期刊论文详细信息
Retrovirology
Recombination-mediated escape from primary CD8+ T cells in acute HIV-1 infection
Nilu Goonetilleke5  Feng Gao2  Andrew J McMichael3  Bette T Korber1  Salim S Abdool Karim6  Simon Brackenridge3  Hongshuo Song7  Sheri Chen7  Nicola MG Smith3  Fangping Cai7  Adam John Ritchie4 
[1] The Sante Fe Institute, Sante Fe 87501, NM, USA;National Engineering Laboratory for AIDS Vaccine, College of Life Science, Jilin University, Changchun, Jilin, China;Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK;Blavatnik School of Government, University of Oxford, Oxford OX1 4JJ, UK;Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill 27599, NC, USA;University of KwaZulu-Natal, Durban 4041, South Africa;Department of Medicine, Duke University, Durham 27710, NC, USA
关键词: Acute infection;    Immunodominance;    Recombination;    Multiple infection;    T cell;    HIV-1;   
Others  :  1152480
DOI  :  10.1186/s12977-014-0069-9
 received in 2013-12-13, accepted in 2014-07-31,  发布年份 2014
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【 摘 要 】

Background

A major immune evasion mechanism of HIV-1 is the accumulation of non-synonymous mutations in and around T cell epitopes, resulting in loss of T cell recognition and virus escape.

Results

Here we analyze primary CD8+ T cell responses and virus escape in a HLA B*81 expressing subject who was infected with two T/F viruses from a single donor. In addition to classic escape through non-synonymous mutation/s, we also observed rapid selection of multiple recombinant viruses that conferred escape from T cells specific for two epitopes in Nef.

Conclusions

Our study shows that recombination between multiple T/F viruses provide greater options for acute escape from CD8+ T cell responses than seen in cases of single T/F virus infection. This process may contribute to the rapid disease progression in patients infected by multiple T/F viruses.

【 授权许可】

   
2014 Ritchie et al.; licensee BioMed Central Ltd.

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【 参考文献 】
  • [1]Borrow P, Lewicki H, Hahn BH, Shaw GM, Oldstone MB: Virus-specific CD8+ cytotoxic T-lymphocyte activity associated with control of viremia in primary human immunodeficiency virus type 1 infection. J Virol 1994, 68:6103-6110.
  • [2]Koup RA, Safrit JT, Cao Y, Andrews CA, McLeod G, Borkowsky W, Farthing C, Ho DD: Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency virus type 1 syndrome. J Virol 1994, 68:4650-4655.
  • [3]Altfeld M, Kalife ET, Qi Y, Streeck H, Lichterfeld M, Johnston MN, Burgett N, Swartz ME, Yang A, Alter G, Yu XG, Meier A, Rockstroh JK, Allen TM, Jessen H, Rosenberg ES, Carrington M, Walker BD: HLA Alleles Associated with Delayed Progression to AIDS Contribute Strongly to the Initial CD8 (+) T Cell Response against HIV-1. PLoS Med 2006, 3:e403.
  • [4]Kaslow RA, Carrington M, Apple R, Park L, Munoz A, Saah AJ, Goedert JJ, Winkler C, O¿Brien SJ, Rinaldo C, Detels R, Blattner W, Phair J, Erlich H, Mann DL: Influence of combinations of human major histocompatibility complex genes on the course of HIV-1 infection. Nat Med 1996, 2:405-411.
  • [5]Leslie A, Kavanagh D, Honeyborne I, Pfafferott K, Edwards C, Pillay T, Hilton L, Thobakgale C, Ramduth D, Draenert R, Le Gall S, Luzzi G, Edwards A, Brander C, Sewell AK, Moore S, Mullins J, Moore C, Mallal S, Bhardwaj N, Yusim K, Phillips R, Klenerman P, Korber B, Kiepiela P, Walker B, Goulder P: Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA. J Exp Med 2005, 201:891-902.
  • [6]International HIVCS, Pereyra F, Jia X, McLaren PJ, Telenti A, de Bakker PI, Walker BD, Ripke S, Brumme CJ, Pulit SL, Carrington M, Kadie CM, Carlson JM, Heckerman D, Graham RR, Plenge RM, Deeks SG, Gianniny L, Crawford G, Sullivan J, Gonzalez E, Davies L, Camargo A, Moore JM, Beattie N, Gupta S, Crenshaw A, Burtt NP, Guiducci C, Gupta N, et al.: The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science 2010, 330:1551-1557.
  • [7]Allen TM, Altfeld M, Geer SC, Kalife ET, Moore C, O¿Sullivan KM, Desouza I, Feeney ME, Eldridge RL, Maier EL, Kaufmann DE, Lahaie MP, Reyor L, Tanzi G, Johnston MN, Brander C, Draenert R, Rockstroh JK, Jessen H, Rosenberg ES, Mallal SA, Walker BD: Selective escape from CD8+ T-cell responses represents a major driving force of human immunodeficiency virus type 1 (HIV-1) sequence diversity and reveals constraints on HIV-1 evolution. J Virol 2005, 79:13239-13249.
  • [8]Phillips RE, Rowland-Jones S, Nixon DF, Gotch FM, Edwards JP, Ogunlesi AO, Elvin JG, Rothbard JA, Bangham CR, Rizza CR, Phillips RE, Rowland-Jones S, Nixon DF, Gotch FM, Edwards JP, Ogunlesi AO, Elvin JG, Rothbard JA, Bangham CRM, Rizza CR, McMichael AJ: Human immunodeficiency virus genetic variation that can escape cytotoxic T cell recognition. Nature 1991, 354:453-459.
  • [9]Goonetilleke N, Liu MK, Salazar-Gonzalez JF, Ferrari G, Giorgi E, Ganusov VV, Keele BF, Learn GH, Turnbull EL, Salazar MG, Weinhold KJ, Moore S, Letvin N, Haynes BF, Cohen MS, Hraber P, Bhattacharya T, Borrow P, Perelson AS, Hahn BH, Shaw GM, Korber BT, McMichael AJ: The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J Exp Med 2009, 206:1253-1272.
  • [10]Liu MK, Hawkins N, Ritchie AJ, Ganusov VV, Whale V, Brackenridge S, Li H, Pavlicek JW, Cai F, Rose-Abrahams M, Treurnicht F, Hraber P, Riou C, Gray C, Ferrari G, Tanner R, Ping LH, Anderson JA, Swanstrom R, Cohen M, Karim SS, Haynes B, Borrow P, Perelson AS, Shaw GM, Hahn BH, Williamson C, Korber BT, Gao F, et al.: Vertical T cell immunodominance and epitope entropy determine HIV-1 escape. J Clin Invest 2013, 123:380-393.
  • [11]Ferrari G, Korber B, Goonetilleke N, Liu MK, Turnbull EL, Salazar-Gonzalez JF, Hawkins N, Self S, Watson S, Betts MR, Gay C, McGhee K, Pellegrino P, Williams I, Tomaras GD, Haynes BF, Gray CM, Borrow P, Roederer M, McMichael AJ, Weinhold KJ: Relationship between functional profile of HIV-1 specific CD8 T cells and epitope variability with the selection of escape mutants in acute HIV-1 infection. PLoS Pathog 2011, 7:e1001273.
  • [12]Keele BF, Giorgi EE, Salazar-Gonzalez JF, Decker JM, Pham KT, Salazar MG, Sun C, Grayson T, Wang S, Li H, Wei X, Jiang C, Kirchherr JL, Gao F, Anderson JA, Ping LH, Swanstrom R, Tomaras GD, Blattner WA, Goepfert PA, Kilby JM, Saag MS, Delwart EL, Busch MP, Cohen MS, Montefiori DC, Haynes BF, Gaschen B, Athreya GS, Lee HY, et al.: Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci U S A 2008, 105:7552-7557.
  • [13]Salazar-Gonzalez JF, Salazar MG, Keele BF, Learn GH, Giorgi EE, Li H, Decker JM, Wang S, Baalwa J, Kraus MH, Parrish NF, Shaw KS, Guffey MB, Bar KJ, Davis KL, Ochsenbauer-Jambor C, Kappes JC, Saag MS, Cohen MS, Mulenga J, Derdeyn CA, Allen S, Hunter E, Markowitz M, Hraber P, Perelson AS, Bhattacharya T, Haynes BF, Korber BT, Hahn BH, et al.: Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. J Exp Med 2009, 206:1273-1289.
  • [14]Abrahams MR, Anderson JA, Giorgi EE, Seoighe C, Mlisana K, Ping LH, Athreya GS, Treurnicht FK, Keele BF, Wood N, Salazar-Gonzalez JF, Bhattacharya T, Chu H, Hoffman I, Galvin S, Mapanje C, Kazembe P, Thebus R, Fiscus S, Hide W, Cohen MS, Karim SA, Haynes BF, Shaw GM, Hahn BH, Korber BT, Swanstrom R, Williamson C, Team CAIS: Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distribution of transmitted variants. J Virol 2009, 83:3556-3567.
  • [15]Bar KJ, Li H, Chamberland A, Tremblay C, Routy JP, Grayson T, Sun C, Wang S, Learn GH, Morgan CJ, Schumacher JE, Haynes BF, Keele BF, Hahn BH, Shaw GM: Wide variation in the multiplicity of HIV-1 infection among injection drug users. J Virol 2010, 84:6241-6247.
  • [16]Haaland RE, Hawkins PA, Salazar-Gonzalez J, Johnson A, Tichacek A, Karita E, Manigart O, Mulenga J, Keele BF, Shaw GM, Hahn BH, Allen SA, Derdeyn CA, Hunter E: Inflammatory genital infections mitigate a severe genetic bottleneck in heterosexual transmission of subtype A and C HIV-1. PLoS Pathog 2009, 5:e1000274.
  • [17]Li H, Bar KJ, Wang S, Decker JM, Chen Y, Sun C, Salazar-Gonzalez JF, Salazar MG, Learn GH, Morgan CJ, Schumacher JE, Hraber P, Giorgi EE, Bhattacharya T, Korber BT, Perelson AS, Eron JJ, Cohen MS, Hicks CB, Haynes BF, Markowitz M, Keele BF, Hahn BH, Shaw GM: High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men. PLoS Pathog 2010, 6:e1000890.
  • [18]Masharsky AE, Dukhovlinova EN, Verevochkin SV, Toussova OV, Skochilov RV, Anderson JA, Hoffman I, Cohen MS, Swanstrom R, Kozlov AP: A substantial transmission bottleneck among newly and recently HIV-1-infected injection drug users in St Petersburg, Russia. J Infect Dis 2010, 201:1697-1702.
  • [19]Novitsky V, Wang R, Margolin L, Baca J, Rossenkhan R, Moyo S, van Widenfelt E, Essex M: Transmission of single and multiple viral variants in primary HIV-1 subtype C infection. PLoS One 2011, 6:e16714.
  • [20]Cornelissen M, Pasternak AO, Grijsen ML, Zorgdrager F, Bakker M, Blom P, Prins JM, Jurriaans S, van der Kuyl AC: HIV-1 dual infection is associated with faster CD4+ T-cell decline in a cohort of men with primary HIV infection. Clin Infect Dis 2012, 54:539-547.
  • [21]Gottlieb GS, Nickle DC, Jensen MA, Wong KG, Grobler J, Li F, Liu SL, Rademeyer C, Learn GH, Karim SS, Williamson C, Corey L, Margolick JB, Mullins JI: Dual HIV-1 infection associated with rapid disease progression. Lancet 2004, 363:619-622.
  • [22]Grobler J, Gray CM, Rademeyer C, Seoighe C, Ramjee G, Karim SA, Morris L, Williamson C: Incidence of HIV-1 dual infection and its association with increased viral load set point in a cohort of HIV-1 subtype C-infected female sex workers. J Infect Dis 2004, 190:1355-1359.
  • [23]Saathoff E, Pritsch M, Geldmacher C, Hoffmann O, Koehler RN, Maboko L, Maganga L, Geis S, McCutchan FE, Kijak GH, Kim JH, Arroyo MA, Gerhardt M, Tovanabutra S, Robb ML, Williamson C, Michael NL, Hoelscher M: Viral and host factors associated with the HIV-1 viral load setpoint in adults from Mbeya Region, Tanzania. J Acquir Immune Defic Syndr 2010, 54:324-330.
  • [24]Sagar M, Lavreys L, Baeten JM, Richardson BA, Mandaliya K, Chohan BH, Kreiss JK, Overbaugh J: Infection with multiple human immunodeficiency virus type 1 variants is associated with faster disease progression. J Virol 2003, 77:12921-12926.
  • [25]Hu WS, Temin HM: Retroviral recombination and reverse transcription. Science 1990, 250:1227-1233.
  • [26]Levy DN, Aldrovandi GM, Kutsch O, Shaw GM: Dynamics of HIV-1 recombination in its natural target cells. Proc Natl Acad Sci U S A 2004, 101:4204-4209.
  • [27]Althaus CL, De Boer RJ: Impaired immune evasion in HIV through intracellular delays and multiple infection of cells. Proc Biol Sci 2012, 279:3003-3010.
  • [28]Mostowy R, Kouyos RD, Fouchet D, Bonhoeffer S: The role of recombination for the coevolutionary dynamics of HIV and the immune response. PLoS One 2011, 6:e16052.
  • [29]Streeck H, Li B, Poon AF, Schneidewind A, Gladden AD, Power KA, Daskalakis D, Bazner S, Zuniga R, Brander C, Rosenberg ES, Frost SD, Altfeld M, Allen TM: Immune-driven recombination and loss of control after HIV superinfection. J Exp Med 2008, 205:1789-1796.
  • [30]Fiebig EW, Wright DJ, Rawal BD, Garrett PE, Schumacher RT, Peddada L, Heldebrant C, Smith R, Conrad A, Kleinman SH, Busch MP: Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection. AIDS 2003, 17:1871-1879.
  • [31]Lee HY, Giorgi EE, Keele BF, Gaschen B, Athreya GS, Salazar-Gonzalez JF, Pham KT, Goepfert PA, Kilby JM, Saag MS, Delwart EL, Busch MP, Hahn BH, Shaw GM, Korber BT, Bhattacharya T, Perelson AS: Modeling sequence evolution in acute HIV-1 infection. J Theor Biol 2009, 261:341-360.
  • [32]Boily MC, Baggaley RF, Wang L, Masse B, White RG, Hayes RJ, Alary M: Heterosexual risk of HIV-1 infection per sexual act: systematic review and meta-analysis of observational studies. Lancet Infect Dis 2009, 9:118-129.
  • [33]Ladell K, Hashimoto M, Iglesias MC, Wilmann PG, McLaren JE, Gras S, Chikata T, Kuse N, Fastenackels S, Gostick E, Bridgeman JS, Venturi V, Arkoub ZA, Agut H, van Bockel DJ, Almeida JR, Douek DC, Meyer L, Venet A, Takiguchi M, Rossjohn J, Price DA, Appay V: A molecular basis for the control of preimmune escape variants by HIV-specific CD8+ T cells. Immunity 2013, 38:425-436.
  • [34]Pacold ME, Pond SL, Wagner GA, Delport W, Bourque DL, Richman DD, Little SJ, Smith DM: Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with men. AIDS 2012, 26:157-165.
  • [35]Fischer W, Ganusov VV, Giorgi EE, Hraber PT, Keele BF, Leitner T, Han CS, Gleasner CD, Green L, Lo CC, Nag A, Wallstrom TC, Wang S, McMichael AJ, Haynes BF, Hahn BH, Perelson AS, Borrow P, Shaw GM, Bhattacharya T, Korber BT: Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing. PLoS One 2010, 5:e12303.
  • [36]Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, Macalalad AR, Berlin AM, Malboeuf CM, Ryan EM, Gnerre S, Zody MC, Erlich RL, Green LM, Berical A, Wang Y, Casali M, Streeck H, Bloom AK, Dudek T, Tully D, Newman R, Axten KL, Gladden AD, Battis L, Kemper M, Zeng Q, Shea TP, Gujja S, Zedlack C, Gasser O, et al.: Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog 2012, 8:e1002529.
  • [37]Emu B, Sinclair E, Favre D, Moretto WJ, Hsue P, Hoh R, Martin JN, Nixon DF, McCune JM, Deeks SG: Phenotypic, functional, and kinetic parameters associated with apparent T-cell control of human immunodeficiency virus replication in individuals with and without antiretroviral treatment. J Virol 2005, 79:14169-14178.
  • [38]Mann JK, Byakwaga H, Kuang XT, Le AQ, Brumme CJ, Mwimanzi P, Omarjee S, Martin E, Lee GQ, Baraki B, Danroth R, McCloskey R, Muzoora C, Bangsberg DR, Hunt PW, Goulder PJ, Walker BD, Harrigan PR, Martin JN, Ndung¿u T, Brockman MA, Brumme ZL: Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes. Retrovirology 2013, 10:100. BioMed Central Full Text
  • [39]Kuang XT, Li X, Anmole G, Mwimanzi P, Shahid A, Le AQ, Chong L, Qian H, Miura T, Markle T, Baraki B, Connick E, Daar ES, Jessen H, Kelleher AD, Little S, Markowitz M, Pereyra F, Rosenberg ES, Walker BD, Ueno T, Brumme ZL, Brockman MA: Impaired Nef function is associated with early control of HIV-1 viremia. J Virol 2014, ?:?. in press
  • [40]Miura T, Brumme ZL, Brockman MA, Rosato P, Sela J, Brumme CJ, Pereyra F, Kaufmann DE, Trocha A, Block BL, Daar ES, Connick E, Jessen H, Kelleher AD, Rosenberg E, Markowitz M, Schafer K, Vaida F, Iwamoto A, Little S, Walker BD: Impaired replication capacity of acute/early viruses in persons who become HIV controllers. J Virol 2010, 84:7581-7591.
  • [41]Shan L, Deng K, Shroff NS, Durand CM, Rabi SA, Yang HC, Zhang H, Margolick JB, Blankson JN, Siliciano RF: Stimulation of HIV-1-specific cytolytic T lymphocytes facilitates elimination of latent viral reservoir after virus reactivation. Immunity 2012, 36:491-501.
  • [42]Jiang C, Parrish NF, Wilen CB, Li H, Chen Y, Pavlicek JW, Berg A, Lu X, Song H, Tilton JC, Pfaff JM, Henning EA, Decker JM, Moody MA, Drinker MS, Schutte R, Freel S, Tomaras GD, Nedellec R, Mosier DE, Haynes BF, Shaw GM, Hahn BH, Doms RW, Gao F: Primary infection by a human immunodeficiency virus with atypical coreceptor tropism. J Virol 2011, 85:10669-10681.
  • [43]Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680.
  • [44]Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P: RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 2010, 26:2462-2463.
  • [45]Shannon C: A mathematical theory of communication. Bell Syst Tech J 1948, 27:79-423.
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