for cross-species transmission from African green monkeys (Cercopithecus aethiops sabaeus) in the wild. J Gen Virol, 1996. 77 ( Pt 4): p. 773-81.
34. Bailes, E., et al., Hybrid origin of SIV in chimpanzees. Science, 2003. 300(5626): p. 1713.
35. Courgnaud, V., et al., Identification of a new simian immunodeficiency virus lineage with a vpu gene present among different cercopithecus monkeys (C. mona, C. cephus, and C. nictitans) from Cameroon. J Virol, 2003. 77(23): p. 12523-34.
36. Beer, B.E., et al., Characterization of novel simian immunodeficiency viruses from red- capped mangabeys from Nigeria (SIVrcmNG409 and -NG411). J Virol, 2001. 75(24): p. 12014-27.
37. Hu, J., et al., Characterization and comparison of recombinant simian immunodeficiency virus from drill (Mandrillus leucophaeus) and mandrill (Mandrillus sphinx) isolates. J Virol, 2003. 77(8): p. 4867-80.
38. Klatt, N.R., G. Silvestri, and V. Hirsch, Nonpathogenic simian immunodeficiency virus infections. Cold Spring Harb Perspect Med, 2012. 2(1): p. a007153.
39. Keele, B.F., et al., Chimpanzee reservoirs of pandemic and nonpandemic HIV-1.
Science, 2006. 313(5786): p. 523-6.
40. Van Heuverswyn, F., et al., Genetic diversity and phylogeographic clustering of SIVcpzPtt in wild chimpanzees in Cameroon. Virology, 2007. 368(1): p. 155-71.
41. Korber, B., et al., Timing the ancestor of the HIV-1 pandemic strains. Science, 2000.
288(5472): p. 1789-96.
42. Gao, F., et al., Human infection by genetically diverse SIVSM-related HIV-2 in west Africa. Nature, 1992. 358(6386): p. 495-9.
43. Apetrei, C., et al., Molecular epidemiology of simian immunodeficiency virus SIVsm in U.S. primate centers unravels the origin of SIVmac and SIVstm. J Virol, 2005. 79(14): p. 8991-9005.
44. Apetrei, C., et al., Kuru experiments triggered the emergence of pathogenic SIVmac.
AIDS, 2006. 20(3): p. 317-21.
45. Harrison, S.C., Mechanism of membrane fusion by viral envelope proteins. Adv Virus Res, 2005. 64: p. 231-61.
46. Rambaut, A., et al., The causes and consequences of HIV evolution. Nat Rev Genet, 2004. 5(1): p. 52-61.
47. Dalgleish, A.G., et al., The CD4 (T4) antigen is an essential component of the receptor for the AIDS retrovirus. Nature, 1984. 312(5996): p. 763-7.
48. Maddon, P.J., et al., The T4 gene encodes the AIDS virus receptor and is expressed in the immune system and the brain. Cell, 1986. 47(3): p. 333-48.
49. McDougal, J.S., et al., Binding of HTLV-III/LAV to T4+ T cells by a complex of the 110K viral protein and the T4 molecule. Science, 1986. 231(4736): p. 382-5.
50. Bartesaghi, A., et al., Prefusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy. Nat Struct Mol Biol, 2013. 20(12): p. 1352-7.
51. Meyerson, J.R., et al., Molecular structures of trimeric HIV-1 Env in complex with small antibody derivatives. Proc Natl Acad Sci U S A, 2013. 110(2): p. 513-8.
52. Tran, E.E., et al., Structural mechanism of trimeric HIV-1 envelope glycoprotein activation. PLoS Pathog, 2012. 8(7): p. e1002797.
53. Choe, H., et al., The beta-chemokine receptors CCR3 and CCR5 facilitate infection by primary HIV-1 isolates. Cell, 1996. 85(7): p. 1135-48.
54. Deng, H., et al., Identification of a major co-receptor for primary isolates of HIV-1.
Nature, 1996. 381(6584): p. 661-6.
55. Dragic, T., et al., HIV-1 entry into CD4+ cells is mediated by the chemokine receptor CC- CKR-5. Nature, 1996. 381(6584): p. 667-73.
56. Feng, Y., et al., HIV-1 entry cofactor: functional cDNA cloning of a seven-
transmembrane, G protein-coupled receptor. Science, 1996. 272(5263): p. 872-7.
57. Chan, D.C., et al., Core structure of gp41 from the HIV envelope glycoprotein. Cell, 1997. 89(2): p. 263-73.
58. Tan, K., et al., Atomic structure of a thermostable subdomain of HIV-1 gp41. Proc Natl Acad Sci U S A, 1997. 94(23): p. 12303-8.
59. Weissenhorn, W., et al., Atomic structure of the ectodomain from HIV-1 gp41. Nature, 1997. 387(6631): p. 426-30.
60. Caffrey, M., et al., Three-dimensional solution structure of the 44 kDa ectodomain of SIV gp41. EMBO J, 1998. 17(16): p. 4572-84.
61. Wilen, C.B., J.C. Tilton, and R.W. Doms, HIV: cell binding and entry. Cold Spring Harb Perspect Med, 2012. 2(8).
62. Telesnitsky, A. and S.P. Goff, Reverse Transcriptase and the Generation of Retroviral DNA, in Retroviruses, J. Coffin, S.H. Hughes, and H.E. Varmus, Editors. 1997, Cold Spring Harbor Laboratory Press: Plainview.
63. Heinzinger, N.K., et al., The Vpr protein of human immunodeficiency virus type 1 influences nuclear localization of viral nucleic acids in nondividing host cells. Proc Natl Acad Sci U S A, 1994. 91(15): p. 7311-5.
64. Gallay, P., et al., HIV nuclear import is governed by the phosphotyrosine-mediated binding of matrix to the core domain of integrase. Cell, 1995. 83(4): p. 569-76.
65. Hindmarsh, P. and J. Leis, Retroviral DNA integration. Microbiol Mol Biol Rev, 1999.
63(4): p. 836-43, table of contents.
66. Brown, P.O., Integration, in Retroviruses, J. Coffin, S.H. Hughes, and H.E. Varmus, Editors. 1997, Cold Spring Harbor Laboratory Press: Plainview.
67. Freed, E.O., et al., Single amino acid changes in the human immunodeficiency virus type 1 matrix protein block virus particle production. J Virol, 1994. 68(8): p. 5311-20.
68. Ono, A., J.M. Orenstein, and E.O. Freed, Role of the Gag matrix domain in targeting human immunodeficiency virus type 1 assembly. J Virol, 2000. 74(6): p. 2855-66.
69. Yu, X., et al., The matrix protein of human immunodeficiency virus type 1 is required for incorporation of viral envelope protein into mature virions. J Virol, 1992. 66(8): p. 4966- 71.
70. Dorfman, T., et al., Role of the matrix protein in the virion association of the human immunodeficiency virus type 1 envelope glycoprotein. J Virol, 1994. 68(3): p. 1689-96.
71. Freed, E.O. and M.A. Martin, 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): p. 1984-9.
72. Freed, E.O. and M.A. Martin, Domains of the human immunodeficiency virus type 1 matrix and gp41 cytoplasmic tail required for envelope incorporation into virions. J Virol, 1996. 70(1): p. 341-51.
73. Murakami, T. and E.O. Freed, Genetic evidence for an interaction between human immunodeficiency virus type 1 matrix and alpha-helix 2 of the gp41 cytoplasmic tail. J Virol, 2000. 74(8): p. 3548-54.
74. Mammano, F., et al., Rescue of human immunodeficiency virus type 1 matrix protein mutants by envelope glycoproteins with short cytoplasmic domains. J Virol, 1995. 69(6): p. 3824-30.
75. Gottlinger, H.G., et al., Effect of mutations affecting the p6 gag protein on human
immunodeficiency virus particle release. Proc Natl Acad Sci U S A, 1991. 88(8): p. 3195- 9.
76. Garrus, J.E., et al., Tsg101 and the vacuolar protein sorting pathway are essential for HIV-1 budding. Cell, 2001. 107(1): p. 55-65.
77. Huang, M., et al., p6Gag is required for particle production from full-length human immunodeficiency virus type 1 molecular clones expressing protease. J Virol, 1995.
69(11): p. 6810-8.
78. VerPlank, L., et al., Tsg101, a homologue of ubiquitin-conjugating (E2) enzymes, binds the L domain in HIV type 1 Pr55(Gag). Proc Natl Acad Sci U S A, 2001. 98(14): p. 7724- 9.
79. Johnson, W.E. and R.C. Desrosiers, Viral persistence: HIV's strategies of immune system evasion. Annu Rev Med, 2002. 53: p. 499-518.
80. Evans, D.T. and R.C. Desrosiers, Immune evasion strategies of the primate lentiviruses.
Immunol Rev, 2001. 183: p. 141-58.
81. Wyatt, R. and J. Sodroski, The HIV-1 envelope glycoproteins: fusogens, antigens, and immunogens. Science, 1998. 280(5371): p. 1884-8.
82. Li, Y., et al., Glycosylation is necessary for the correct folding of human immunodeficiency virus gp120 in CD4 binding. J Virol, 1993. 67(1): p. 584-8.
83. Zhu, P., et al., Electron tomography analysis of envelope glycoprotein trimers on HIV and simian immunodeficiency virus virions. Proc Natl Acad Sci U S A, 2003. 100(26): p. 15812-7.
84. Zhu, P., et al., Distribution and three-dimensional structure of AIDS virus envelope spikes. Nature, 2006. 441(7095): p. 847-52.
85. Chertova, E., et al., Envelope glycoprotein incorporation, not shedding of surface envelope glycoprotein (gp120/SU), Is the primary determinant of SU content of purified human immunodeficiency virus type 1 and simian immunodeficiency virus. J Virol, 2002.
76(11): p. 5315-25.
86. Yuste, E., et al., Modulation of Env content in virions of simian immunodeficiency virus: correlation with cell surface expression and virion infectivity. J Virol, 2004. 78(13): p. 6775-85.
87. Kwong, P.D., et al., Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature, 1998. 393(6686): p. 648-59.
88. Burton, D.R. and J.R. Mascola, Antibody responses to envelope glycoproteins in HIV-1 infection. Nat Immunol, 2015. 16(6): p. 571-6.
89. Rizzuto, C.D., et al., A conserved HIV gp120 glycoprotein structure involved in chemokine receptor binding. Science, 1998. 280(5371): p. 1949-53.
90. Huang, C.C., et al., Structure of a V3-containing HIV-1 gp120 core. Science, 2005.
310(5750): p. 1025-8.
91. Farzan, M., et al., Tyrosine sulfation of the amino terminus of CCR5 facilitates HIV-1 entry. Cell, 1999. 96(5): p. 667-76.
92. Huang, C.C., et al., Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4. Science, 2007. 317(5846): p. 1930-4.
93. Cormier, E.G. and T. Dragic, The crown and stem of the V3 loop play distinct roles in human immunodeficiency virus type 1 envelope glycoprotein interactions with the CCR5 coreceptor. J Virol, 2002. 76(17): p. 8953-7.
94. Lindemann, D., I. Steffen, and S. Pohlmann, Cellular Entry of Retroviruses, in Viral Entry into Host Cells, S. Pohlmann and G. Simmonds, Editors. 2013, Landes BioScience and Springer Science+Business Media, LLC: Austin.
95. Connor, R.I., et al., Change in coreceptor use correlates with disease progression in HIV-1--infected individuals. J Exp Med, 1997. 185(4): p. 621-8.
96. Margolis, L. and R. Shattock, Selective transmission of CCR5-utilizing HIV-1: the 'gatekeeper' problem resolved? Nat Rev Microbiol, 2006. 4(4): p. 312-7.
97. Dean, M., et al., Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Hemophilia Growth and Development Study, Multicenter AIDS Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort, ALIVE Study. Science, 1996. 273(5283): p. 1856-62.
98. Garred, P., et al., Dual effect of CCR5 delta 32 gene deletion in HIV-1-infected patients. Copenhagen AIDS Study Group. Lancet, 1997. 349(9069): p. 1884.
99. Huang, Y., et al., The role of a mutant CCR5 allele in HIV-1 transmission and disease progression. Nat Med, 1996. 2(11): p. 1240-3.
100. Michael, N.L., et al., The role of viral phenotype and CCR-5 gene defects in HIV-1 transmission and disease progression. Nat Med, 1997. 3(3): p. 338-40.
101. Samson, M., et al., Resistance to HIV-1 infection in caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene. Nature, 1996. 382(6593): p. 722-5.
102. Hutter, G., et al., Long-term control of HIV by CCR5 Delta32/Delta32 stem-cell transplantation. N Engl J Med, 2009. 360(7): p. 692-8.
103. Hutter, G. and E. Thiel, Allogeneic transplantation of CCR5-deficient progenitor cells in a patient with HIV infection: an update after 3 years and the search for patient no. 2. AIDS, 2011. 25(2): p. 273-4.
104. Calado, M., et al., Coreceptor usage by HIV-1 and HIV-2 primary isolates: the relevance of CCR8 chemokine receptor as an alternative coreceptor. Virology, 2010. 408(2): p. 174-82.
105. Deng, H.K., et al., Expression cloning of new receptors used by simian and human immunodeficiency viruses. Nature, 1997. 388(6639): p. 296-300.
106. Blaak, H., et al., CCR5, GPR15, and CXCR6 are major coreceptors of human
immunodeficiency virus type 2 variants isolated from individuals with and without plasma viremia. J Virol, 2005. 79(3): p. 1686-700.
107. Neil, S.J., et al., The promiscuous CC chemokine receptor D6 is a functional coreceptor for primary isolates of human immunodeficiency virus type 1 (HIV-1) and HIV-2 on astrocytes. J Virol, 2005. 79(15): p. 9618-24.
108. Farzan, M., et al., Two orphan seven-transmembrane segment receptors which are expressed in CD4-positive cells support simian immunodeficiency virus infection. J Exp Med, 1997. 186(3): p. 405-11.
109. Mori, K., et al., Complex determinants of macrophage tropism in env of simian immunodeficiency virus. J Virol, 1992. 66(4): p. 2067-75.
110. Johnson, W.E., et al., Assorted mutations in the envelope gene of simian
immunodeficiency virus lead to loss of neutralization resistance against antibodies representing a broad spectrum of specificities. J Virol, 2003. 77(18): p. 9993-10003.
111. Means, R.E., et al., Ability of the V3 loop of simian immunodeficiency virus to serve as a target for antibody-mediated neutralization: correlation of neutralization sensitivity,
growth in macrophages, and decreased dependence on CD4. J Virol, 2001. 75(8): p. 3903-15.
112. Yen, P.J., et al., Identification and characterization of a macrophage-tropic SIV envelope glycoprotein variant in blood from early infection in SIVmac251-infected macaques.
Virology, 2014. 458-459: p. 53-68.
113. Yen, P.J., et al., Loss of a conserved N-linked glycosylation site in the simian
immunodeficiency virus envelope glycoprotein V2 region enhances macrophage tropism by increasing CD4-independent cell-to-cell transmission. J Virol, 2014. 88(9): p. 5014- 28.
114. Liu, J., et al., Molecular architecture of native HIV-1 gp120 trimers. Nature, 2008.
455(7209): p. 109-13.
115. White, T.A., et al., Molecular architectures of trimeric SIV and HIV-1 envelope
glycoproteins on intact viruses: strain-dependent variation in quaternary structure. PLoS Pathog, 2010. 6(12): p. e1001249.
116. White, T.A., et al., Three-dimensional structures of soluble CD4-bound states of trimeric simian immunodeficiency virus envelope glycoproteins determined by using cryo-
electron tomography. J Virol, 2011. 85(23): p. 12114-23.
117. Li, M., 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(16): p. 10108-25.
118. Li, M., 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(23): p. 11776-90.
119. Richman, D.D., et al., Rapid evolution of the neutralizing antibody response to HIV type 1 infection. Proc Natl Acad Sci U S A, 2003. 100(7): p. 4144-9.
120. Gray, E.S., et al., Neutralizing antibody responses in acute human immunodeficiency