The role of MHC class I allele Mamu-A *07 during SIV mac239 infection

Immunogenetics

Volumn 63, Issue 12, 2011, Pages 789-807

  Reed, Jason S ^a   Sidney, John ^b   Piaskowski, Shari M ^a   Glidden, Chrystal E ^a   León, Enrique J ^a   Burwitz, Benjamin J ^a   Kolar, Holly L ^a   Eernisse, Christopher M ^a   Furlott, Jessica R ^a   Maness, Nicholas J ^a   Walsh, Andrew D ^a   Rudersdorf, Richard A ^a   Bardet, Wilfried ^c   McMurtrey, Curtis P ^c   O'Connor, David H ^a   Hildebrand, William H ^c   Sette, Alessandro ^b   Watkins, David I ^a   Wilson, Nancy A ^a  

^a UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

^b LA JOLLA INSTITUTE FOR ALLERGY AND IMMUNOLOGY   (United States)

^c UNIVERSITY OF OKLAHOMA COLLEGE OF MEDICINE   (United States)

Author keywords

Epitope; Escape; Macaque; MHC; SIV

Indexed keywords

ALANINE; ENVELOPE PROTEIN; EPITOPE; GAG PROTEIN; GAMMA INTERFERON; ISOLEUCINE; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; METHIONINE; PEPTIDE; POL PROTEIN; SERINE; SIMIAN IMMUNODEFICIENCY VIRUS VACCINE; TUMOR NECROSIS FACTOR ALPHA; UNCLASSIFIED DRUG; VALINE; VIF PROTEIN; VIRUS PROTEIN; VPR PROTEIN; VPX PROTEIN;

ALLELE; AMINO ACID SUBSTITUTION; ANIMAL CELL; ARTICLE; BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; CD8+ T LYMPHOCYTE; ENZYME LINKED IMMUNOSPOT ASSAY; GENE DELETION; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IN VITRO STUDY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; PYROSEQUENCING; RHESUS MONKEY; SIMIAN IMMUNODEFICIENCY VIRUS; VIRUS REPLICATION;

ALLELES; AMINO ACID SEQUENCE; ANIMALS; CD8-POSITIVE T-LYMPHOCYTES; EPITOPES, T-LYMPHOCYTE; GENES, MHC CLASS I; HISTOCOMPATIBILITY ANTIGENS CLASS I; INTERFERON-GAMMA; MACACA MULATTA; PROTEIN BINDING; RNA, VIRAL; SEQUENCE ANALYSIS, PROTEIN; SIMIAN ACQUIRED IMMUNODEFICIENCY SYNDROME; SIMIAN IMMUNODEFICIENCY VIRUS; T-LYMPHOCYTES, CYTOTOXIC; VIRAL LOAD; VIRAL VACCINES;

MACACA MULATTA; SIMIAN IMMUNODEFICIENCY VIRUS;

EID: 82755198004     PISSN: 00937711     EISSN: 14321211     Source Type: Journal    
DOI: 10.1007/s00251-011-0541-9     Document Type: Article

References (100)

1. L Alexander L Denekamp S Czajak R Desrosiers 2001 Suboptimal nucleotides in the infectious, pathogenic simian immunodeficiency virus clone SIVmac239 J Virol 75 4019 4022 10.1128/JVI.75.8.4019-4022.2001 11264395 10.1128/JVI.75.8. 4019-4022.2001 1:CAS:528:DC%2BD3MXisVSmtr4%3D (Pubitemid 32246415)
2. TM Allen J Sidney MF Del Guercio R Glickman G Lensmeyer D Wiebe R Demars C Pauza R Johnson A Sette D Watkins 1998 Characterization of the peptide binding motif of a rhesus MHC class I molecule (Mamu-A*01) that binds an immunodominant CTL epitope from simian immunodeficiency virus J Immunol 160 6062 6071 9637523 1:CAS:528:DyaK1cXjvVahsr0%3D (Pubitemid 28298070)
3. TM Allen DH O'Connor P Jing J Dzuris B Mothe T Vogel E Dunphy M Liebl C Emerson N Wilson K Kunstman X Wang D Allison A Hughes R Desrosiers J Altman S Wolinsky A Sette D Watkins 2000 Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia Nature 407 386 390 10.1038/35030124 11014195 10.1038/35036559 1:CAS:528:DC%2BD3cXntF2ntr0%3D
4. TM Allen B Mothe J Sidney P Jing J Dzuris M Liebl T Vogel DH O'Connor X Wang M Wussow J Thomson J Altman D Watkins A Sette 2001 CD8(+) lymphocytes from simian immunodeficiency virus-infected rhesus macaques recognize 14 different epitopes bound by the major histocompatibility complex class I molecule mamu-A*01: implications for vaccine design and testing J Virol 75 738 749 10.1128/JVI.75.2.738-749.2001 11134287 10.1128/JVI.75.2.738-749.2001 1:CAS:528:DC%2BD3MXhsFWqsg%3D%3D (Pubitemid 32037277)
5. M Altfeld E Kalife Y Qi H Streeck M Lichterfeld M Johnston N Burgett M Swartz A Yang G Alter XG Yu A Meier J Rockstroh T Allen H Jessen E Rosenberg M Carrington B Walker 2006 HLA alleles associated with delayed progression to AIDS contribute strongly to the initial CD8(+) T cell response against HIV-1 PLoS Med 3 e403 10.1371/journal.pmed.0030403 17076553 10.1371/journal.pmed.0030403 (Pubitemid 44721824)
6. JD Altman P Moss P Goulder D Barouch MG Mcheyzer-Williams J Bell A Mcmichael M Davis 1996 Phenotypic analysis of antigen-specific T lymphocytes Science 274 94 96 8810254 10.1126/science.274.5284.94 1:CAS:528: DyaK28XmtVyns7k%3D (Pubitemid 26332731)
7. E Assarsson J Sidney C Oseroff V Pasquetto H Bui N Frahm C Brander B Peters H Grey A Sette 2007 A quantitative analysis of the variables affecting the repertoire of T cell specificities recognized after vaccinia virus infection J Immunol 178 7890 7901 17548627 1:CAS:528:DC%2BD2sXmtVKns78%3D (Pubitemid 46898061)
8. C Barnstable W Bodmer G Brown G Galfre C Milstein A Williams A Ziegler 1978 Production of monoclonal antibodies to group A erythrocytes, HLA and other human cell surface antigens-new tools for genetic analysis Cell 14 9 20 667938 10.1016/0092-8674(78)90296-9 1:CAS:528:DyaE1cXkslCjs7g%3D (Pubitemid 8340429)
9. DH Barouch J Kunstman M Kuroda J Schmitz S Santra F Peyerl G Krivulka K Beaudry M Lifton D Gorgone D Montefiori M Lewis S Wolinsky N Letvin 2002 Eventual AIDS vaccine failure in a rhesus monkey by viral escape from cytotoxic T lymphocytes Nature 415 335 339 10.1038/415335a 11797012 10.1038/415335a 1:CAS:528:DC%2BD38XptlamsA%3D%3D (Pubitemid 34087556)
10. D Barouch J Kunstman J Glowczwskie K Kunstman M Egan F Peyerl S Santra M Kuroda J Schmitz K Beaudry G Krivulka M Lifton D Gorgone S Wolinsky N Letvin 2003 Viral escape from dominant simian immunodeficiency virus epitope-specific cytotoxic T lymphocytes in DNA-vaccinated rhesus monkeys J Virol 77 7367 7375 12805435 10.1128/JVI.77.13.7367-7375.2003 1:CAS:528:DC%2BD3sXkvV2qur8%3D (Pubitemid 36734505)
11. BN Bimber B Burwitz S O'Connor A Detmer E Gostick S Lank D Price A Hughes D O'Connor 2009 Ultradeep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in simian immunodeficiency virus-infected macaques J Virol 83 8247 8253 10.1128/JVI.00897-09 19515775 10.1128/JVI.00897-09 1:CAS:528:DC%2BD1MXpsFOltbo%3D
12. P Borrow H Lewicki B Hahn G Shaw M Oldstone 1994 Virus-specific CD8+ cytotoxic T-lymphocyte activity associated with control of viremia in primary human immunodeficiency virus type 1 infection J Virol 68 6103 6110 8057491 1:CAS:528:DyaK2cXlsFGmt7w%3D (Pubitemid 24258634)
13. P Borrow H Lewicki X Wei M Horwitz N Peffer H Meyers J Nelson J Gairin B Hahn M Oldstone G Shaw 1997 Antiviral pressure exerted by HIV-1-specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus Nat Med 3 205 211 9018240 10.1038/nm0297-205 1:CAS:528:DyaK2sXpsV2rug%3D%3D (Pubitemid 27064706)
14. J Boyson C Shufflebotham L Cadavid J Urvater L Knapp A Hughes D Watkins 1996 The MHC class I genes of the rhesus monkey. Different evolutionary histories of MHC class I and II genes in primates J Immunol 156 4656 4665 8648109 1:CAS:528:DyaK28XjsFamtL0%3D (Pubitemid 26174447)
15. B Burwitz C Pendley J Greene A Detmer J Lhost J Karl S Piaskowski R Rudersdorf L Wallace B Bimber J Loffredo D Cox W Bardet W Hildebrand R Wiseman SL O'Connor DH O'Connor 2009 Mauritian cynomolgus macaques share two exceptionally common major histocompatibility complex class I alleles that restrict simian immunodeficiency virus-specific CD8+ T cells J Virol 83 6011 6019 10.1128/JVI.00199-09 19339351 10.1128/JVI.00199-09 1:CAS:528: DC%2BD1MXntFWqtL0%3D
16. M Carrington SJ O'Brien 2003 The influence of HLA genotype on AIDS Annu Rev Med 54 535 551 10.1146/annurev.med.54.101601.152346 12525683 10.1146/annurev.med.54.101601.152346 1:CAS:528:DC%2BD3sXit1ejtr0%3D (Pubitemid 37386411)
17. M Carrington GW Nelson M Martin T Kissner D Vlahov J Goedert R Kaslow S Buchbinder K Hoots SJ O'Brien 1999 HLA and HIV-1: heterozygote advantage and B 35-Cw 04 disadvantage Science 283 1748 1752 10073943 10.1126/science.283.5408. 1748 1:CAS:528:DyaK1MXhvFSnu7s%3D (Pubitemid 29143811)
18. Z Chen A Craiu L Shen M Kuroda U Iroku D Watkins G Voss N Letvin 2000 Simian immunodeficiency virus evades a dominant epitope-specific cytotoxic T lymphocyte response through a mutation resulting in the accelerated dissociation of viral peptide and MHC class I J Immunol 164 6474 6479 10843704 1:CAS:528:DC%2BD3cXktFWltb4%3D (Pubitemid 30408831)
19. Y Cheng W Prusoff 1973 Relationship between the inhibition constant (K1) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction Biochem Pharmacol 22 3099 3108 4202581 10.1016/0006-2952(73)90196-2 1:CAS:528:DyaE2cXhtVGgs7c%3D
20. S Deeks B Walker 2007 Human immunodeficiency virus controllers: mechanisms of durable virus control in the absence of antiretroviral therapy Immunity 27 406 416 10.1016/j.immuni.2007.08.010 17892849 10.1016/j.immuni.2007. 08.010 1:CAS:528:DC%2BD2sXhtFWmu7bL (Pubitemid 47418678)
21. R Demars R Rudersdorf C Chang J Petersen J Strandtmann N Korn B Sidwell H Orr 1985 Mutations that impair a posttranscriptional step in expression of HLA-A and -B antigens Proc Natl Acad Sci USA 82 8183 8187 3906658 10.1073/pnas.82.23.8183 1:CAS:528:DyaL28Xks1KjsA%3D%3D (Pubitemid 16171058)
22. D Evans DH O'Connor P Jing J Dzuris J Sidney J Da Silva T Allen H Horton J Venham R Rudersdorf T Vogel C Pauza R Bontrop R Demars A Sette A Hughes D Watkins 1999 Virus-specific cytotoxic T-lymphocyte responses select for amino-acid variation in simian immunodeficiency virus Env and Nef Nat Med 5 1270 1276 10.1038/15224 10545993 10.1038/15224 1:CAS:528:DyaK1MXnt1yntro%3D (Pubitemid 29535604)
23. K Falk O Rotzschke S Stevanovic G Jung H Rammensee 1991 Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules Nature 351 290 296 10.1038/351290a0 1709722 10.1038/351290a0 1:CAS:528: DyaK3MXkt1Ogs78%3D (Pubitemid 21896578)
24. T Friedrich C Frye L Yant DH O'Connor N Kriewaldt M Benson L Vojnov E Dodds C Cullen R Rudersdorf A Hughes N Wilson D Watkins 2004 Extraepitopic compensatory substitutions partially restore fitness to simian immunodeficiency virus variants that escape from an immunodominant cytotoxic-T-lymphocyte response J Virol 78 2581 2585 14963161 10.1128/JVI.78.5.2581-2585.2004 1:CAS:528:DC%2BD2cXhs1Sltbk%3D (Pubitemid 38228953)
25. T Friedrich A Mcdermott M Reynolds S Piaskowski S Fuenger IP De Souza R Rudersdorf C Cullen L Yant L Vojnov J Stephany S Martin DH O'Connor N Wilson D Watkins 2004 Consequences of cytotoxic T-lymphocyte escape: common escape mutations in simian immunodeficiency virus are poorly recognized in naive hosts J Virol 78 10064 10073 10.1128/JVI.78.18.10064-10073.2004 15331739 10.1128/JVI.78.18.10064-10073.2004 1:CAS:528:DC%2BD2cXnvVarsb0%3D (Pubitemid 39187124)
26. T Friedrich L Valentine L Yant E Rakasz S Piaskowski J Furlott K Weisgrau B Burwitz G May E Leon T Soma G Napoe SR Capuano N Wilson D Watkins 2007 Subdominant CD8+ T-cell responses are involved in durable control of AIDS virus replication J Virol 81 3465 3476 10.1128/JVI.02392-06 17251286 10.1128/JVI.02392-06 1:CAS:528:DC%2BD2sXjslWqs7k%3D (Pubitemid 46456655)
27. X Gao A Bashirova A Iversen J Phair J Goedert S Buchbinder K Hoots D Vlahov M Altfeld SJ O'Brien M Carrington 2005 AIDS restriction HLA allotypes target distinct intervals of HIV-1 pathogenesis Nat Med 11 1290 1292 10.1038/nm1333 16288280 10.1038/nm1333 1:CAS:528:DC%2BD2MXht1yisrrF (Pubitemid 41752907)
28. P Goulder R Phillips R Colbert S Mcadam G Ogg M Nowak P Giangrande G Luzzi B Morgan A Edwards A Mcmichael S Rowland-Jones 1997 Late escape from an immunodominant cytotoxic T-lymphocyte response associated with progression to AIDS Nat Med 3 212 217 9018241 10.1038/nm0297-212 1:CAS:528:DyaK2sXpsFShtg%3D%3D (Pubitemid 27064707)
29. K Gulukota J Sidney A Sette C Delisi 1997 Two complementary methods for predicting peptides binding major histocompatibility complex molecules J Mol Biol 267 1258 1267 10.1006/jmbi.1997.0937 9150410 10.1006/jmbi.1997.0937 1:CAS:528:DyaK2sXjtFWhur0%3D (Pubitemid 27192636)
30. H Hendel S Caillat-Zucman H Lebuanec M Carrington S O'Brien J Andrieu F Schachter D Zagury J Rappaport C Winkler G Nelson J Zagury 1999 New class I and II HLA alleles strongly associated with opposite patterns of progression to AIDS J Immunol 162 6942 6946 10352317 1:CAS:528:DyaK1MXjtlKiu7s%3D (Pubitemid 29309424)
31. X Jin D Bauer S Tuttleton S Lewin A Gettie J Blanchard C Irwin J Safrit J Mittler L Weinberger L Kostrikis L Zhang A Perelson DD Ho 1999 Dramatic rise in plasma viremia after CD8(+) T cell depletion in simian immunodeficiency virus-infected macaques J Exp Med 189 991 998 10075982 10.1084/jem.189.6.991 1:CAS:528:DyaK1MXhvVOit7o%3D (Pubitemid 29149355)
32. M Kaizu G Borchardt C Glidden D Fisk J Loffredo D Watkins W Rehrauer 2007 Molecular typing of major histocompatibility complex class I alleles in the Indian rhesus macaque which restrict SIV CD8+ T cell epitopes Immunogenetics 59 693 703 10.1007/s00251-007-0233-7 17641886 10.1007/s00251-007-0233-7 1:CAS:528:DC%2BD2sXhtVCnsrjM (Pubitemid 47415561)
33. RA Kaslow M Carrington R Apple L Park A Munoz A Saah J Goedert C Winkler SJ O'Brien C Rinaldo R Detels W Blattner J Phair H Erlich D Mann 1996 Influence of combinations of human major histocompatibility complex genes on the course of HIV-1 infection Nat Med 2 405 411 8597949 10.1038/nm0496-405 1:CAS:528:DyaK28XitVKmsbc%3D (Pubitemid 26193012)
34. R Kaslow C Rivers J Tang T Bender P Goepfert R El Habib K Weinhold M Mulligan 2001 Polymorphisms in HLA class I genes associated with both favorable prognosis of human immunodeficiency virus (HIV) type 1 infection and positive cytotoxic T-lymphocyte responses to ALVAC-HIV recombinant canarypox vaccines J Virol 75 8681 8689 11507213 10.1128/JVI.75.18.8681-8689.2001 1:CAS:528:DC%2BD3MXmsVaqs7w%3D (Pubitemid 32768972)
35. WM Kast RM Brandt J Sidney J Drijfhout R Kubo H Grey C Melief A Sette 1994 Role of HLA-A motifs in identification of potential CTL epitopes in human papillomavirus type 16 E6 and E7 proteins J Immunol 152 3904 3912 7511661 1:CAS:528:DyaK2MXotlCl (Pubitemid 24111062)
36. H Kestler T Kodama D Ringler M Marthas N Pedersen A Lackner D Regier P Sehgal M Daniel N King A Et 1990 Induction of AIDS in rhesus monkeys by molecularly cloned simian immunodeficiency virus Science 248 1109 1112 2160735 10.1126/science.2160735 1:STN:280:DyaK3c3mtVKmtQ%3D%3D
37. M Klein CA Van Baalen A Holwerda SR Kerkhof Garde R Bende I Keet JK Eeftinck-Schattenkerk A Osterhaus H Schuitemaker F Miedema 1995 Kinetics of Gag-specific cytotoxic T lymphocyte responses during the clinical course of HIV-1 infection: a longitudinal analysis of rapid progressors and long-term asymptomatics J Exp Med 181 1365 1372 7699324 10.1084/jem.181.4.1365 1:CAS:528:DyaK2MXkslWntrc%3D
38. A Kondo J Sidney S Southwood MF Del Guercio E Appella H Sakamoto E Celis H Grey RW Chesnut R Kubo A Sette 1995 Prominent roles of secondary anchor residues in peptide binding to HLA-A24 human class I molecules J Immunol 155 4307 4312 7594589 1:CAS:528:DyaK2MXovFWltbo%3D
39. M Kotturi B Peters FJ Buendia-Laysa J Sidney C Oseroff J Botten H Grey M Buchmeier A Sette 2007 The CD8+ T-cell response to lymphocytic choriomeningitis virus involves the L antigen: uncovering new tricks for an old virus J Virol 81 4928 4940 10.1128/JVI.02632-06 17329346 10.1128/JVI.02632-06 1:CAS:528:DC%2BD2sXls1Grsrk%3D (Pubitemid 46744404)
40. RA Koup J Safrit Y Cao C Andrews G Mcleod W Borkowsky C Farthing DD Ho 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 8207839 1:STN:280:DyaK2c3msl2huw%3D%3D (Pubitemid 24183063)
41. RT Kubo A Sette H Grey E Appella K Sakaguchi N Zhu D Arnott N Sherman J Shabanowitz H Michel A Et 1994 Definition of specific peptide motifs for four major HLA-A alleles J Immunol 152 3913 3924 8144960 1:CAS:528:DyaK2MXotlCk (Pubitemid 24111063)
42. M Kuroda J Schmitz D Barouch A Craiu T Allen A Sette D Watkins M Forman N Letvin 1998 Analysis of Gag-specific cytotoxic T lymphocytes in simian immunodeficiency virus-infected rhesus monkeys by cell staining with a tetrameric major histocompatibility complex class I-peptide complex J Exp Med 187 1373 1381 9565630 10.1084/jem.187.9.1373 1:CAS:528:DyaK1cXivVGjtLw%3D (Pubitemid 28215397)
43. S Lauemoller A Holm J Hilden S Brunak M Holst Nissen A Stryhn L Ostergaard Pedersen S Buus 2001 Quantitative predictions of peptide binding to MHC class I molecules using specificity matrices and anchor-stratified calibrations Tissue Antigens 57 405 414 11556965 10.1034/j.1399-0039.2001. 057005405.x 1:CAS:528:DC%2BD3MXlsV2rur0%3D (Pubitemid 32590839)
44. J Loffredo J Sidney C Wojewoda E Dodds M Reynolds G Napoe B Mothe DH O'Connor N Wilson D Watkins A Sette 2004 Identification of seventeen new simian immunodeficiency virus-derived CD8+ T cell epitopes restricted by the high frequency molecule, Mamu-A*02, and potential escape from CTL recognition J Immunol 173 5064 5076 15470050 1:CAS:528:DC%2BD2cXotFCqu78%3D (Pubitemid 39387789)
45. J Loffredo J Sidney S Piaskowski A Szymanski J Furlott R Rudersdorf J Reed B Peters HD Hickman-Miller W Bardet W Rehrauer DH O'Connor N Wilson W Hildebrand A Sette D Watkins 2005 The high frequency Indian rhesus macaque MHC class I molecule, Mamu-B*01, does not appear to be involved in CD8+ T lymphocyte responses to SIVmac239 J Immunol 175 5986 5997 16237093 1:CAS:528:DC%2BD2MXhtFahurbO (Pubitemid 41508084)
46. J Loffredo T Friedrich E Leon J Stephany D Rodrigues S Spencer A Bean D Beal B Burwitz R Rudersdorf L Wallace S Piaskowski G May J Sidney E Gostick N Wilson D Price E Kallas H Piontkivska A Hughes A Sette D Watkins 2007 CD8+ T cells from SIV elite controller macaques recognize Mamu-B*08-bound epitopes and select for widespread viral variation PLoS ONE 2 e1152 10.1371/journal.pone.0001152 18000532 10.1371/journal.pone.0001152 (Pubitemid 351637971)
47. J Loffredo J Maxwell Y Qi C Glidden G Borchardt T Soma A Bean D Beal N Wilson W Rehrauer J Lifson M Carrington D Watkins 2007 Mamu-B*08-positive macaques control simian immunodeficiency virus replication J Virol 81 8827 8832 10.1128/JVI.00895-07 17537848 10.1128/JVI.00895-07 1:CAS:528: DC%2BD2sXoslOitb0%3D (Pubitemid 47242856)
48. J Loffredo J Sidney A Bean D Beal W Bardet A Wahl O Hawkins S Piaskowski N Wilson W Hildebrand D Watkins A Sette 2009 Two MHC class I molecules associated with elite control of immunodeficiency virus replication, Mamu-B*08 and HLA-B*2705, bind peptides with sequence similarity J Immunol 182 7763 7775 10.4049/jimmunol.0900111 19494300 10.4049/jimmunol.0900111 1:CAS:528:DC%2BD1MXmslCntro%3D
49. O Lund M Nielsen C Kesmir A Petersen C Lundegaard P Worning C Sylvester-Hvid K Lamberth G Roder S Justesen S Buus S Brunak 2004 Definition of supertypes for HLA molecules using clustering of specificity matrices Immunogenetics 55 797 810 10.1007/s00251-004-0647-4 14963618 10.1007/s00251-004-0647-4 1:CAS:528:DC%2BD2cXisV2isLg%3D (Pubitemid 38650985)
50. T Matano R Shibata C Siemon M Connors HC Lane M Martin 1998 Administration of an anti-CD8 monoclonal antibody interferes with the clearance of chimeric simian/human immunodeficiency virus during primary infections of rhesus macaques J Virol 72 164 169 9420212 1:CAS:528:DyaK1cXhvVChsg%3D%3D (Pubitemid 28048825)
51. A Mcneil P Yap S Gore R Brettle M Mccoll R Wyld S Davidson R Weightman A Richardson J Robertson 1996 Association of HLA types A1-B8-DR3 and B27 with rapid and slow progression of HIV disease QJM 89 177 185 8731561 1:STN:280:DyaK283pslyitQ%3D%3D (Pubitemid 26086136)
52. K Metzner X Jin F Lee A Gettie D Bauer M Di Mascio A Perelson P Marx DD Ho L Kostrikis R Connor 2000 Effects of in vivo CD8(+) T cell depletion on virus replication in rhesus macaques immunized with a live, attenuated simian immunodeficiency virus vaccine J Exp Med 191 1921 1931 10839807 10.1084/jem.191.11.1921 1:CAS:528:DC%2BD3cXjvFyntLc%3D (Pubitemid 30390354)
53. S Migueles M Sabbaghian W Shupert M Bettinotti F Marincola L Martino C Hallahan S Selig D Schwartz J Sullivan M Connors 2000 HLA B*5701 is highly associated with restriction of virus replication in a subgroup of HIV-infected long term nonprogressors Proc Natl Acad Sci USA 97 2709 2714 10.1073/pnas.050567397 10694578 10.1073/pnas.050567397 1:CAS:528: DC%2BD3cXitVahs70%3D (Pubitemid 30159236)
54. L Mortara F Letourneur H Gras-Masse A Venet J Guillet I Bourgault-Villada 1998 Selection of virus variants and emergence of virus escape mutants after immunization with an epitope vaccine J Virol 72 1403 1410 9445041 1:CAS:528:DyaK1cXlt1Gnug%3D%3D (Pubitemid 28116926)
55. BR Mothe J Sidney J Dzuris M Liebl S Fuenger D Watkins A Sette 2002 Characterization of the peptide-binding specificity of Mamu-B*17 and identification of Mamu-B*17-restricted epitopes derived from simian immunodeficiency virus proteins J Immunol 169 210 219 12077247 1:CAS:528:DC%2BD38XltVKisr4%3D (Pubitemid 34686138)
56. M Moutaftsi B Peters V Pasquetto D Tscharke J Sidney H Bui H Grey A Sette 2006 A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus Nat Biotechnol 24 817 819 10.1038/nbt1215 16767078 10.1038/nbt1215 1:CAS:528:DC%2BD28XmvFans74%3D (Pubitemid 44086622)
57. TK Naruse Z Chen R Yanagida T Yamashita Y Saito K Mori H Akari Y Yasutomi M Miyazawa T Matano A Kimura 2010 Diversity of MHC class I genes in Burmese-origin rhesus macaques Immunogenetics 62 601 611 10.1007/s00251-010- 0462-z 20640416 10.1007/s00251-010-0462-z 1:CAS:528:DC%2BC3cXhtVyls7jN
58. M Oberste M Gonda 1992 Conservation of amino-acid sequence motifs in lentivirus Vif proteins Virus Genes 6 95 102 1312756 10.1007/BF01703760 1:CAS:528:DyaK38Xlt1Klt78%3D
59. DH O'Connor T Allen T Vogel P Jing I Desouza E Dodds E Dunphy C Melsaether B Mothe H Yamamoto H Horton N Wilson A Hughes D Watkins 2002 Acute phase cytotoxic T lymphocyte escape is a hallmark of simian immunodeficiency virus infection Nat Med 8 493 499 10.1038/nm0502-493 11984594 10.1038/nm0502-493 (Pubitemid 34546752)
60. DH O'Connor A Mcdermott K Krebs E Dodds J Miller E Gonzalez T Jacoby L Yant H Piontkivska R Pantophlet D Burton W Rehrauer N Wilson A Hughes D Watkins 2004 A dominant role for CD8+-T-lymphocyte selection in simian immunodeficiency virus sequence variation J Virol 78 14012 14022 10.1128/JVI.78.24.14012-14022. 2004 15564508 10.1128/JVI.78.24.14012-14022.2004 (Pubitemid 39612797)
61. G Ogg X Jin S Bonhoeffer P Dunbar M Nowak S Monard J Segal Y Cao SL Rowland-Jones V Cerundolo A Hurley M Markowitz DD Ho D Nixon A Mcmichael 1998 Quantitation of HIV-1-specific cytotoxic T lymphocytes and plasma load of viral RNA Science 279 2103 2106 9516110 10.1126/science.279.5359.2103 1:CAS:528:DyaK1cXitFGksrg%3D (Pubitemid 28196353)
62. N Otting AJ De Vos-Rouweler C Heijmans NG De Groot G Doxiadis R Bontrop 2007 MHC class I A region diversity and polymorphism in macaque species Immunogenetics 59 367 375 10.1007/s00251-007-0201-2 17334754 10.1007/s00251-007-0201-2 1:CAS:528:DC%2BD2sXjslOntbs%3D (Pubitemid 46537502)
63. N Otting A Morner R Bontrop 2011 Novel major histocompatibility complex class I alleles extracted from two rhesus macaque populations Tissue Antigens 77 79 80 10.1111/j.1399-0039.2010.01565.x 20946193 10.1111/j.1399-0039.2010.01565. x 1:CAS:528:DC%2BC3MXhtlOmu78%3D
64. B Peters H Bui S Frankild M Nielson C Lundegaard E Kostem D Basch K Lamberth M Harndahl W Fleri S Wilson J Sidney O Lund S Buus A Sette 2006 A community resource benchmarking predictions of peptide binding to MHC-I molecules PLoS Comput Biol 2 e65 10.1371/journal.pcbi.0020065 16789818 10.1371/journal.pcbi.0020065 (Pubitemid 43990673)
65. FW Peyerl D Barouch W Yeh H Bazick J Kunstman K Kunstman S Wolinsky NL Letvin 2003 Simian-human immunodeficiency virus escape from cytotoxic T-lymphocyte recognition at a structurally constrained epitope J Virol 77 12572 12578 14610180 10.1128/JVI.77.23.12572-12578.2003 1:CAS:528:DC%2BD3sXptFOjsr0%3D (Pubitemid 37430653)
66. R Phillips S Rowland-Jones D Nixon F Gotch J Edwards A Ogunlesi J Elvin J Rothbard C Bangham C Rizza A Et 1991 Human immunodeficiency virus genetic variation that can escape cytotoxic T cell recognition Nature 354 453 459 10.1038/354453a0 1721107 10.1038/354453a0 1:CAS:528:DyaK38XjvFGlug%3D%3D (Pubitemid 21896855)
67. C Pinilla J Appel P Blanc R Houghten 1992 Rapid identification of high affinity peptide ligands using positional scanning synthetic peptide combinatorial libraries Biotechniques 13 901 905 1476743 1:CAS:528: DyaK3sXhsVGgt7s%3D
68. DA Price P Goulder P Klenerman A Sewell P Easterbrook M Troop C Bangham R Phillips 1997 Positive selection of HIV-1 cytotoxic T lymphocyte escape variants during primary infection Proc Natl Acad Sci USA 94 1890 1895 9050875 10.1073/pnas.94.5.1890 1:CAS:528:DyaK2sXhslejsr0%3D (Pubitemid 27113932)
69. H Rammensee T Friede S Stevanoviic 1995 MHC ligands and peptide motifs: first listing Immunogenetics 41 178 228 7890324 10.1007/BF00172063 1:CAS:528:DyaK2MXlvVemu7g%3D
70. K Reimann K Tenner-Racz P Racz D Montefiori Y Yasutomi W Lin B Ransil N Letvin 1994 Immunopathogenic events in acute infection of rhesus monkeys with simian immunodeficiency virus of macaques J Virol 68 2362 2370 8139022 1:STN:280:DyaK2c7oslSktQ%3D%3D (Pubitemid 24091915)
71. J Ruppert J Sidney E Celis R Kubo H Grey A Sette 1993 Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules Cell 74 929 937 8104103 10.1016/0092-8674(93)90472-3 1:CAS:528:DyaK3sXms1yns7k%3D (Pubitemid 23270612)
72. JB Sacha C Chung J Reed A Jonas A Bean S Spencer W Lee L Vojnov R Rudersdorf T Friedrich NA Wilson JD Lifson DI Watkins 2007 Pol-specific CD8+ T cells recognize simian immunodeficiency virus-infected cells prior to Nef-mediated major histocompatibility complex class I downregulation J Virol 81 11703 11712 10.1128/JVI.00926-07 17699580 10.1128/JVI.00926-07 1:CAS:528:DC%2BD2sXht1aisrnI (Pubitemid 47623802)
73. J Sacha M Buechler L Newman J Reed L Wallace J Loffredo N Wilson D Watkins 2010 Simian immunodeficiency virus-specific CD8+ T cells recognize Vpr- and Rev-derived epitopes early after infection J Virol 84 10907 10912 10.1128/JVI.01357-10 20686015 10.1128/JVI.01357-10 1:CAS:528:DC%2BC3cXhtlaku7rF
74. M Salgado A Simon B Sanz-Minguela N Rallon M Lopez J Vicario J Benito B Rodes 2010 An additive effect of protective host genetic factors correlates with HIV-non progression status J Acquir Immune Defic Syndr 10.1097/QAI. 0b013e3182036f14
75. J Schmitz M Kuroda S Santra V Sasseville M Simon M Lifton P Racz K Tenner-Racz M Dalesandro B Scallon J Ghrayeb M Forman D Montefiori E Rieber N Letvin K Reimann 1999 Control of viremia in simian immunodeficiency virus infection by CD8+ lymphocytes Science 283 857 860 9933172 10.1126/science.283. 5403.857 1:CAS:528:DyaK1MXhtFSgurg%3D (Pubitemid 29072328)
76. A Sette J Sidney MF Del Guercio S Southwood J Ruppert C Dahlberg H Grey R Kubo 1994 Peptide binding to the most frequent HLA-A class I alleles measured by quantitative molecular binding assays Mol Immunol 31 813 822 8047072 10.1016/0161-5890(94)90019-1 1:CAS:528:DyaK2cXlsFGjtrk%3D (Pubitemid 24254672)
77. A Sette A Vitiello B Reherman P Fowler R Nayersina W Kast C Melief C Oseroff L Yuan J Ruppert J Sidney MF Del Guercio S Southwood R Kubo R Chesnut H Grey F Chisari 1994 The relationship between class I binding affinity and immunogenicity of potential cytotoxic T cell epitopes J Immunol 153 5586 5592 7527444 1:CAS:528:DyaK2MXis12ksbs%3D (Pubitemid 24377694)
78. A Sette J Sidney H Bui MF Del Guercio J Alexander J Loffredo D Watkins B Mothe 2005 Characterization of the peptide-binding specificity of Mamu-A*11 results in the identification of SIV-derived epitopes and interspecies cross-reactivity Immunogenetics 57 53 68 10.1007/s00251-004-0749-z 15747117 10.1007/s00251-004-0749-z 1:CAS:528:DC%2BD2MXjtlartbY%3D (Pubitemid 40598019)
79. J Sidney S Southwood MF Del Guercio H Grey RW Chesnut R Kubo A Sette 1996 Specificity and degeneracy in peptide binding to HLA-B7-like class I molecules J Immunol 157 3480 3490 8871647 1:CAS:528:DyaK28Xmtlant7Y%3D (Pubitemid 126449161)
80. J Sidney JL Dzuris M Newman R Johnson A Kaur K Amitinder C Walker E Appella B Mothe D Watkins A Sette 2000 Definition of the Mamu A*01 peptide binding specificity: application to the identification of wild-type and optimized ligands from simian immunodeficiency virus regulatory proteins J Immunol 165 6387 6399 11086077 1:CAS:528:DC%2BD3cXosFOhs7w%3D
81. Sidney J, Southwood S, Oseroff C, Del Guercio MF, Sette A, Grey H (2001) Measurement of MHC/peptide interactions by gel filtration. Curr Protoc Immunol Chapter 18:Unit 18.3. doi: 10.1002/0471142735.im1803s31
82. J Sidney B Peters C Moore T Pencille S Ngo K Masterman S Asabe C Pinilla F Chisari A Sette 2007 Characterization of the peptide-binding specificity of the chimpanzee class I alleles A 0301 and A 0401 using a combinatorial peptide library Immunogenetics 59 745 751 10.1007/s00251-007-0243-5 17701407 10.1007/s00251-007-0243-5 1:CAS:528:DC%2BD2sXhtVCnsrvL (Pubitemid 47415567)
83. J Sidney E Assarsson C Moore S Ngo C Pinilla A Sette B Peters 2008a Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries Immunome Res 4 2 10.1186/1745-7580-4-2 10.1186/1745-7580-4-2 (Pubitemid 351278399)
84. J Sidney B Peters N Frahm C Brander A Sette 2008b HLA class I supertypes: a revised and updated classification BMC Immunol 9 1 10.1186/1471-2172-9-1 10.1186/1471-2172-9-1 (Pubitemid 351283143)
85. H Soudeyns S Paolucci C Chappey M Daucher C Graziosi M Vaccarezza O Cohen A Fauci G Pantaleo 1999 Selective pressure exerted by immunodominant HIV-1-specific cytotoxic T lymphocyte responses during primary infection drives genetic variation restricted to the cognate epitope Eur J Immunol 29 3629 3635 10.1002/(SICI)1521-4141(199911)29:11<3629::AID-IMMU3629>3.0.CO;2-O 10556818 10.1002/(SICI)1521-4141(199911)29:11<3629::AID-IMMU3629>3.0.CO;2- O 1:CAS:528:DyaK1MXnt1Ogtbw%3D (Pubitemid 29527811)
86. E Stephens D Singh E Pacyniak C Mccormick 2001 Comparison of Vif sequences from diverse geographical isolates of HIV type 1 and SIV(cpz) identifies substitutions common to subtype C isolates and extensive variation in a proposed nuclear transport inhibition signal AIDS Res Hum Retroviruses 17 169 177 10.1089/08892220150217256 11177396 10.1089/08892220150217256 1:CAS:528:DC%2BD3MXhtFCnt78%3D (Pubitemid 32099301)
87. A Stryhn L Pedersen T Romme C Holm A Holm S Buus 1996 Peptide binding specificity of major histocompatibility complex class I resolved into an array of apparently independent subspecificities: quantitation by peptide libraries and improved prediction of binding Eur J Immunol 26 1911 1918 10.1002/eji.1830260836 8765039 10.1002/eji.1830260836 1:CAS:528: DyaK28XkvVOhsLc%3D (Pubitemid 26283169)
88. J Tang S Tang E Lobashevsky A Myracle U Fideli G Aldrovandi S Allen R Musonda R Kaslow 2002 Favorable and unfavorable HLA class I alleles and haplotypes in Zambians predominantly infected with clade C human immunodeficiency virus type 1 J Virol 76 8276 8284 12134033 10.1128/JVI.76.16. 8276-8284.2002 1:CAS:528:DC%2BD38XlslOksb0%3D (Pubitemid 34809082)
89. K Udaka K Wiesmuller S Kienle G Jung P Walden 1995 Decrypting the structure of major histocompatibility complex class I-restricted cytotoxic T lymphocyte epitopes with complex peptide libraries J Exp Med 181 2097 2108 7539039 10.1084/jem.181.6.2097 1:CAS:528:DyaK2MXlvFSjtLk%3D
90. K Udaka K Wiesmuller S Kienle G Jung H Tamamura H Yamagishi K Okumura P Walden T Suto T Kawasaki 2000 An automated prediction of MHC class I-binding peptides based on positional scanning with peptide libraries Immunogenetics 51 816 828 10970096 10.1007/s002510000217 1:CAS:528:DC%2BD3cXmvFOqsrk%3D (Pubitemid 30612045)
91. J Urvater N Otting J Loehrke R Rudersdorf I Slukvin M Piekarczyk T Golos A Hughes R Bontrop D Watkins 2000 Mamu-I: a novel primate MHC class I B-related locus with unusually low variability J Immunol 164 1386 1398 10640754 1:CAS:528:DC%2BD3cXot1Gruw%3D%3D (Pubitemid 30067253)
92. CA Van Baalen M Schutten R Huisman P Boers R Gruters A Osterhaus 1998 Kinetics of antiviral activity by human immunodeficiency virus type 1-specific cytotoxic T lymphocytes (CTL) and rapid selection of CTL escape virus in vitro J Virol 72 6851 6857 9658134 (Pubitemid 28324005)
93. GM Van Bleek S Nathenson 1990 Isolation of an endogenously processed immunodominant viral peptide from the class I H-2Kb molecule Nature 348 213 216 10.1038/348213a0 1700303 10.1038/348213a0 (Pubitemid 20383086)
94. T Vogel T Friedrich DH O'Connor W Rehrauer E Dodds H Hickman W Hildebrand J Sidney A Sette A Hughes H Horton K Vielhuber R Rudersdorf IP De Souza M Reynolds T Allen N Wilson D Watkins 2002 Escape in one of two cytotoxic T-lymphocyte epitopes bound by a high-frequency major histocompatibility complex class I molecule, Mamu-A*02: a paradigm for virus evolution and persistence? J Virol 76 11623 11636 12388723 10.1128/JVI.76.22.11623-11636.2002 1:CAS:528:DC%2BD38XoslKjt7w%3D (Pubitemid 35231318)
95. CC Wilson R Brown B Korber B Wilkes D Ruhl D Sakamoto K Kunstman K Luzuriaga I Hanson S Widmayer A Wiznia S Clapp A Ammann R Koup S Wolinsky B Walker 1999 Frequent detection of escape from cytotoxic T-lymphocyte recognition in perinatal human immunodeficiency virus (HIV) type 1 transmission: the ariel project for the prevention of transmission of HIV from mother to infant J Virol 73 3975 3985 10196293 1:CAS:528:DyaK1MXis1entrs%3D (Pubitemid 29189842)
96. N Wilson J Reed G Napoe S Piaskowski A Szymanski J Furlott E Gonzalez L Yant N Maness G May T Soma M Reynolds E Rakasz R Rudersdorf A Mcdermott DH O'Connor T Friedrich D Allison A Patki L Picker D Burton J Lin L Huang D Patel G Heindecker J Fan M Citron M Horton F Wang X Liang J Shiver D Casimiro D Watkins 2006 Vaccine-induced cellular immune responses reduce plasma viral concentrations after repeated low-dose challenge with pathogenic simian immunodeficiency virus SIVmac239 J Virol 80 5875 5885 10.1128/JVI.00171-06
97. NA Wilson B Keele J Reed S Piaskowski C Macnair A Bett X Liang F Wang E Thoryk G Heidecker M Citron L Huang J Lin S Vitelli C Ahn M Kaizu N Maness M Reynolds T Friedrich J Loffredo E Rakasz S Erickson D Allison MJ Piatak J Lifson J Shiver D Casimiro G Shaw B Hahn D Watkins 2009 Vaccine-induced cellular responses control simian immunodeficiency virus replication after heterologous challenge J Virol 83 6508 6521 10.1128/JVI.00272-09 19403685 10.1128/JVI.00272-09 1:CAS:528:DC%2BD1MXnvF2lt7c%3D
98. S Wolinsky B Korber A Neumann M Daniels K Kunstman A Whetsell M Furtado Y Cao DD Ho J Safrit 1996 Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection Science 272 537 542 8614801 10.1126/science.272.5261.537 1:CAS:528:DyaK28XisFOmsbc%3D (Pubitemid 26138195)
99. LJ Yant T Friedrich R Johnson G May N Maness A Enz J Lifson DH O'Connor M Carrington D Watkins 2006 The high-frequency major histocompatibility complex class I allele Mamu-B*17 is associated with control of simian immunodeficiency virus SIVmac239 replication J Virol 80 5074 5077 10.1128/JVI.80.10.5074-5077.2006 16641299 10.1128/JVI.80.10.5074-5077.2006 1:CAS:528:DC%2BD28XkslChurg%3D
100. Y Yasutomi K Reimann C Lord M Miller N Letvin 1993 Simian immunodeficiency virus-specific CD8+ lymphocyte response in acutely infected rhesus monkeys J Virol 67 1707 1711 8437240 1:CAS:528:DyaK3sXhs1Ohu7g%3D (Pubitemid 23067685)