Viral escape from neutralizing antibodies in early subtype A HIV-1 infection drives an increase in autologous neutralization breadth

Antibodies that neutralize (nAbs) genetically diverse HIV-1 strains have been recovered from a subset of HIV-1 infected subjects during chronic infection. Exact mechanisms that expand the otherwise narrow neutralization capacity observed during early infection are, however, currently undefined. Here...

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Published inPLoS pathogens Vol. 9; no. 2; p. e1003173
Main Authors Murphy, Megan K, Yue, Ling, Pan, Ruimin, Boliar, Saikat, Sethi, Anurag, Tian, Jianhui, Pfafferot, Katja, Karita, Etienne, Allen, Susan A, Cormier, Emmanuel, Goepfert, Paul A, Borrow, Persephone, Robinson, James E, Gnanakaran, S, Hunter, Eric, Kong, Xiang-Peng, Derdeyn, Cynthia A
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 01.02.2013
Public Library of Science (PLoS)
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Abstract Antibodies that neutralize (nAbs) genetically diverse HIV-1 strains have been recovered from a subset of HIV-1 infected subjects during chronic infection. Exact mechanisms that expand the otherwise narrow neutralization capacity observed during early infection are, however, currently undefined. Here we characterized the earliest nAb responses in a subtype A HIV-1 infected Rwandan seroconverter who later developed moderate cross-clade nAb breadth, using (i) envelope (Env) glycoproteins from the transmitted/founder virus and twenty longitudinal nAb escape variants, (ii) longitudinal autologous plasma, and (iii) autologous monoclonal antibodies (mAbs). Initially, nAbs targeted a single region of gp120, which flanked the V3 domain and involved the alpha2 helix. A single amino acid change at one of three positions in this region conferred early escape. One immunoglobulin heavy chain and two light chains recovered from autologous B cells comprised two mAbs, 19.3H-L1 and 19.3H-L3, which neutralized the founder Env along with one or three of the early escape variants carrying these mutations, respectively. Neither mAb neutralized later nAb escape or heterologous Envs. Crystal structures of the antigen-binding fragments (Fabs) revealed flat epitope contact surfaces, where minimal light chain mutation in 19.3H-L3 allowed for additional antigenic interactions. Resistance to mAb neutralization arose in later Envs through alteration of two glycans spatially adjacent to the initial escape signatures. The cross-neutralizing nAbs that ultimately developed failed to target any of the defined V3-proximal changes generated during the first year of infection in this subject. Our data demonstrate that this subject's first recognized nAb epitope elicited strain-specific mAbs, which incrementally acquired autologous breadth, and directed later B cell responses to target distinct portions of Env. This immune re-focusing could have triggered the evolution of cross-clade antibodies and suggests that exposure to a specific sequence of immune escape variants might promote broad humoral responses during HIV-1 infection.
AbstractList Antibodies that neutralize (nAbs) genetically diverse HIV-1 strains have been recovered from a subset of HIV-1 infected subjects during chronic infection. Exact mechanisms that expand the otherwise narrow neutralization capacity observed during early infection are, however, currently undefined. Here we characterized the earliest nAb responses in a subtype A HIV-1 infected Rwandan seroconverter who later developed moderate cross-clade nAb breadth, using (i) envelope (Env) glycoproteins from the transmitted/founder virus and twenty longitudinal nAb escape variants, (ii) longitudinal autologous plasma, and (iii) autologous monoclonal antibodies (mAbs). Initially, nAbs targeted a single region of gp120, which flanked the V3 domain and involved the alpha2 helix. A single amino acid change at one of three positions in this region conferred early escape. One immunoglobulin heavy chain and two light chains recovered from autologous B cells comprised two mAbs, 19.3H-L1 and 19.3H-L3, which neutralized the founder Env along with one or three of the early escape variants carrying these mutations, respectively. Neither mAb neutralized later nAb escape or heterologous Envs. Crystal structures of the antigen-binding fragments (Fabs) revealed flat epitope contact surfaces, where minimal light chain mutation in 19.3H-L3 allowed for additional antigenic interactions. Resistance to mAb neutralization arose in later Envs through alteration of two glycans spatially adjacent to the initial escape signatures. The cross-neutralizing nAbs that ultimately developed failed to target any of the defined V3-proximal changes generated during the first year of infection in this subject. Our data demonstrate that this subject's first recognized nAb epitope elicited strain-specific mAbs, which incrementally acquired autologous breadth, and directed later B cell responses to target distinct portions of Env. This immune re-focusing could have triggered the evolution of cross-clade antibodies and suggests that exposure to a specific sequence of immune escape variants might promote broad humoral responses during HIV-1 infection.
Antibodies that neutralize (nAbs) genetically diverse HIV-1 strains have been recovered from a subset of HIV-1 infected subjects during chronic infection. Exact mechanisms that expand the otherwise narrow neutralization capacity observed during early infection are, however, currently undefined. Here we characterized the earliest nAb responses in a subtype A HIV-1 infected Rwandan seroconverter who later developed moderate cross-clade nAb breadth, using (i) envelope (Env) glycoproteins from the transmitted/founder virus and twenty longitudinal nAb escape variants, (ii) longitudinal autologous plasma, and (iii) autologous monoclonal antibodies (mAbs). Initially, nAbs targeted a single region of gp120, which flanked the V3 domain and involved the alpha2 helix. A single amino acid change at one of three positions in this region conferred early escape. One immunoglobulin heavy chain and two light chains recovered from autologous B cells comprised two mAbs, 19.3H-L1 and 19.3H-L3, which neutralized the founder Env along with one or three of the early escape variants carrying these mutations, respectively. Neither mAb neutralized later nAb escape or heterologous Envs. Crystal structures of the antigen-binding fragments (Fabs) revealed flat epitope contact surfaces, where minimal light chain mutation in 19.3H-L3 allowed for additional antigenic interactions. Resistance to mAb neutralization arose in later Envs through alteration of two glycans spatially adjacent to the initial escape signatures. The cross-neutralizing nAbs that ultimately developed failed to target any of the defined V3-proximal changes generated during the first year of infection in this subject. Our data demonstrate that this subject's first recognized nAb epitope elicited strain-specific mAbs, which incrementally acquired autologous breadth, and directed later B cell responses to target distinct portions of Env. This immune re-focusing could have triggered the evolution of cross-clade antibodies and suggests that exposure to a specific sequence of immune escape variants might promote broad humoral responses during HIV-1 infection. Since cases were first recognized in the United States in 1981, human immunodeficiency virus (HIV-1) has infected over one million Americans. Globally, this scale reaches into the tens of millions, but no effective vaccine exists. Of those infected, approximately 20–30% of patients will develop broadly neutralizing antibodies. The reasons for maturation of these potentially protective responses are presently unknown, but being able to elicit such antibodies via vaccination could curb the pandemic. Here, we defined the earliest neutralizing antibody targets and the consequent routes of viral escape in one subtype A HIV-1 infected subject who developed modest breadth. We also determined the genetic and structural characteristics of early neutralizing monoclonal antibodies circulating in this subject and found that subtle light chain alteration enhanced target contact and neutralization. Overall, our data support the idea that exposure to a specific sequence of viral variants, which have escaped from immune pressure, could program long-term potential for antibody breadth.
Author Goepfert, Paul A
Pfafferot, Katja
Pan, Ruimin
Sethi, Anurag
Tian, Jianhui
Allen, Susan A
Karita, Etienne
Borrow, Persephone
Robinson, James E
Yue, Ling
Kong, Xiang-Peng
Hunter, Eric
Cormier, Emmanuel
Murphy, Megan K
Derdeyn, Cynthia A
Boliar, Saikat
Gnanakaran, S
AuthorAffiliation 6 Projet San Francisco, Kigali, Rwanda
10 Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
2 Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
7 Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
9 International AIDS Vaccine Initiative, Human Immunology Laboratory, Imperial College, London, United Kingdom
3 Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
4 Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
8 Departments of Epidemiology and Global Health, Emory University, Atlanta, Georgia, United States of America
University of Zurich, Switzerland
1 Immunology and Molecular Pathogenesis Graduate Program, Emory University, Atla
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Cites_doi 10.1371/journal.ppat.1001251
10.1128/JVI.76.14.7293-7305.2002
10.1073/pnas.1006498107
10.1089/aid.2010.0030
10.1371/journal.ppat.1000594
10.1128/JVI.02660-07
10.1126/science.1207227
10.1128/JVI.00198-11
10.1128/JVI.02036-08
10.1128/JVI.06973-11
10.1107/S0907444904019158
10.1016/j.virol.2006.10.017
10.1038/nature05580
10.1016/S0076-6879(97)76066-X
10.1073/pnas.0912914107
10.1038/nm.2985
10.1126/science.1093137
10.1056/NEJMoa1113425
10.1038/nature07159
10.1128/CVI.00131-10
10.1002/prot.21123
10.1016/S0021-9673(01)87461-6
10.1128/JVI.79.16.10108-10125.2005
10.1128/JVI.75.22.10892-10905.2001
10.1126/science.1118398
10.1128/JVI.02286-10
10.1126/science.1213782
10.4049/jimmunol.147.5.1709
10.1038/nature01470
10.1107/S0907444909042589
10.1038/nature10766
10.1371/journal.ppat.1000598
10.1128/JVI.02419-10
10.1128/JVI.00201-06
10.1016/j.molimm.2008.09.005
10.1128/JVI.01839-06
10.1128/JVI.76.14.7306-7321.2002
10.1371/journal.ppat.1000274
10.1038/nsmb.1861
10.1016/S0969-2126(00)00547-5
10.1016/j.jim.2007.09.017
10.1016/j.str.2009.09.012
10.1128/JVI.73.7.5255-5264.1999
10.1073/pnas.0911004107
10.1038/nprot.2009.3
10.1371/journal.ppat.1002721
10.1128/JVI.02335-10
10.1107/S0907444902016657
10.1089/088922202753747914
10.1016/j.str.2011.02.012
10.1016/j.virol.2010.04.010
10.1128/JVI.00110-09
10.1073/pnas.0630530100
10.1016/j.virol.2006.05.011
10.1107/S0907444910045749
10.1086/514243
10.1016/j.pep.2005.09.022
10.1016/j.jviromet.2009.02.014
10.1002/jcc.20289
10.1371/journal.pone.0023532
10.1002/jcc.540150503
10.1128/JVI.05312-11
10.1128/JVI.05045-11
10.1126/science.1192819
10.1126/science.1207532
10.1038/nature10373
10.1128/JVI.02006-10
10.1098/rstb.2011.0096
10.1371/journal.pone.0025606
10.1126/science.1213256
10.1097/QAD.0b013e32805e8727
10.1002/jcc.20820
10.1128/JVI.00257-07
10.1128/JVI.01730-06
10.1073/pnas.0308527100
10.1038/nature10696
10.1073/pnas.0901474106
10.1126/science.1178746
10.1093/bioinformatics/btk004
10.1371/journal.pone.0027780
10.1016/j.virol.2009.11.032
10.1038/nature11544
10.1128/JVI.02187-07
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DocumentTitleAlternate NAbs in Early Subtype A HIV-1 Infection
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The authors have declared that no competing interests exist.
Conceived and designed the experiments: MKM CAD XPK PB PAG LY EH JER. Performed the experiments: MKM RP SB LY KP. Analyzed the data: MKM CAD XPK AS JT SG PB PAG EH. Contributed reagents/materials/analysis tools: JER EC SAA EK XPK RP. Wrote the manuscript: MKM CAD XPK JER SG. Contributed to participant recruitment, follow-up, and field site management: SAA EK EC.
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References R Rong (ref58) 2007; 81
T Zhou (ref7) 2010; 329
L Morris (ref10) 2011; 6
A Changela (ref44) 2011; 85
MD Simek (ref18) 2009; 83
PL Moore (ref28) 2009; 5
B Li (ref37) 2006; 80
R Pejchal (ref8) 2011; 334
CC Huang (ref22) 2004; 101
LM Walker (ref76) 2009; 326
X Wei (ref27) 2003; 422
MA Price (ref48) 2011; 27
CN Scanlan (ref35) 2002; 76
EA Kabat (ref33) 1991; 147
T Zhou (ref65) 2007; 445
KN Kirschner (ref70) 2008; 29
HX Liao (ref72) 2009; 158
KJ Bar (ref25) 2012; 8
M Pancera (ref66) 2010; 107
V Hornak (ref69) 2006; 65
DD Richman (ref26) 2003; 100
JF Salazar-Gonzalez (ref49) 2008; 82
DN Sather (ref20) 2009; 83
K Smith (ref75) 2009; 4
X Wu (ref13) 2011; 333
M Bonsignori (ref40) 2011; 85
I Mikell (ref16) 2011; 7
MB Zwick (ref9) 2001; 75
R Rong (ref29) 2009; 5
N Eswar (ref61) 2006; 5
V Burke (ref79) 2009; 17
RE Haaland (ref47) 2009; 5
A Vagin (ref81) 2010; 66
E Falkowska (ref5) 2012; 86
PL Moore (ref36) 2007; 82
MK Gorny (ref42) 2009; 46
CA Blish (ref50) 2007; 21
ES Gray (ref17) 2011; 85
ref80
J Huang (ref11) 2012; 491
R Rong (ref60) 2007; 81
PD Adams (ref84) 2002; 58
RW Sanders (ref34) 2002; 76
CA Derdeyn (ref57) 2004; 303
L Verkoczy (ref19) 2010; 107
KA Bosch (ref30) 2009; 398
T Tiller (ref74) 2008; 329
RM Lynch (ref31) 2011; 85
M Li (ref53) 2005; 79
R Diskin (ref43) 2011; 334
R Abagyan (ref85) 1994; 15
EM Long (ref51) 2002; 18
KJ Doores (ref68) 2010; 107
J Liu (ref67) 2008; 455
LM Walker (ref6) 2011; 477
V Racanelli (ref21) 2011; 6
MK Gorny (ref41) 2011; 6
RM Benoit (ref73) 2006; 45
JS McLellan (ref12) 2011; 480
H Tang (ref38) 2011; 85
PL Moore (ref24) 2012; 18
DC Malherbe (ref46) 2011; 85
DL Kothe (ref55) 2006; 352
B Spurrier (ref78) 2011; 19
SA Plotkin (ref1) 2010; 17
ref23
HW Lahm (ref71) 1985; 326
KS MacDonald (ref45) 1998; 177
RM Lynch (ref59) 2010; 404
DH Barouch (ref3) 2012; 482
M Li (ref56) 2006; 80
BF Haynes (ref2) 2012; 366
JC Phillips (ref62) 2005; 26
L Song (ref14) 2009; 106
Z Zhu (ref39) 2011; 85
JM Volpe (ref32) 2006; 22
PD Kwong (ref63) 2000; 8
JF Scheid (ref15) 2011; 333
P Emsley (ref83) 2004; 60
DL Kothe (ref54) 2007; 360
MD Winn (ref82) 2011; 67
GJ Nabel (ref4) 2011; 366
M Poss (ref52) 1999; 73
X Jiang (ref77) 2010; 17
CC Huang (ref64) 2005; 310
References_xml – volume: 7
  start-page: e1001251
  year: 2011
  ident: ref16
  article-title: Characteristics of the earliest cross-neutralizing antibody response to HIV-1
  publication-title: PLoS Pathog
  doi: 10.1371/journal.ppat.1001251
  contributor:
    fullname: I Mikell
– volume: 76
  start-page: 7293
  year: 2002
  ident: ref34
  article-title: The mannose-dependent epitope for neutralizing antibody 2G12 on human immunodeficiency virus type 1 glycoprotein gp120
  publication-title: J Virol
  doi: 10.1128/JVI.76.14.7293-7305.2002
  contributor:
    fullname: RW Sanders
– volume: 107
  start-page: 13800
  year: 2010
  ident: ref68
  article-title: Envelope glycans of immunodeficiency virions are almost entirely oligomannose antigens
  publication-title: Proc Natl Acad Sci U S A
  doi: 10.1073/pnas.1006498107
  contributor:
    fullname: KJ Doores
– volume: 27
  start-page: 5
  year: 2011
  ident: ref48
  article-title: Transmitted HIV type 1 drug resistance among individuals with recent HIV infection in East and Southern Africa
  publication-title: AIDS Res Hum Retroviruses
  doi: 10.1089/aid.2010.0030
  contributor:
    fullname: MA Price
– volume: 5
  start-page: e1000594
  year: 2009
  ident: ref29
  article-title: Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways
  publication-title: PLoS Pathog
  doi: 10.1371/journal.ppat.1000594
  contributor:
    fullname: R Rong
– volume: 5
  start-page: Unit 5 6
  year: 2006
  ident: ref61
  article-title: Comparative protein structure modeling using Modeller
  publication-title: Curr Protoc Bioinformatics Chapter
  contributor:
    fullname: N Eswar
– volume: 82
  start-page: 3952
  year: 2008
  ident: ref49
  article-title: Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing
  publication-title: J Virol
  doi: 10.1128/JVI.02660-07
  contributor:
    fullname: JF Salazar-Gonzalez
– volume: 333
  start-page: 1633
  year: 2011
  ident: ref15
  article-title: Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding
  publication-title: Science
  doi: 10.1126/science.1207227
  contributor:
    fullname: JF Scheid
– volume: 85
  start-page: 4828
  year: 2011
  ident: ref17
  article-title: The neutralization breadth of HIV-1 develops incrementally over four years and is associated with CD4+ T cell decline and high viral load during acute infection
  publication-title: J Virol
  doi: 10.1128/JVI.00198-11
  contributor:
    fullname: ES Gray
– volume: 83
  start-page: 757
  year: 2009
  ident: ref20
  article-title: Factors associated with the development of cross-reactive neutralizing antibodies during human immunodeficiency virus type 1 infection
  publication-title: J Virol
  doi: 10.1128/JVI.02036-08
  contributor:
    fullname: DN Sather
– volume: 86
  start-page: 4394
  year: 2012
  ident: ref5
  article-title: PGV04, an HIV-1 gp120 CD4 Binding Site Antibody, Is Broad and Potent in Neutralization but Does Not Induce Conformational Changes Characteristic of CD4
  publication-title: J Virol
  doi: 10.1128/JVI.06973-11
  contributor:
    fullname: E Falkowska
– volume: 60
  start-page: 2126
  year: 2004
  ident: ref83
  article-title: Coot: model-building tools for molecular graphics
  publication-title: Acta Crystallogr D Biol Crystallogr
  doi: 10.1107/S0907444904019158
  contributor:
    fullname: P Emsley
– volume: 360
  start-page: 218
  year: 2007
  ident: ref54
  article-title: Antigenicity and immunogenicity of HIV-1 consensus subtype B envelope glycoproteins
  publication-title: Virology
  doi: 10.1016/j.virol.2006.10.017
  contributor:
    fullname: DL Kothe
– volume: 445
  start-page: 732
  year: 2007
  ident: ref65
  article-title: Structural definition of a conserved neutralization epitope on HIV-1 gp120
  publication-title: Nature
  doi: 10.1038/nature05580
  contributor:
    fullname: T Zhou
– ident: ref80
  doi: 10.1016/S0076-6879(97)76066-X
– volume: 107
  start-page: 181
  year: 2010
  ident: ref19
  article-title: Autoreactivity in an HIV-1 broadly reactive neutralizing antibody variable region heavy chain induces immunologic tolerance
  publication-title: Proc Natl Acad Sci U S A
  doi: 10.1073/pnas.0912914107
  contributor:
    fullname: L Verkoczy
– volume: 18
  start-page: 1688
  year: 2012
  ident: ref24
  article-title: Evolution of an HIV glycan-dependent broadly neutralizing antibody epitope through immune escape
  publication-title: Nat Med
  doi: 10.1038/nm.2985
  contributor:
    fullname: PL Moore
– volume: 303
  start-page: 2019
  year: 2004
  ident: ref57
  article-title: Envelope-Constrained Neutralization-Sensitive HIV-1 After Heterosexual Transmission
  publication-title: Science
  doi: 10.1126/science.1093137
  contributor:
    fullname: CA Derdeyn
– volume: 366
  start-page: 1275
  year: 2012
  ident: ref2
  article-title: Immune-correlates analysis of an HIV-1 vaccine efficacy trial
  publication-title: N Engl J Med
  doi: 10.1056/NEJMoa1113425
  contributor:
    fullname: BF Haynes
– volume: 455
  start-page: 109
  year: 2008
  ident: ref67
  article-title: Molecular architecture of native HIV-1 gp120 trimers
  publication-title: Nature
  doi: 10.1038/nature07159
  contributor:
    fullname: J Liu
– volume: 17
  start-page: 1055
  year: 2010
  ident: ref1
  article-title: Correlates of protection induced by vaccination
  publication-title: Clin Vaccine Immunol
  doi: 10.1128/CVI.00131-10
  contributor:
    fullname: SA Plotkin
– volume: 65
  start-page: 712
  year: 2006
  ident: ref69
  article-title: Comparison of multiple Amber force fields and development of improved protein backbone parameters
  publication-title: Proteins
  doi: 10.1002/prot.21123
  contributor:
    fullname: V Hornak
– volume: 326
  start-page: 357
  year: 1985
  ident: ref71
  article-title: Characterization of recombinant human interleukin-2 with micromethods
  publication-title: J Chromatogr
  doi: 10.1016/S0021-9673(01)87461-6
  contributor:
    fullname: HW Lahm
– volume: 79
  start-page: 10108
  year: 2005
  ident: ref53
  article-title: Human immunodeficiency virus type 1 env clones from acute and early subtype B infections for standardized assessments of vaccine-elicited neutralizing antibodies
  publication-title: J Virol
  doi: 10.1128/JVI.79.16.10108-10125.2005
  contributor:
    fullname: M Li
– volume: 75
  start-page: 10892
  year: 2001
  ident: ref9
  article-title: Broadly neutralizing antibodies targeted to the membrane-proximal external region of human immunodeficiency virus type 1 glycoprotein gp41
  publication-title: J Virol
  doi: 10.1128/JVI.75.22.10892-10905.2001
  contributor:
    fullname: MB Zwick
– volume: 310
  start-page: 1025
  year: 2005
  ident: ref64
  article-title: Structure of a V3-containing HIV-1 gp120 core
  publication-title: Science
  doi: 10.1126/science.1118398
  contributor:
    fullname: CC Huang
– volume: 85
  start-page: 9286
  year: 2011
  ident: ref38
  article-title: Epitopes immediately below the base of the V3 loop of gp120 as targets for the initial autologous neutralizing antibody response in two HIV-1 subtype B-infected individuals
  publication-title: J Virol
  doi: 10.1128/JVI.02286-10
  contributor:
    fullname: H Tang
– volume: 334
  start-page: 1289
  year: 2011
  ident: ref43
  article-title: Increasing the potency and breadth of an HIV antibody by using structure-based rational design
  publication-title: Science
  doi: 10.1126/science.1213782
  contributor:
    fullname: R Diskin
– volume: 147
  start-page: 1709
  year: 1991
  ident: ref33
  article-title: Identical V region amino acid sequences and segments of sequences in antibodies of different specificities. Relative contributions of VH and VL genes, minigenes, and complementarity-determining regions to binding of antibody-combining sites
  publication-title: J Immunol
  doi: 10.4049/jimmunol.147.5.1709
  contributor:
    fullname: EA Kabat
– volume: 422
  start-page: 307
  year: 2003
  ident: ref27
  article-title: Antibody Neutralization and Escape by HIV-1
  publication-title: Nature
  doi: 10.1038/nature01470
  contributor:
    fullname: X Wei
– volume: 66
  start-page: 22
  year: 2010
  ident: ref81
  article-title: Molecular replacement with MOLREP
  publication-title: Acta Crystallogr D Biol Crystallogr
  doi: 10.1107/S0907444909042589
  contributor:
    fullname: A Vagin
– volume: 482
  start-page: 89
  year: 2012
  ident: ref3
  article-title: Vaccine protection against acquisition of neutralization-resistant SIV challenges in rhesus monkeys
  publication-title: Nature
  doi: 10.1038/nature10766
  contributor:
    fullname: DH Barouch
– volume: 5
  start-page: e1000598
  year: 2009
  ident: ref28
  article-title: Limited neutralizing antibody specificities drive neutralization escape in early HIV-1 subtype C infection
  publication-title: PLoS Pathog
  doi: 10.1371/journal.ppat.1000598
  contributor:
    fullname: PL Moore
– ident: ref23
– volume: 85
  start-page: 5262
  year: 2011
  ident: ref46
  article-title: Sequential immunization with a subtype B HIV-1 envelope quasispecies partially mimics the in vivo development of neutralizing antibodies
  publication-title: J Virol
  doi: 10.1128/JVI.02419-10
  contributor:
    fullname: DC Malherbe
– volume: 80
  start-page: 5211
  year: 2006
  ident: ref37
  article-title: Evidence for potent autologous neutralizing antibody titers and compact envelopes in early infection with subtype C human immunodeficiency virus type 1
  publication-title: J Virol
  doi: 10.1128/JVI.00201-06
  contributor:
    fullname: B Li
– volume: 46
  start-page: 917
  year: 2009
  ident: ref42
  article-title: Preferential use of the VH5-51 gene segment by the human immune response to code for antibodies against the V3 domain of HIV-1
  publication-title: Mol Immunol
  doi: 10.1016/j.molimm.2008.09.005
  contributor:
    fullname: MK Gorny
– volume: 81
  start-page: 1350
  year: 2007
  ident: ref58
  article-title: Role of V1V2 and other human immunodeficiency virus type 1 envelope domains in resistance to autologous neutralization during clade C infection
  publication-title: J Virol
  doi: 10.1128/JVI.01839-06
  contributor:
    fullname: R Rong
– volume: 76
  start-page: 7306
  year: 2002
  ident: ref35
  article-title: 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
  publication-title: J Virol
  doi: 10.1128/JVI.76.14.7306-7321.2002
  contributor:
    fullname: CN Scanlan
– volume: 5
  start-page: e1000274
  year: 2009
  ident: ref47
  article-title: Inflammatory genital infections mitigate a severe genetic bottleneck in heterosexual transmission of subtype A and C HIV-1
  publication-title: PLoS Pathog
  doi: 10.1371/journal.ppat.1000274
  contributor:
    fullname: RE Haaland
– volume: 17
  start-page: 955
  year: 2010
  ident: ref77
  article-title: Conserved structural elements in the V3 crown of HIV-1 gp120
  publication-title: Nat Struct Mol Biol
  doi: 10.1038/nsmb.1861
  contributor:
    fullname: X Jiang
– volume: 8
  start-page: 1329
  year: 2000
  ident: ref63
  article-title: Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates
  publication-title: Structure Fold Des
  doi: 10.1016/S0969-2126(00)00547-5
  contributor:
    fullname: PD Kwong
– volume: 329
  start-page: 112
  year: 2008
  ident: ref74
  article-title: Efficient generation of monoclonal antibodies from single human B cells by single cell RT-PCR and expression vector cloning
  publication-title: J Immunol Methods
  doi: 10.1016/j.jim.2007.09.017
  contributor:
    fullname: T Tiller
– volume: 17
  start-page: 1538
  year: 2009
  ident: ref79
  article-title: Structural basis of the cross-reactivity of genetically related human anti-HIV-1 mAbs: implications for design of V3-based immunogens
  publication-title: Structure
  doi: 10.1016/j.str.2009.09.012
  contributor:
    fullname: V Burke
– volume: 73
  start-page: 5255
  year: 1999
  ident: ref52
  article-title: Variants from the diverse virus population identified at seroconversion of a clade A human immunodeficiency virus type 1-infected woman have distinct biological properties
  publication-title: J Virol
  doi: 10.1128/JVI.73.7.5255-5264.1999
  contributor:
    fullname: M Poss
– volume: 107
  start-page: 1166
  year: 2010
  ident: ref66
  article-title: Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility
  publication-title: Proc Natl Acad Sci U S A
  doi: 10.1073/pnas.0911004107
  contributor:
    fullname: M Pancera
– volume: 4
  start-page: 372
  year: 2009
  ident: ref75
  article-title: Rapid generation of fully human monoclonal antibodies specific to a vaccinating antigen
  publication-title: Nat Protoc
  doi: 10.1038/nprot.2009.3
  contributor:
    fullname: K Smith
– volume: 8
  start-page: e1002721
  year: 2012
  ident: ref25
  article-title: Early Low-Titer Neutralizing Antibodies Impede HIV-1 Replication and Select for Virus Escape
  publication-title: PLoS Pathog
  doi: 10.1371/journal.ppat.1002721
  contributor:
    fullname: KJ Bar
– volume: 85
  start-page: 2524
  year: 2011
  ident: ref44
  article-title: Crystal structure of human antibody 2909 reveals conserved features of quaternary structure-specific antibodies that potently neutralize HIV-1
  publication-title: J Virol
  doi: 10.1128/JVI.02335-10
  contributor:
    fullname: A Changela
– volume: 58
  start-page: 1948
  year: 2002
  ident: ref84
  article-title: PHENIX: building new software for automated crystallographic structure determination
  publication-title: Acta Crystallogr D Biol Crystallogr
  doi: 10.1107/S0907444902016657
  contributor:
    fullname: PD Adams
– volume: 18
  start-page: 567
  year: 2002
  ident: ref51
  article-title: HIV type 1 variants transmitted to women in Kenya require the CCR5 coreceptor for entry, regardless of the genetic complexity of the infecting virus
  publication-title: AIDS Res Hum Retroviruses
  doi: 10.1089/088922202753747914
  contributor:
    fullname: EM Long
– volume: 19
  start-page: 691
  year: 2011
  ident: ref78
  article-title: Structural analysis of human and macaque mAbs 2909 and 2.5B: implications for the configuration of the quaternary neutralizing epitope of HIV-1 gp120
  publication-title: Structure
  doi: 10.1016/j.str.2011.02.012
  contributor:
    fullname: B Spurrier
– volume: 404
  start-page: 59
  year: 2010
  ident: ref59
  article-title: Subtype-specific conservation of isoleucine 309 in the envelope V3 domain is linked to immune evasion in subtype C HIV-1 infection
  publication-title: Virology
  doi: 10.1016/j.virol.2010.04.010
  contributor:
    fullname: RM Lynch
– volume: 83
  start-page: 7337
  year: 2009
  ident: ref18
  article-title: Human immunodeficiency virus type 1 elite neutralizers: individuals with broad and potent neutralizing activity identified by using a high-throughput neutralization assay together with an analytical selection algorithm
  publication-title: J Virol
  doi: 10.1128/JVI.00110-09
  contributor:
    fullname: MD Simek
– volume: 100
  start-page: 4144
  year: 2003
  ident: ref26
  article-title: Rapid evolution of the neutralizing antibody response to HIV type 1 infection
  publication-title: Proc Natl Acad Sci U S A
  doi: 10.1073/pnas.0630530100
  contributor:
    fullname: DD Richman
– volume: 352
  start-page: 438
  year: 2006
  ident: ref55
  article-title: Ancestral and consensus envelope immunogens for HIV-1 subtype C
  publication-title: Virology
  doi: 10.1016/j.virol.2006.05.011
  contributor:
    fullname: DL Kothe
– volume: 67
  start-page: 235
  year: 2011
  ident: ref82
  article-title: Overview of the CCP4 suite and current developments
  publication-title: Acta Crystallogr D Biol Crystallogr
  doi: 10.1107/S0907444910045749
  contributor:
    fullname: MD Winn
– volume: 177
  start-page: 551
  year: 1998
  ident: ref45
  article-title: Mother-child class I HLA concordance increases perinatal human immunodeficiency virus type 1 transmission
  publication-title: J Infect Dis
  doi: 10.1086/514243
  contributor:
    fullname: KS MacDonald
– volume: 45
  start-page: 66
  year: 2006
  ident: ref73
  article-title: An improved method for fast, robust, and seamless integration of DNA fragments into multiple plasmids
  publication-title: Protein Expr Purif
  doi: 10.1016/j.pep.2005.09.022
  contributor:
    fullname: RM Benoit
– volume: 158
  start-page: 171
  year: 2009
  ident: ref72
  article-title: High-throughput isolation of immunoglobulin genes from single human B cells and expression as monoclonal antibodies
  publication-title: J Virol Methods
  doi: 10.1016/j.jviromet.2009.02.014
  contributor:
    fullname: HX Liao
– volume: 26
  start-page: 1781
  year: 2005
  ident: ref62
  article-title: Scalable molecular dynamics with NAMD
  publication-title: J Comput Chem
  doi: 10.1002/jcc.20289
  contributor:
    fullname: JC Phillips
– volume: 6
  start-page: e23532
  year: 2011
  ident: ref10
  article-title: Isolation of a human anti-HIV gp41 membrane proximal region neutralizing antibody by antigen-specific single B cell sorting
  publication-title: PLoS One
  doi: 10.1371/journal.pone.0023532
  contributor:
    fullname: L Morris
– volume: 15
  start-page: 488
  year: 1994
  ident: ref85
  article-title: ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
  publication-title: J Comput Chem
  doi: 10.1002/jcc.540150503
  contributor:
    fullname: R Abagyan
– volume: 85
  start-page: 11401
  year: 2011
  ident: ref39
  article-title: Cross-reactive HIV-1-neutralizing human monoclonal antibodies identified from a patient with 2F5-like antibodies
  publication-title: J Virol
  doi: 10.1128/JVI.05312-11
  contributor:
    fullname: Z Zhu
– volume: 85
  start-page: 9998
  year: 2011
  ident: ref40
  article-title: Analysis of a clonal lineage of HIV-1 envelope V2/V3 conformational epitope-specific broadly neutralizing antibodies and their inferred unmutated common ancestors
  publication-title: J Virol
  doi: 10.1128/JVI.05045-11
  contributor:
    fullname: M Bonsignori
– volume: 329
  start-page: 811
  year: 2010
  ident: ref7
  article-title: Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01
  publication-title: Science
  doi: 10.1126/science.1192819
  contributor:
    fullname: T Zhou
– volume: 333
  start-page: 1593
  year: 2011
  ident: ref13
  article-title: Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing
  publication-title: Science
  doi: 10.1126/science.1207532
  contributor:
    fullname: X Wu
– volume: 477
  start-page: 466
  year: 2011
  ident: ref6
  article-title: Broad neutralization coverage of HIV by multiple highly potent antibodies
  publication-title: Nature
  doi: 10.1038/nature10373
  contributor:
    fullname: LM Walker
– volume: 85
  start-page: 905
  year: 2011
  ident: ref31
  article-title: The B cell response is redundant and highly focused on V1V2 during early subtype C infection in a Zambian seroconverter
  publication-title: J Virol
  doi: 10.1128/JVI.02006-10
  contributor:
    fullname: RM Lynch
– volume: 366
  start-page: 2759
  year: 2011
  ident: ref4
  article-title: Progress in the rational design of an AIDS vaccine
  publication-title: Philos Trans R Soc Lond B Biol Sci
  doi: 10.1098/rstb.2011.0096
  contributor:
    fullname: GJ Nabel
– volume: 6
  start-page: e25606
  year: 2011
  ident: ref21
  article-title: Antibody V(h) repertoire differences between resolving and chronically evolving hepatitis C virus infections
  publication-title: PLoS One
  doi: 10.1371/journal.pone.0025606
  contributor:
    fullname: V Racanelli
– volume: 334
  start-page: 1097
  year: 2011
  ident: ref8
  article-title: A potent and broad neutralizing antibody recognizes and penetrates the HIV glycan shield
  publication-title: Science
  doi: 10.1126/science.1213256
  contributor:
    fullname: R Pejchal
– volume: 21
  start-page: 693
  year: 2007
  ident: ref50
  article-title: HIV-1 subtype A envelope variants from early in infection have variable sensitivity to neutralization and to inhibitors of viral entry
  publication-title: Aids
  doi: 10.1097/QAD.0b013e32805e8727
  contributor:
    fullname: CA Blish
– volume: 29
  start-page: 622
  year: 2008
  ident: ref70
  article-title: GLYCAM06: a generalizable biomolecular force field. Carbohydrates
  publication-title: J Comput Chem
  doi: 10.1002/jcc.20820
  contributor:
    fullname: KN Kirschner
– volume: 81
  start-page: 5658
  year: 2007
  ident: ref60
  article-title: Unique Mutational Patterns in the Envelope {alpha}2 Amphipathic Helix and Acquisition of Length in gp120 Hyper-variable Domains are Associated with Resistance to Autologous Neutralization of Subtype C Human Immunodeficiency Virus type 1
  publication-title: J Virol
  doi: 10.1128/JVI.00257-07
  contributor:
    fullname: R Rong
– volume: 80
  start-page: 11776
  year: 2006
  ident: ref56
  article-title: 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
  publication-title: J Virol
  doi: 10.1128/JVI.01730-06
  contributor:
    fullname: M Li
– volume: 101
  start-page: 2706
  year: 2004
  ident: ref22
  article-title: Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120
  publication-title: Proc Natl Acad Sci U S A
  doi: 10.1073/pnas.0308527100
  contributor:
    fullname: CC Huang
– volume: 480
  start-page: 336
  year: 2011
  ident: ref12
  article-title: Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9
  publication-title: Nature
  doi: 10.1038/nature10696
  contributor:
    fullname: JS McLellan
– volume: 106
  start-page: 9057
  year: 2009
  ident: ref14
  article-title: Broadly neutralizing anti-HIV-1 antibodies disrupt a hinge-related function of gp41 at the membrane interface
  publication-title: Proc Natl Acad Sci U S A
  doi: 10.1073/pnas.0901474106
  contributor:
    fullname: L Song
– volume: 326
  start-page: 285
  year: 2009
  ident: ref76
  article-title: Broad and potent neutralizing antibodies from an African donor reveal a new HIV-1 vaccine target
  publication-title: Science
  doi: 10.1126/science.1178746
  contributor:
    fullname: LM Walker
– volume: 22
  start-page: 438
  year: 2006
  ident: ref32
  article-title: SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btk004
  contributor:
    fullname: JM Volpe
– volume: 6
  start-page: e27780
  year: 2011
  ident: ref41
  article-title: Human Anti-V3 HIV-1 Monoclonal Antibodies Encoded by the VH5-51/VL Lambda Genes Define a Conserved Antigenic Structure
  publication-title: PLoS One
  doi: 10.1371/journal.pone.0027780
  contributor:
    fullname: MK Gorny
– volume: 398
  start-page: 115
  year: 2009
  ident: ref30
  article-title: Temporal analysis of HIV envelope sequence evolution and antibody escape in a subtype A-infected individual with a broad neutralizing antibody response
  publication-title: Virology
  doi: 10.1016/j.virol.2009.11.032
  contributor:
    fullname: KA Bosch
– volume: 491
  start-page: 406
  year: 2012
  ident: ref11
  article-title: Broad and potent neutralization of HIV-1 by a gp41-specific human antibody
  publication-title: Nature
  doi: 10.1038/nature11544
  contributor:
    fullname: J Huang
– volume: 82
  start-page: 1860
  year: 2007
  ident: ref36
  article-title: The C3-V4 Region Is a Major Target of Autologous Neutralizing Antibodies in Hiv-1 Subtype C Infection
  publication-title: J Virol
  doi: 10.1128/JVI.02187-07
  contributor:
    fullname: PL Moore
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Snippet Antibodies that neutralize (nAbs) genetically diverse HIV-1 strains have been recovered from a subset of HIV-1 infected subjects during chronic infection....
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StartPage e1003173
SubjectTerms Amino Acid Sequence
Antibodies, Neutralizing - chemistry
Antibodies, Neutralizing - immunology
Antibodies, Viral - immunology
Biology
Cross Reactions - immunology
Female
HIV Infections - immunology
HIV Infections - virology
HIV Seropositivity - immunology
HIV Seropositivity - virology
HIV-1 - immunology
Humans
Immune Evasion - immunology
Immunoglobulin Heavy Chains - immunology
Immunoglobulin Light Chains - immunology
Male
Medicine
Molecular Sequence Data
Protein Structure, Tertiary
Sequence Alignment
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Title Viral escape from neutralizing antibodies in early subtype A HIV-1 infection drives an increase in autologous neutralization breadth
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