Spatiotemporal hierarchy in antibody recognition against transmitted HIV-1 envelope glycoprotein during natural infection
© Jin et al. 2016
Received: 17 September 2015
Accepted: 4 February 2016
Published: 17 February 2016
Majority of HIV-1 infection is established by one transmitted/founder virus and understanding how the neutralizing antibodies develop against this virus is critical for our rational design an HIV-1 vaccine.
We report here antibody profiling of sequential plasma samples against transmitted/founder HIV-1 envelope glycoprotein in an epidemiologically linked transmission pair using our previously reported antigen library approach. We have decomposed the antibody recognition into three major subdomains on the envelope and showed their development in vivo followed a spatiotemporal hierarchy: starting with the ectodomain of gp41 at membrane proximal region, then the V3C3V4 and the V1V2 of gp120 at the membrane distal region. While antibodies to these subdomains appeared to undergo avidity maturation, the early anti-gp41 antibodies failed to translate into detectable autologous neutralization. Instead, it was the much delayed anti-V3C3V4 and anti-V1V2 antibodies constituted the major neutralizing activities.
Our results indicate that the initial antibody response was severely misguided by the transmitted/founder virus and future vaccine design would need to avoid the ectodomain of gp41 and focus on the neutralizing targets in the V3C3V4 and V1V2 subdomains of gp120.
KeywordsHIV Transmission Antibody Vaccine
Neutralizing antibodies are the major component of protective immunity against viral infection in humans. Polyclonal by nature, they exert their function by targeting the crucial antigenic domains on the viral envelop glycoprotein. Identifying the neutralizing antibodies and their recognized antigenic domains have therefore become the first crucial step for better understanding of the protective antibody response and the rational design of immunogens capable of eliciting the neutralizing antibodies [1–5]. In human immunodeficiency virus type I (HIV-1) infection, viral glycoprotein gp160 that mediates infection of CD4+ T lymphocytes is the sole target for neutralizing antibodies. The gp160 is composed of exterior, receptor-binding gp120 and the fusion-mediating, transmembrane gp41 subunits. The unique feature of gp160 is its extensive glycosylation and genetic diversity manifested by rapid generation and high turnover of viral variants during infection . Sequence and structural analysis has revealed the glycosylation and mutations are largely distributed in the hypervarible regions V1–V5 on the exterior surface of gp160 and function to protect the virus from antibody recognition and neutralization [1–5, 7, 8].
Majority of HIV-1 infection is established by one transmitted/founder virus with distinct genetic and phenotypic properties compared to those in the later stages of infection [9–12]. The development of neutralizing antibodies against this virus, however, follows an unusual pathway of inefficiency [2, 4, 13–18]. Most of the antibodies generated during the first few weeks lack neutralizing activities but reactive to gp41 as well as some non-HIV-1 antigens [19–21]. Only after a few months into the infection, autologous neutralizing antibodies become detectable, largely directed to gp120 and invariably strain-specific [4, 13, 14, 22]. Cross-reactive and broadly neutralizing antibodies (bnAbs) capable of neutralizing heterologous viruses across many genetic subtypes can only be generated after years into the infection and most notably in individuals who remain healthy despite prolonged period of infection [1–5, 15, 23]. Isolation and characterization of bnAbs from these individuals have identified five major targets on the gp160. These include the CD4-binding site (CD4bs), the glycan-associated V1V2 and V3/C3 subdomains of gp120, the membrane proximal external regions (MPER) of gp41, and the interface between gp120 and gp41 [1–5, 15]. But how exactly the autologous and bnAbs are generated during the course of HIV-1 infection remain largely unknown. Several elegant studies highlighted the critical role of interplay between viral evolution and antibody development. At the monoclonal levels, germline ancestors for neutralizing antibodies require stimulation by evolving or incoming viral variants during infection [24–29]. Different B cell lineages within the same individuals also appeared to work in concert to drive the development of neutralizing antibodies . At the polyclonal levels, however, dissecting the mechanism underlying the development of neutralizing antibodies is much more complex as polyclonal antibodies function through a dynamic and complex mixture of monoclonal antibodies with diverse targets on the gp160. Studies based on short peptides, chimeric and epitope-specific mutant viruses have identified a few subdomains of gp120 are the major targets for neutralizing activities in polyclonal sera [30–33]. However, the detailed understanding on the scope, specificities and dynamic features of polyclonal antibody recognition against the transmitted/founder virus remain elusive.
Here, we report antibody profiling of sequential plasma samples against transmitted/founder HIV-1 envelope glycoprotein in an epidemiologically linked transmission pair. Using our previously reported approach based on combinatorial antigen library displayed on the surface of the yeast Saccharomyces cerevisiae, we were able to delineate polyclonal antibody recognition in both qualitative and quantitative terms . Through sequential analysis of plasma-reactive antigenic sequences over the first 2 years of infection, we decomposed the polyclonal antibody recognition into three major subdomains and showed their development in vivo followed spatiotemporal hierarchy: starting at the ectodomain of gp41, then at the V3C3V4 and V1V2 of gp120. While antibodies to all three subdomains appeared to undergo avidity maturation, the early anti-gp41 antibodies demonstrated no detectable autologous neutralization and only those delayed anti-V3C3V4 and anti-V1V2 antibodies constituted the major neutralizing activities. Our results indicate that the initial antibody response was severely misguided by the transmitted/founder virus and future vaccine design would need to avoid the ectodomain of gp41 and focus on the neutralizing targets in the V3C3V4 and V1V2 subdomains of gp120.
Construction and validation of combinatorial antigen library from the transmitted HIV-1 envelopes
Neutralization sensitivity of transmitted/founder P08 and P11 pseudoviruses to various bnAbs
Spatiotemporal hierarchy in antibody development against distinct subdomains of HIV-1 envelope during natural infection
Avidity maturation of antibody recognition against distinct subdomains of HIV-1 envelope during natural infection
V3C3V4 and V1V2 but not gp41 contain the major targets for autologous neutralization
We report here the systematic characterization of antibody recognition against transmitted/founder HIV-1 envelope glycoprotein during natural infection in an epidemiologically linked transmission pair infected by highly homologous CRF01_AE strains. Based on several complementary approaches to determine the specificities of binding as well as neutralizing antibodies, we were able to decompose the complex plasma antibody recognition into three discrete subdomains on the HIV-1 envelope: ectodomain of gp41, V3C3V4 and V1V2 of gp120. The development of these subdomain-specific antibodies appeared to follow a spatiotemporal hierarchy with distinct dynamic, biochemical and neutralizing properties. While antibodies to all three subdomains appeared to undergo avidity maturation, the early and strong anti-gp41 antibodies failed to translate into detectable autologous neutralization. Instead, it was the much delayed anti-V3C3V4 and anti-V1V2 antibodies constituted the major neutralizing activities. In particular, it reinforced the early discoveries in that the majority of the initial antibody response was severely misguided by the transmitted/founder virus towards its gp41 subdomain and therefore missed the most critical window of opportunity to contain or clear the virus replication through recognizing the neutralizing epitopes in the V3C3V4 and V1V2 subdomains [19, 20]. By the time when the neutralizing antibody response was indeed mounted in a substantial manner, it was much too late and virus had already established its permanent residence in the target cells. Such defects in mistargeting and mistiming have provided some explanations for the failure of human immune system to contain viral replication during early infection, and strongly recommend that future vaccine design would need to avoid the ectodomain of gp41 and focus more on those neutralizing targets in the V3C3V4 and V1V2 subdomains of gp120.
At the current stage, we are uncertain about the underlying mechanisms leading to the spatiotemporal hierarchy for antibody recognition against the three major envelope subdomains. The overwhelming response against gp41 during early infection could be due to the pre-existing gp41 cross-reactive memory B cells that acquired reactivity with autologous gp41 [19, 44, 45]. A recent study showing majority of gut-derived anti-gp41 antibodies cross-reacted with commensal bacteria supports this hypothesis . It could also be due to the shedding of gp120 leading to the exposure of preferred structures during early infection although the exact step and timing of such preference during viral replication are currently unknown. Generally speaking, gp41 exhibits at least three distinct conformational states during the viral fusion process: the prefusion, the prehairpin intermediate, and the postfusion conformation. It is believed that the conformational differences among the three states are so great that each of them likely presents distinct antigenic surface to the immune system [46–48]. So far, only the prehairpin intermediate was found to be the target of bnAbs such as 2F5, 4E10 and 10E8 while the other two states were largely recognized by non-neutralizing antibodies. In particular, the non-neutralizing antibodies against gp41 appeared to group in two clusters based on the location of their respective epitopes. Cluster I antibodies recognize the immunodominant C–C loop of gp41 (aa590–600), and the cluster II antibodies react with the downstream immunodominant segment (aa644–663) [46–49]. But whether the two clusters of antibodies specifically react with prefusion and postfusion conformation remain to be determined. As the antibody recognition found in our study subjects overlapped with cluster I antibodies, the conformational state against which they were initially generated was unlikely to be the prehairpin intermediate. Whatever the conformational state was recognized, it must be the one to be avoided in our vaccine design to prevent non-neutralizing epitopes as well as severe misguidance and mistiming found during natural infection.
Neutralizing activity of P08 and P11 plasma samples against a panel of pseudoviruses with distinct genotypic and phenotypic features from China and abroad
Our study has unraveled the complex and dynamic feature of antibody development against transmitted/founder HIV-1 envelope glycoprotein during natural infection. The major binding and neutralizing antigenic subdomains identified here will provide critical reference for our better understanding of the spatiotemporal feature of protective antibody response during natural infection and assist our rational design of vaccines that will empower the strengths while minimize the weaknesses of human immune recognition.
Study subjects and plasma samples
Two acutely infected individuals, P08 and P11, were chosen for the study. P08 was 37 and P11 38 years old when identified through China’s largest acute infection cohort for man who have sex with man (MSM) that followed several thousands of high risk individuals over the last decade. P08 and P11 were epidemiologically linked transmission pair and P08 infected P11 during acute infection based on epidemiologic and clinic documentation. When enrolled on day 30 after infection for P08 and day 18 for P11, both individuals were negative for HIV-1 antibody measured by enzyme-linked immunosorbent assay (ELISA) and indeterminate Western blot test, and therefore fell into Fiebig II-IV substage of acute infection . P08 and P11 had baseline CD4 lymphocyte count of 339 and 369 per cubic millimeter (FACS Calibur, BD) and plasma viral load of 30,600 and 889,000 RNA copies per milliliter (Cobas AmpliPrep/Cobas TaqMan HIV-1 version 5.1 Assay, Roche), respectively. Both individuals progressed to diseases relatively fast and by 2 years into the infection, the CD4 lymphocyte count dropped to 147 for P08 and 181 for P11 per cubic millimeter and plasma viral load remained as high as 12,500 for P08 and 40,429 for P11 RNA copies per milliliter. Sequential plasma and peripheral blood mononuclear cells (PBMCs) were collected over the first 2 years of infection and stored at −80 °C until use. Neither P08 nor P11 received any antiretroviral therapy during the study period. This study was reviewed and approved by the institutional research ethics committee at the No. 1 Hospital of China Medical University in Shenyang, Liaoning Province, China.
Full-length envelopes, phylogenetic analysis, pseudoviruses and neutralization assay
The full-length envelope genes from P08 (P08-gp160) and P11 (P11-gp160) were obtained through PCR amplification of single HIV-1 RNA molecules directly from the plasma samples. The reference envelopes from subtype A (KER2018.11 and RW020.2), subtype B (JRFL, Bal.01, YU2.DG) and subtype C (ZA012.29, ZM106.9, ZM55.28a) were kindly provided by John Mascola of Vaccine Research Center at National Institute of Health (NIH). The representative envelopes from HIV-1 infected individuals in China came from our previously studies including those from CRF01_AE, subtype B′, subtype B′C, and CRF07_BC and CRF_08BC. These full-length envelope sequences were aligned using the Clustal W program together with selected subtypes/CRFs of geographical importance from the Genbank database. Phylogenetic analysis was conducted using the neighbor-joining method and the reliability of the branching orders was tested by bootstrap analysis of 1000 replicates .
These envelope clones were also used to generate pseudoviruses by co-transfection with backbone construct pNL43R-E-luciferase into the 293 cells. Forty-eight hours later, the culture supernatant containing the pseudoviruses was collected and tested for luciferase activity to standardize viral input in the subsequent neutralization analysis. Neutralizing activities of plasma samples from P08 and P11 and neutralizing sensitivity of P08 and P11 pseudoviruses to various bnAbs were analyzed as previously described . In brief, 100 TCID50 of pseudoviruses was incubated with serially diluted plasma, or various bnAb in a 96-well plate in triplicate for 1 h at 37 °C. Approximately 2 × 104 TZM-bl cells were then added and the cultures were maintained for an additional 48 h at 37 °C. Neutralizing activity was measured by the reduction in luciferase activity compared with controls (Bright-Glo luciferase assay system, E2650, Promega). Half-maximal inhibitory concentrations or dilutions (IC50 or ID50) were reported as the concentration for bnAbs or dilution for plasma required to inhibit infection by 50 % compared with the controls. The values were calculated using the dose–response inhibition model with a variable slope in GraphPad Prism, version 5.0 (GraphPad Software Inc., La Jolla, CA, USA). The bnAb PG9 and PG16 were kindly provided by Wayne Koff at International AIDS Vaccine Initiative (IAVI), VRC01 by John Mascola of Vaccine Research Center at NIH, 3BNC117 by Michel Nussenzweig at Rockefeller University, and Ibalizumab by David Ho at Aaron Diamond AIDS Research Center of Rockefeller University. The rest of the bnAbs were obtained from NIH reference and reagents program.
Generation and verification of envelope chimeras
Chimeric gp160 envelopes were generated using an overlapping PCR strategy with gp120, gp41, V3C3V4, V1V2 subdomains amplified separately and then together with the flanking regions from the backbone of CNE6. The resultant envelope chimeras were cloned into the pcDNA3.1 (Invitrogen), verified by sequencing before used for pseudovirus production. Sensitivity of chimeric pseudoviruses to plasma neutralization was measured as described above.
Construction and expression of transmitted/founder HIV-1 envelope combinatorial libraries on the surface of yeast Saccharomyces cerevisiae
Construction of yeast library displaying the combinatorial antigens was carried out as described previously . In brief, the full-length P08 and P11 envelope gene from the day 30 and day 18 after infection, respectively, was amplified by single molecule PCR, purified (QIAquick DNA purification kit, QIAGEN) and digested by DNase I into fragments about 50 base pair (bp) in length. The digested fragments were reassembled to approximately 100–600 bp fragments through controlled number of PCR cycles, added A-tails (DNA A-tailing kit, TAKARA) and ligated to the modified yeast surface displayed vector pCTCON2-T. The ligation products were transformed into the Escherichia coli competent cells, amplified, extracted and then further transformed into the competent yeast cell line EBY100 using electroporation. Transformed yeast cells were partially spread on SDCAA Amp plates and incubated overnight at 30 °C to estimate the number and insert sequences of colonies for quality control purpose. Conditions for yeast growing and induction of surface antigen expression in solution have been previously described . In short, EBY100 yeasts were first grown in SDCAA media at 30 °C for 48 h. At the exponential growth phase, yeasts were transferred to SGCAA media for induction of antigen expression at 20 °C for 48 h before incubating with either plasma samples or monoclonal antibodies for subsequent analysis .
Immunofluorescence staining, sorting, sequencing and sequence analysis of bnAb- or plasma-reactive yeast clones by FACS
The entire procedure was conducted as previously described . Induced yeast cells (106–107) were collected by centrifugation (6000 rmp/s, 1 min), washed twice with cold PBS and incubated with either bnAb or patient plasma (1:100 dilution) on ice for 1 h with occasional agitation. After washed three times with cold PBS, the cells were incubated with PE labeled anti-human IgG secondary antibody (1:200 dilution, rabbit anti-human IgG-PE, Santa Cruz) on ice for another 45 min, washed again with PBS for three times, analyzed and sorted for positive clones using FACS Aria II (BD, USA). The positive yeast clones were grown in SDCAA before plasmids were extracted (Yeast plasmid kit, Omega Bio-Tek) for sequencing and sequence analysis (Sequencher 5.0, Gene Codes Corp.). The most frequently recognized amino acid residues within each subdomain were calculated as over 90 % percentile among the selected fragments for each subdomain.
Measurement of Kd and Ka for each antigenic subdomain
The technique relies on measuring the MFI of the bound polyclonal antibodies, at and variety of concentrations of polyclonal antibodies, on the c-myc positive yeast . Specifically, four representative yeast clones were selected from each envelope subdomain based on their coverage and mixed in equal proportion (106 cells) before incubated with a serial 1:3 dilution of sequential plasma samples from P08 and P11. After washed twice with cold PBS, the mixture was resuspended in PE labeled anti-human secondary antibody (1:200 dilution, rabbit anti-human IgG-PE, Santa Cruz) and incubated for another hour. Antibody recognition of yeast clones expressing the distinct envelope subdomains were detected by FACS. The MFI was recorded, plotted and fitted using a nonlinear least square curve against the reciprocal plasma dilution. Kd value was determined using the following equation: y = MFImax × Plasmadilution−1/(Kd + Plasmadilution−1). Ka is the reciprocal of Kd.
Measurement of plasma binding to trimeric and monomeric gp120 and gp140 by ELISA
Trimeric ectodomain of NL4-3 (subtype B) constructed based on BG505 SOSIP.664  was kindly provided by Dr. Yi Shi at Institute of Microbiology, Chinese Academy of Sciences. Monomeric gp120 and monomeric gp140 (CRF01_AE) derived from a CRF01_AE circulating strain CM235 (Genebank #: AAG28611) isolated in Thailand in year 2000 were purchased and produced from 293T cells (Immune Technology Corp, China). Recombinant envelope glycoprotein was coated overnight at 4 °C on the 96-well plate (100 ng/well), blocked for 2 h at 37 °C with 1 % bovine serum albumin (BSA) in PBS before addition of ten serial threefold dilutions of plasma samples. After incubating for 1 h at 37 °C and three-time thorough washes with PBST (PBS with 0.05 % Tween), the secondary antibody conjugated with horseradish peroxidase (1:4000 dilution, anti-human IgG-HRP, Promega) was added before applying substrate for detectioin. Maximum absorbance at 450 nm and corresponding plasma dilution were recorded (Microplate Reader, Bio-Rad). Plasma samples from HIV-1 negative individuals were included as negative controls.
SJ, YJ, QW, HW, XS, and XH conducted experiments. TZ analyzed the antigenic subdomains in the context of gp160 sequence. HS and LZ designed the study and were involved in writing of the manuscript. All authors read and approved the final manuscript.
We thank Drs. K. Dane Wittrup and Annie Gai at Massachusetts Institute of Technology for providing yeast surface display vector pCTCON2 and Drs. John Mascola of Vaccine Research Center at NIH, Wayne Koff at IAVI, Michel Nussenzweig and David Ho at Rockefeller University for providing bnAbs. We also thank patients for their participation.
The authors declare that they have no competing interests.
This work was supported by the funds from National Natural Science Foundation Award 81530065, the National Science and Technology Major Projects (2012ZX10001-006, -004 and -009), Ministry of Science and Technology of China (2014CB542500-03), also in part by the Tsinghua University Initiative Scientific Research Program (20124812029) and Janssen Investigator Award to Linqi Zhang.
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
- Corti D, Lanzavecchia A. Broadly neutralizing antiviral antibodies. Annu Rev Immunol. 2013;31:705–42.View ArticlePubMedGoogle Scholar
- West AP Jr, Scharf L, Scheid JF, Klein F, Bjorkman PJ, Nussenzweig MC. Structural insights on the role of antibodies in HIV-1 vaccine and therapy. Cell. 2014;156:633–48.PubMed CentralView ArticlePubMedGoogle Scholar
- Burton DR, Mascola JR. Antibody responses to envelope glycoproteins in HIV-1 infection. Nat Immunol. 2015;16:571–6.View ArticlePubMedGoogle Scholar
- Mascola JR, Haynes BF. HIV-1 neutralizing antibodies: understanding natur’s pathways. Immunol Rev. 2013;254:225–44.PubMed CentralView ArticlePubMedGoogle Scholar
- Kwong PD, Mascola JR. Human antibodies that neutralize HIV-1: identification, structures, and B cell ontogenies. Immunity. 2012;37:412–25.PubMed CentralView ArticlePubMedGoogle Scholar
- Simon V, Ho DD. HIV-1 dynamics in vivo: implications for therapy. Nat Rev Microbiol. 2003;1:181–90.View ArticlePubMedGoogle Scholar
- Julien JP, Cupo A, Sok D, Stanfield RL, Lyumkis D, Deller MC, Klasse PJ, Burton DR, Sanders RW, Moore JP, et al. Crystal structure of a soluble cleaved HIV-1 envelope trimer. Science. 2013;342:1477–83.View ArticlePubMedGoogle Scholar
- Pancera M, Zhou T, Druz A, Georgiev IS, Soto C, Gorman J, Huang J, Acharya P, Chuang GY, Ofek G, et al. Structure and immune recognition of trimeric pre-fusion HIV-1 Env. Nature. 2014;514:455–61.PubMed CentralView ArticlePubMedGoogle Scholar
- Zhang LQ, MacKenzie P, Cleland A, Holmes EC, Brown AJ, Simmonds P. Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection. J Virol. 1993;67:3345–56.PubMed CentralPubMedGoogle Scholar
- Keele BF, Giorgi EE, Salazar-Gonzalez JF, Decker JM, Pham KT, Salazar MG, Sun C, Grayson T, Wang S, Li H, et al. Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci USA. 2008;105:7552–7.PubMed CentralView ArticlePubMedGoogle Scholar
- Zhu T, Mo H, Wang N, Nam DS, Cao Y, Koup RA, Ho DD. Genotypic and phenotypic characterization of HIV-1 patients with primary infection. Science. 1993;261:1179–81.View ArticlePubMedGoogle Scholar
- Salazar-Gonzalez JF, Salazar MG, Keele BF, Learn GH, Giorgi EE, Li H, Decker JM, Wang S, Baalwa J, Kraus MH, et al. Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. J Exp Med. 2009;206:1273–89.PubMed CentralView ArticlePubMedGoogle Scholar
- Derdeyn CA, Moore PL, Morris L. Development of broadly neutralizing antibodies from autologous neutralizing antibody responses in HIV infection. Curr Opin HIV AIDS. 2014;9:210–6.PubMed CentralView ArticlePubMedGoogle Scholar
- Moore PL, Gray ES, Morris L. Specificity of the autologous neutralizing antibody response. Curr Opin HIV AIDS. 2009;4:358–63.PubMed CentralView ArticlePubMedGoogle Scholar
- Klein F, Mouquet H, Dosenovic P, Scheid JF, Scharf L, Nussenzweig MC. Antibodies in HIV-1 vaccine development and therapy. Science. 2013;341:1199–204.PubMed CentralView ArticlePubMedGoogle Scholar
- Stamatatos L, Morris L, Burton DR, Mascola JR. Neutralizing antibodies generated during natural HIV-1 infection: good news for an HIV-1 vaccine? Nat Med. 2009;15:866–70.PubMedGoogle Scholar
- Wei X, Decker JM, Wang S, Hui H, Kappes JC, Wu X, Salazar-Gonzalez JF, Salazar MG, Kilby JM, Saag MS, et al. Antibody neutralization and escape by HIV-1. Nature. 2003;422:307–12.View ArticlePubMedGoogle Scholar
- McMichael AJ, Borrow P, Tomaras GD, Goonetilleke N, Haynes BF. The immune response during acute HIV-1 infection: clues for vaccine development. Nat Rev Immunol. 2009;10:11–23.PubMed CentralView ArticlePubMedGoogle Scholar
- Liao HX, Chen X, Munshaw S, Zhang R, Marshall DJ, Vandergrift N, Whitesides JF, Lu X, Yu JS, Hwang KK, et al. Initial antibodies binding to HIV-1 gp41 in acutely infected subjects are polyreactive and highly mutated. J Exp Med. 2011;208:2237–49.PubMed CentralView ArticlePubMedGoogle Scholar
- Tomaras GD, Yates NL, Liu P, Qin L, Fouda GG, Chavez LL, Decamp AC, Parks RJ, Ashley VC, Lucas JT, et al. Initial B-cell responses to transmitted human immunodeficiency virus type 1: virion-binding immunoglobulin M (IgM) and IgG antibodies followed by plasma anti-gp41 antibodies with ineffective control of initial viremia. J Virol. 2008;82:12449–63.PubMed CentralView ArticlePubMedGoogle Scholar
- Trama AM, Moody MA, Alam SM, Jaeger FH, Lockwood B, Parks R, Lloyd KE, Stolarchuk C, Scearce R, Foulger A, et al. HIV-1 envelope gp41 antibodies can originate from terminal ileum B cells that share cross-reactivity with commensal bacteria. Cell Host Microbe. 2014;16:215–26.PubMed CentralView ArticlePubMedGoogle Scholar
- Moore PL, Ranchobe N, Lambson BE, Gray ES, Cave E, Abrahams MR, Bandawe G, Mlisana K, Abdool Karim SS, Williamson C, Morris L. Limited neutralizing antibody specificities drive neutralization escape in early HIV-1 subtype C infection. PLoS Pathog. 2009;5:e1000598.PubMed CentralView ArticlePubMedGoogle Scholar
- Hraber P, Seaman MS, Bailer RT, Mascola JR, Montefiori DC, Korber BT. Prevalence of broadly neutralizing antibody responses during chronic HIV-1 infection. AIDS. 2013;28:163–9.View ArticleGoogle Scholar
- Doria-Rose NA, Schramm CA, Gorman J, Moore PL, Bhiman JN, DeKosky BJ, Ernandes MJ, Georgiev IS, Kim HJ, Pancera M, et al. Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies. Nature. 2014;509:55–62.PubMed CentralView ArticlePubMedGoogle Scholar
- Gao F, Bonsignori M, Liao HX, Kumar A, Xia SM, Lu X, Cai F, Hwang KK, Song H, Zhou T, et al. Cooperation of B cell lineages in induction of HIV-1-broadly neutralizing antibodies. Cell. 2014;158:481–91.PubMed CentralView ArticlePubMedGoogle Scholar
- Liao HX, Lynch R, Zhou T, Gao F, Alam SM, Boyd SD, Fire AZ, Roskin KM, Schramm CA, Zhang Z, et al. Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature. 2013;496:469–76.PubMed CentralView ArticlePubMedGoogle Scholar
- Moore PL, Gray ES, Wibmer CK, Bhiman JN, Nonyane M, Sheward DJ, Hermanus T, Bajimaya S, Tumba NL, Abrahams MR, et al. Evolution of an HIV glycan-dependent broadly neutralizing antibody epitope through immune escape. Nat Med. 2012;18:1688–92.PubMed CentralView ArticlePubMedGoogle Scholar
- Wu X, Zhang Z, Schramm CA, Joyce MG, Do Kwon Y, Zhou T, Sheng Z, Zhang B, O’Dell S, McKee K, et al. Maturation and diversity of the VRC01-antibody lineage over 15 years of chronic HIV-1 infection. Cell. 2015;161:470–85.View ArticlePubMedGoogle Scholar
- Wu X, Zhou T, Zhu J, Zhang B, Georgiev I, Wang C, Chen X, Longo NS, Louder M, McKee K, et al. Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing. Science. 2011;333:1593–602.PubMed CentralView ArticlePubMedGoogle Scholar
- Binley JM, Lybarger EA, Crooks ET, Seaman MS, Gray E, Davis KL, Decker JM, Wycuff D, Harris L, Hawkins N, et al. Profiling the specificity of neutralizing antibodies in a large panel of plasmas from patients chronically infected with human immunodeficiency virus type 1 subtypes B and C. J Virol. 2008;82:11651–68.PubMed CentralView ArticlePubMedGoogle Scholar
- Dhillon AK, Donners H, Pantophlet R, Johnson WE, Decker JM, Shaw GM, Lee FH, Richman DD, Doms RW, Vanham G, Burton DR. Dissecting the neutralizing antibody specificities of broadly neutralizing sera from human immunodeficiency virus type 1-infected donors. J Virol. 2007;81:6548–62.PubMed CentralView ArticlePubMedGoogle Scholar
- Georgiev IS, Doria-Rose NA, Zhou T, Kwon YD, Staupe RP, Moquin S, Chuang GY, Louder MK, Schmidt SD, Altae-Tran HR, et al. Delineating antibody recognition in polyclonal sera from patterns of HIV-1 isolate neutralization. Science. 2013;340:751–6.View ArticlePubMedGoogle Scholar
- Li Y, Svehla K, Louder MK, Wycuff D, Phogat S, Tang M, Migueles SA, Wu X, Phogat A, Shaw GM, et al. Analysis of neutralization specificities in polyclonal sera derived from human immunodeficiency virus type 1-infected individuals. J Virol. 2009;83:1045–59.PubMed CentralView ArticlePubMedGoogle Scholar
- Zuo T, Shi X, Liu Z, Guo L, Zhao Q, Guan T, Pan X, Jia N, Cao W, Zhou B, et al. Comprehensive analysis of pathogen-specific antibody response in vivo based on an antigen library displayed on surface of yeast. J Biol Chem. 2011;286:33511–9.PubMed CentralView ArticlePubMedGoogle Scholar
- Luo K, Li S, Jiang L, Zuo T, Qing J, Shi X, Liu Y, Wu H, Chen X, Zhang L. Combinatorial library-based profiling of the antibody response against hepatitis C virus in humans. J Gen Virol. 2014;96:52–63.View ArticlePubMedGoogle Scholar
- Huang J, Ofek G, Laub L, Louder MK, Doria-Rose NA, Longo NS, Imamichi H, Bailer RT, Chakrabarti B, Sharma SK, et al. Broad and potent neutralization of HIV-1 by a gp41-specific human antibody. Nature. 2012;491:406–12.View ArticlePubMedGoogle Scholar
- McLellan JS, Pancera M, Carrico C, Gorman J, Julien JP, Khayat R, Louder R, Pejchal R, Sastry M, Dai K, et al. Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9. Nature. 2011;480:336–43.PubMed CentralView ArticlePubMedGoogle Scholar
- Zhou T, Zhu J, Wu X, Moquin S, Zhang B, Acharya P, Georgiev IS, Altae-Tran HR, Chuang GY, Joyce MG, et al. Multidonor analysis reveals structural elements, genetic determinants, and maturation pathway for HIV-1 neutralization by VRC01-class antibodies. Immunity. 2013;39:245–58.PubMed CentralView ArticlePubMedGoogle Scholar
- Gnann JW Jr, Schwimmbeck PL, Nelson JA, Truax AB, Oldstone MB. Diagnosis of AIDS by using a 12-amino acid peptide representing an immunodominant epitope of the human immunodeficiency virus. J Infect Dis. 1987;156:261–7.View ArticlePubMedGoogle Scholar
- Zwart G, Langedijk H, van der Hoek L, de Jong JJ, Wolfs TF, Ramautarsing C, Bakker M, de Ronde A, Goudsmit J. Immunodominance and antigenic variation of the principal neutralization domain of HIV-1. Virology. 1991;181:481–9.View ArticlePubMedGoogle Scholar
- Liao HX, Bonsignori M, Alam SM, McLellan JS, Tomaras GD, Moody MA, Kozink DM, Hwang KK, Chen X, Tsao CY, et al. Vaccine induction of antibodies against a structurally heterogeneous site of immune pressure within HIV-1 envelope protein variable regions 1 and 2. Immunity. 2013;38:176–86.PubMed CentralView ArticlePubMedGoogle Scholar
- Sanders RW, Derking R, Cupo A, Julien JP, Yasmeen A, de Val N, Kim HJ, Blattner C, de la Pena AT, Korzun J, et al. A next-generation cleaved, soluble HIV-1 Env trimer, BG505 SOSIP.664 gp140, expresses multiple epitopes for broadly neutralizing but not non-neutralizing antibodies. PLoS Pathog. 2013;9:e1003618.PubMed CentralView ArticlePubMedGoogle Scholar
- Shang H, Han X, Shi X, Zuo T, Goldin M, Chen D, Han B, Sun W, Wu H, Wang X, Zhang L. Genetic and neutralization sensitivity of diverse HIV-1 env clones from chronically infected patients in China. J Biol Chem. 2011;286:14531–41.PubMed CentralView ArticlePubMedGoogle Scholar
- Verkoczy L, Kelsoe G, Haynes BF. HIV-1 envelope gp41 broadly neutralizing antibodies: hurdles for vaccine development. PLoS Pathog. 2014;10:e1004073.PubMed CentralView ArticlePubMedGoogle Scholar
- Yang G, Holl TM, Liu Y, Li Y, Lu X, Nicely NI, Kepler TB, Alam SM, Liao HX, Cain DW, et al. Identification of autoantigens recognized by the 2F5 and 4E10 broadly neutralizing HIV-1 antibodies. J Exp Med. 2013;210:241–56.PubMed CentralView ArticlePubMedGoogle Scholar
- Frey G, Chen J, Rits-Volloch S, Freeman MM, Zolla-Pazner S, Chen B. Distinct conformational states of HIV-1 gp41 are recognized by neutralizing and non-neutralizing antibodies. Nat Struct Mol Biol. 2010;17:1486–91.PubMed CentralView ArticlePubMedGoogle Scholar
- Frey G, Peng H, Rits-Volloch S, Morelli M, Cheng Y, Chen B. A fusion-intermediate state of HIV-1 gp41 targeted by broadly neutralizing antibodies. Proc Natl Acad Sci USA. 2008;105:3739–44.PubMed CentralView ArticlePubMedGoogle Scholar
- Pietzsch J, Scheid JF, Mouquet H, Seaman MS, Broder CC, Nussenzweig MC. Anti-gp41 antibodies cloned from HIV-infected patients with broadly neutralizing serologic activity. J Virol. 2010;84:5032–42.PubMed CentralView ArticlePubMedGoogle Scholar
- Xu JY, Gorny MK, Palker T, Karwowska S, Zolla-Pazner S. Epitope mapping of two immunodominant domains of gp41, the transmembrane protein of human immunodeficiency virus type 1, using ten human monoclonal antibodies. J Virol. 1991;65:4832–8.PubMed CentralPubMedGoogle Scholar
- Moore PL, Gray ES, Choge IA, Ranchobe N, Mlisana K, Abdool Karim SS, Williamson C, Morris L. The c3-v4 region is a major target of autologous neutralizing antibodies in human immunodeficiency virus type 1 subtype C infection. J Virol. 2008;82:1860–9.PubMed CentralView ArticlePubMedGoogle Scholar
- Bar KJ, Tsao CY, Iyer SS, Decker JM, Yang Y, Bonsignori M, Chen X, Hwang KK, Montefiori DC, Liao HX, et al. Early low-titer neutralizing antibodies impede HIV-1 replication and select for virus escape. PLoS Pathog. 2012;8:e1002721.PubMed CentralView ArticlePubMedGoogle Scholar
- Sagar M, Wu X, Lee S, Overbaugh J. Human immunodeficiency virus type 1 V1–V2 envelope loop sequences expand and add glycosylation sites over the course of infection, and these modifications affect antibody neutralization sensitivity. J Virol. 2006;80:9586–98.PubMed CentralView ArticlePubMedGoogle Scholar
- Moore PL, Sheward D, Nonyane M, Ranchobe N, Hermanus T, Gray ES, Abdool Karim SS, Williamson C, Morris L. Multiple pathways of escape from HIV broadly cross-neutralizing V2-dependent antibodies. J Virol. 2013;87:4882–94.PubMed CentralView ArticlePubMedGoogle Scholar
- 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;17:1871–9.View ArticlePubMedGoogle Scholar
- Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–25.PubMedGoogle Scholar
- Feldhaus MJ, Siegel RW, Opresko LK, Coleman JR, Feldhaus JM, Yeung YA, Cochran JR, Heinzelman P, Colby D, Swers J, et al. Flow-cytometric isolation of human antibodies from a nonimmune Saccharomyces cerevisiae surface display library. Nat Biotechnol. 2003;21:163–70.View ArticlePubMedGoogle Scholar