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Volumn 89, Issue 20, 2015, Pages 10303-10318

Fitness-balanced escape determines resolution of dynamic founder virus escape processes in HIV-1 infection

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE; GAG PROTEIN; GAMMA INTERFERON; INTERLEUKIN 2; PROTEIN P17;

EID: 84942133739     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.01876-15     Document Type: Article
Times cited : (27)

References (69)
  • 1
    • 0027980442 scopus 로고
    • Human immunodeficiency virus type 1 evolution in vivo tracked by DNA heteroduplex mobility assays
    • Delwart EL, Sheppard HW, Walker BD, Goudsmit J, Mullins JI. 1994. Human immunodeficiency virus type 1 evolution in vivo tracked by DNA heteroduplex mobility assays. J Virol 68:6672-6683.
    • (1994) J Virol , vol.68 , pp. 6672-6683
    • Delwart, E.L.1    Sheppard, H.W.2    Walker, B.D.3    Goudsmit, J.4    Mullins, J.I.5
  • 2
    • 0027229245 scopus 로고
    • Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection
    • Zhang LQ, MacKenzie P, Cleland A, Holmes EC, Brown AJ, Simmonds P. 1993. Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection. J Virol 67:3345-3356.
    • (1993) J Virol , vol.67 , pp. 3345-3356
    • Zhang, L.Q.1    MacKenzie, P.2    Cleland, A.3    Holmes, E.C.4    Brown, A.J.5    Simmonds, P.6
  • 3
    • 0027422278 scopus 로고
    • Genotypic and phenotypic characterization of HIV-1 patients with primary infection
    • Zhu T, Mo H, Wang N, Nam DS, Cao Y, Koup RA, Ho DD. 1993. Genotypic and phenotypic characterization of HIV-1 patients with primary infection. Science 261:1179-1181. http://dx.doi.org/10.1126/science.8356453.
    • (1993) Science , vol.261 , pp. 1179-1181
    • Zhu, T.1    Mo, H.2    Wang, N.3    Nam, D.S.4    Cao, Y.5    Koup, R.A.6    Ho, D.D.7
  • 9
    • 0028337166 scopus 로고
    • Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency virus type 1 syndrome
    • Koup RA, Safrit JT, Cao Y, Andrews CA, McLeod G, Borkowsky W, Farthing C, Ho DD. 1994. Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency virus type 1 syndrome. J Virol 68:4650-4655.
    • (1994) J Virol , vol.68 , pp. 4650-4655
    • Koup, R.A.1    Safrit, J.T.2    Cao, Y.3    Andrews, C.A.4    McLeod, G.5    Borkowsky, W.6    Farthing, C.7    Ho, D.D.8
  • 19
    • 80055017715 scopus 로고    scopus 로고
    • Fitness costs and diversity of the cytotoxic T lymphocyte (CTL) response determine the rate of CTL escape during acute and chronic phases of HIV infection
    • Ganusov VV, Goonetilleke N, Liu MK, Ferrari G, Shaw GM, McMichael AJ, Borrow P, Korber BT, Perelson AS. 2011. Fitness costs and diversity of the cytotoxic T lymphocyte (CTL) response determine the rate of CTL escape during acute and chronic phases of HIV infection. J Virol 85: 10518-10528. http://dx.doi.org/10.1128/JVI.00655-11.
    • (2011) J Virol , vol.85 , pp. 10518-10528
    • Ganusov, V.V.1    Goonetilleke, N.2    Liu, M.K.3    Ferrari, G.4    Shaw, G.M.5    McMichael, A.J.6    Borrow, P.7    Korber, B.T.8    Perelson, A.S.9
  • 23
    • 84875527661 scopus 로고    scopus 로고
    • Frequent and variable cytotoxic-T-lymphocyte escape-associated fitness costs in the human immunodeficiency virus type 1 subtype B Gag proteins
    • Boutwell CL, Carlson JM, Lin TH, Seese A, Power KA, Peng J, Tang Y, Brumme ZL, Heckerman D, Schneidewind A, Allen TM. 2013. Frequent and variable cytotoxic-T-lymphocyte escape-associated fitness costs in the human immunodeficiency virus type 1 subtype B Gag proteins. J Virol 87:3952-3965. http://dx.doi.org/10.1128/JVI.03233-12.
    • (2013) J Virol , vol.87 , pp. 3952-3965
    • Boutwell, C.L.1    Carlson, J.M.2    Lin, T.H.3    Seese, A.4    Power, K.A.5    Peng, J.6    Tang, Y.7    Brumme, Z.L.8    Heckerman, D.9    Schneidewind, A.10    Allen, T.M.11
  • 25
    • 84878978349 scopus 로고    scopus 로고
    • Fitness costs of mutations at the HIV-1 capsid hexamerization interface
    • Manocheewa S, Swain JV, Lanxon-Cookson E, Rolland M, Mullins JI. 2013. Fitness costs of mutations at the HIV-1 capsid hexamerization interface. PLoS One 8:e66065. http://dx.doi.org/10.1371/journal.pone.0066065.
    • (2013) PLoS One , vol.8
    • Manocheewa, S.1    Swain, J.V.2    Lanxon-Cookson, E.3    Rolland, M.4    Mullins, J.I.5
  • 30
    • 79251616079 scopus 로고    scopus 로고
    • Dynamics of viral evolution and CTL responses in HIV-1 infection
    • Liu Y, McNevin JP, Holte S, McElrath MJ, Mullins JI. 2011. Dynamics of viral evolution and CTL responses in HIV-1 infection. PLoS One 6:e15639. http://dx.doi.org/10.1371/journal.pone.0015639.
    • (2011) PLoS One , vol.6
    • Liu, Y.1    McNevin, J.P.2    Holte, S.3    McElrath, M.J.4    Mullins, J.I.5
  • 31
    • 37348999199 scopus 로고    scopus 로고
    • HIV-1 group M conserved elements vaccine
    • Rolland M, Nickle DC, Mullins JI. 2007. HIV-1 group M conserved elements vaccine. PLoS Pathog 3:e157. http://dx.doi.org/10.1371/journal.ppat.0030157.
    • (2007) PLoS Pathog , vol.3
    • Rolland, M.1    Nickle, D.C.2    Mullins, J.I.3
  • 32
    • 0030586445 scopus 로고    scopus 로고
    • Clinical and epidemiologic features of primary HIV infection
    • Schacker T, Collier AC, Hughes J, Shea T, Corey L. 1996. Clinical and epidemiologic features of primary HIV infection. Ann Intern Med 125: 257-264. http://dx.doi.org/10.7326/0003-4819-125-4-199608150-00001.
    • (1996) Ann Intern Med , vol.125 , pp. 257-264
    • Schacker, T.1    Collier, A.C.2    Hughes, J.3    Shea, T.4    Corey, L.5
  • 33
    • 0032522379 scopus 로고    scopus 로고
    • Biological and virologic characteristics of primary HIV infection
    • Schacker TW, Hughes JP, Shea T, Coombs RW, Corey L. 1998. Biological and virologic characteristics of primary HIV infection. Ann Intern Med 128:613-620. http://dx.doi.org/10.7326/0003-4819-128-8-199804150-00001.
    • (1998) Ann Intern Med , vol.128 , pp. 613-620
    • Schacker, T.W.1    Hughes, J.P.2    Shea, T.3    Coombs, R.W.4    Corey, L.5
  • 36
    • 84891724092 scopus 로고    scopus 로고
    • Increased sequence coverage through combined targeting of variant and conserved epitopes correlates with control of HIV replication
    • Sunshine J, Kim M, Carlson JM, Heckerman D, Czartoski J, Migueles SA, Maenza J, McElrath MJ, Mullins JI, Frahm N. 2014. Increased sequence coverage through combined targeting of variant and conserved epitopes correlates with control of HIV replication. J Virol 88:1354-1365. http://dx.doi.org/10.1128/JVI.02361-13.
    • (2014) J Virol , vol.88 , pp. 1354-1365
    • Sunshine, J.1    Kim, M.2    Carlson, J.M.3    Heckerman, D.4    Czartoski, J.5    Migueles, S.A.6    Maenza, J.7    McElrath, M.J.8    Mullins, J.I.9    Frahm, N.10
  • 37
    • 79951945491 scopus 로고    scopus 로고
    • How to optimally define optimal cytotoxic T lymphocyte epitopes in HIV infection
    • Yusim K, Brander C, Haynes BF, Koup R, Moore JP, Watkins DI (ed). Los Alamos National Laboratory, Theoretical Biology and Biophysics Group, Los Alamos, NM
    • Llano AF, Brander NC. 2009. How to optimally define optimal cytotoxic T lymphocyte epitopes in HIV infection? p 3-24. In Yusim K, Brander C, Haynes BF, Koup R, Moore JP, Watkins DI (ed), HIV molecular immunology. Los Alamos National Laboratory, Theoretical Biology and Biophysics Group, Los Alamos, NM.
    • (2009) HIV molecular immunology , pp. 3-24
    • Llano, A.F.1    Brander, N.C.2
  • 42
    • 33645021327 scopus 로고    scopus 로고
    • RF cloning: a restriction-free method for inserting target genes into plasmids
    • van den Ent F, Lowe J. 2006. RF cloning: a restriction-free method for inserting target genes into plasmids. J Biochem Biophys Methods 67:67-74. http://dx.doi.org/10.1016/j.jbbm.2005.12.008.
    • (2006) J Biochem Biophys Methods , vol.67 , pp. 67-74
    • van den Ent, F.1    Lowe, J.2
  • 44
    • 33745158157 scopus 로고
    • A simple method of estimating fifty percent endpoints
    • Reed LJM, H. 1938. A simple method of estimating fifty percent endpoints. Am J Hyg 27:493-497.
    • (1938) Am J Hyg , vol.27 , pp. 493-497
    • Reed, L.J.M.1    H.2
  • 45
    • 33847254313 scopus 로고    scopus 로고
    • Granulocytemonocyte colony-stimulating factor upregulates HIV-1 replication in monocyte-derived macrophages cultured at low density
    • McClure J, van't Wout AB, Tran T, Mittler JE. 2007. Granulocytemonocyte colony-stimulating factor upregulates HIV-1 replication in monocyte-derived macrophages cultured at low density. J Acquir Immune Defic Syndr 44:254-261. http://dx.doi.org/10.1097/QAI.0b013e318030f5c5.
    • (2007) J Acquir Immune Defic Syndr , vol.44 , pp. 254-261
    • McClure, J.1    van't Wout, A.B.2    Tran, T.3    Mittler, J.E.4
  • 47
    • 17844385106 scopus 로고    scopus 로고
    • The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage
    • Nielsen M, Lundegaard C, Lund O, Kesmir C. 2005. The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics 57: 33-41. http://dx.doi.org/10.1007/s00251-005-0781-7.
    • (2005) Immunogenetics , vol.57 , pp. 33-41
    • Nielsen, M.1    Lundegaard, C.2    Lund, O.3    Kesmir, C.4
  • 48
    • 0036096708 scopus 로고    scopus 로고
    • Prediction of proteasome cleavage motifs by neural networks
    • Kesmir C, Nussbaum AK, Schild H, Detours V, Brunak S. 2002. Prediction of proteasome cleavage motifs by neural networks. Protein Eng 15:287-296. http://dx.doi.org/10.1093/protein/15.4.287.
    • (2002) Protein Eng , vol.15 , pp. 287-296
    • Kesmir, C.1    Nussbaum, A.K.2    Schild, H.3    Detours, V.4    Brunak, S.5
  • 52
    • 80051718223 scopus 로고    scopus 로고
    • Molecular determinants that regulate plasma membrane association of HIV-1 Gag
    • Chukkapalli V, Ono A. 2011. Molecular determinants that regulate plasma membrane association of HIV-1 Gag. J Mol Biol 410:512-524. http://dx.doi.org/10.1016/j.jmb.2011.04.015.
    • (2011) J Mol Biol , vol.410 , pp. 512-524
    • Chukkapalli, V.1    Ono, A.2
  • 55
    • 62749167015 scopus 로고    scopus 로고
    • Reduced viral replication capacity of human immunodeficiency virus type 1 subtype C caused by cytotoxic-T-lymphocyte escape mutations in HLA-B57 epitopes of capsid protein
    • Boutwell CL, Rowley CF, Essex M. 2009. Reduced viral replication capacity of human immunodeficiency virus type 1 subtype C caused by cytotoxic-T-lymphocyte escape mutations in HLA-B57 epitopes of capsid protein. J Virol 83:2460-2468. http://dx.doi.org/10.1128/JVI.01970-08.
    • (2009) J Virol , vol.83 , pp. 2460-2468
    • Boutwell, C.L.1    Rowley, C.F.2    Essex, M.3
  • 57
    • 30844443739 scopus 로고    scopus 로고
    • Decreasing the frameshift efficiency translates into an equivalent reduction of the replication of the human immunodeficiency virus type 1
    • Dulude D, Berchiche YA, Gendron K, Brakier-Gingras L, Heveker N. 2006. Decreasing the frameshift efficiency translates into an equivalent reduction of the replication of the human immunodeficiency virus type 1. Virology 345:127-136. http://dx.doi.org/10.1016/j.virol.2005.08.048.
    • (2006) Virology , vol.345 , pp. 127-136
    • Dulude, D.1    Berchiche, Y.A.2    Gendron, K.3    Brakier-Gingras, L.4    Heveker, N.5
  • 58
    • 34248155890 scopus 로고    scopus 로고
    • HIV gp41 C-terminal heptad repeat contains multifunc-tional domains. Relation to mechanisms of action of anti-HIV peptides
    • Liu S, Jing W, Cheung B, Lu H, Sun J, Yan X, Niu J, Farmar J, Wu S, Jiang S. 2007. HIV gp41 C-terminal heptad repeat contains multifunc-tional domains. Relation to mechanisms of action of anti-HIV peptides. J Biol Chem 282:9612-9620.
    • (2007) J Biol Chem , vol.282 , pp. 9612-9620
    • Liu, S.1    Jing, W.2    Cheung, B.3    Lu, H.4    Sun, J.5    Yan, X.6    Niu, J.7    Farmar, J.8    Wu, S.9    Jiang, S.10
  • 59
    • 39649122106 scopus 로고    scopus 로고
    • HLA class I supertypes: a revised and updated classification
    • Sidney J, Peters B, Frahm N, Brander C, Sette A. 2008. HLA class I supertypes: a revised and updated classification. BMC Immunol 9:1. http://dx.doi.org/10.1186/1471-2172-9-1.
    • (2008) BMC Immunol , vol.9 , pp. 1
    • Sidney, J.1    Peters, B.2    Frahm, N.3    Brander, C.4    Sette, A.5
  • 60
    • 33845756711 scopus 로고    scopus 로고
    • Rapid reversion of sequence polymorphisms dominates early human immunodeficiency virus type 1 evolution
    • Li B, Gladden AD, Altfeld M, Kaldor JM, Cooper DA, Kelleher AD, Allen TM. 2007. Rapid reversion of sequence polymorphisms dominates early human immunodeficiency virus type 1 evolution. J Virol 81:193-201. http://dx.doi.org/10.1128/JVI.01231-06.
    • (2007) J Virol , vol.81 , pp. 193-201
    • Li, B.1    Gladden, A.D.2    Altfeld, M.3    Kaldor, J.M.4    Cooper, D.A.5    Kelleher, A.D.6    Allen, T.M.7
  • 61
    • 84865063695 scopus 로고    scopus 로고
    • Cytotoxic T-lymphocyte escape mutations identified by HLA association favor those which escape and revert rapidly
    • Fryer HR, Frater J, Duda A, Palmer D, Phillips RE, McLean AR. 2012. Cytotoxic T-lymphocyte escape mutations identified by HLA association favor those which escape and revert rapidly. J Virol 86:8568-8580. http://dx.doi.org/10.1128/JVI.07020-11.
    • (2012) J Virol , vol.86 , pp. 8568-8580
    • Fryer, H.R.1    Frater, J.2    Duda, A.3    Palmer, D.4    Phillips, R.E.5    McLean, A.R.6
  • 64
    • 0029965055 scopus 로고    scopus 로고
    • Selective expansion of high-or low-avidity cytotoxic T lymphocytes and efficacy for adoptive immunotherapy
    • Alexander-Miller MA, Leggatt GR, Berzofsky JA. 1996. Selective expansion of high-or low-avidity cytotoxic T lymphocytes and efficacy for adoptive immunotherapy. Proc Natl Acad Sci U S A 93:4102-4107. http://dx.doi.org/10.1073/pnas.93.9.4102.
    • (1996) Proc Natl Acad Sci U S A , vol.93 , pp. 4102-4107
    • Alexander-Miller, M.A.1    Leggatt, G.R.2    Berzofsky, J.A.3
  • 65
    • 0035253434 scopus 로고    scopus 로고
    • High-avidity CTL exploit two complementary mechanisms to provide better protection against viral infection than low-avidity CTL
    • Derby M, Alexander-Miller M, Tse R, Berzofsky J. 2001. High-avidity CTL exploit two complementary mechanisms to provide better protection against viral infection than low-avidity CTL. J Immunol 166:1690-1697. http://dx.doi.org/10.4049/jimmunol.166.3.1690.
    • (2001) J Immunol , vol.166 , pp. 1690-1697
    • Derby, M.1    Alexander-Miller, M.2    Tse, R.3    Berzofsky, J.4
  • 66
    • 84883404887 scopus 로고    scopus 로고
    • Selective induction of CTL helper rather than killer activity by natural epitope variants promotes dendritic cell-mediated HIV-1 dissemination
    • Mailliard RB, Smith KN, Fecek RJ, Rappocciolo G, Nascimento EJ, Marques ET, Watkins SC, Mullins JI, Rinaldo CR. 2013. Selective induction of CTL helper rather than killer activity by natural epitope variants promotes dendritic cell-mediated HIV-1 dissemination. J Immunol 191:2570-2580. http://dx.doi.org/10.4049/jimmunol.1300373.
    • (2013) J Immunol , vol.191 , pp. 2570-2580
    • Mailliard, R.B.1    Smith, K.N.2    Fecek, R.J.3    Rappocciolo, G.4    Nascimento, E.J.5    Marques, E.T.6    Watkins, S.C.7    Mullins, J.I.8    Rinaldo, C.R.9


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