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Analysis of temporal changes in HIV-1 CRF01_AE gag genetic variability and CD8 T-cell epitope evolution. PLoS One 2022; 17:e0267130. [PMID: 35536783 PMCID: PMC9089901 DOI: 10.1371/journal.pone.0267130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 04/02/2022] [Indexed: 11/19/2022] Open
Abstract
Currently, little is known about the time-dependent evolution of human immunodeficiency virus-1 (HIV-1) circulating recombinant forms (CRF) 01_AE, a dominant recombinant form associated with HIV-1 epidemics worldwide. Since gag is a highly immunodominant HIV-1 protein, we performed a comparative analysis of the CRF01_AE gag protein’s time-dependent changes and evolution. A total of 3105 HIV-1 CRF01_AE gag sequences representing 17 countries from the timeline 1990–2017 were obtained. The sequences’ phylogenetic relationship and epidemic dynamics were analyzed through a Maximum Likelihood tree and Bayesian Skyline plot, respectively. Genomic variability was measured through Shannon entropy and time-dependent immunoevolution was analyzed using changes in proteasomal degradation pattern, cytotoxic T lymphocytes (CTL) epitopes, and Human leukocyte antigens (HLA) restriction profile. The most recent common ancestor of the HIV CRF01_AE epidemic was estimated to be 1974±1. A period of exponential growth in effective population size began in 1982, fluctuated, and then stabilized in 1999. Genetic variability (entropy) consistently increased, however, epitope variability remained comparable; the highest number of novel CTL epitopes were present in 1995–1999, which were lost over time. The spread of the HIV-1 CRF01_AE epidemic is predominant in countries within Asia. Population immunogenetic pressures in the region may have contributed to the initial changes and following adaptation/stabilization of epitope diversity within gag sequences.
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Umviligihozo G, Muok E, Nyirimihigo Gisa E, Xu R, Dilernia D, Herard K, Song H, Qin Q, Bizimana J, Farmer P, Hare J, Gilmour J, Allen S, Karita E, Hunter E, Yue L. Increased Frequency of Inter-Subtype HIV-1 Recombinants Identified by Near Full-Length Virus Sequencing in Rwandan Acute Transmission Cohorts. Front Microbiol 2021; 12:734929. [PMID: 34690973 PMCID: PMC8529237 DOI: 10.3389/fmicb.2021.734929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/07/2021] [Indexed: 12/01/2022] Open
Abstract
Most studies of HIV-1 transmission have focused on subtypes B and C. In this study, we determined the genomic sequences of the transmitted founder (TF) viruses from acutely infected individuals enrolled between 2005 and 2011 into IAVI protocol C in Rwanda and have compared these isolates to viruses from more recent (2016–2019) acute/early infections in three at risk populations – MSM, high risk women (HRW), and discordant couples (DC). For the Protocol C samples, we utilized near full-length single genome (NFLG) amplification to generate 288 HIV-1 amplicons from 26 acutely infected seroconverters (SC), while for the 21 recent seroconverter samples (13 from HRW, two from DC, and six from MSM), we PCR amplified overlapping half-genomes. Using PacBio SMRT technology combined with the MDPseq workflow, we performed multiplex sequencing to obtain high accuracy sequences for each amplicon. Phylogenetic analyses indicated that the majority of recent transmitted viruses from DC and HRW clustered within those of the earlier Protocol C cohort. However, five of six sequences from the MSM cohort branched together and were greater than 97% identical. Recombination analyses revealed a high frequency (6/26; 23%) of unique inter-subtype recombination in Protocol C with 19% AC and 4% CD recombinant viruses, which contrasted with only 6.5% of recombinants defined by sequencing of the pol gene previously. The frequency of recombinants was significantly higher (12/21; 57%) in the more recent isolates, although, the five related viruses from the MSM cohort had identical recombination break points. While major drug resistance mutations were absent from Protocol C viruses, 4/21 of recent isolates exhibited transmitted nevirapine resistance. These results demonstrate the ongoing evolution and increased prevalence of recombinant and drug resistant transmitted viruses in Rwanda and highlight the importance of defining NFLG sequences to fully understand the nature of TF viruses and in particular the prevalence of unique recombinant forms (URFs) in transmission cohorts.
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Affiliation(s)
| | - Erick Muok
- Centre for Family Health Research, Kigali, Rwanda
| | | | - Rui Xu
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Dario Dilernia
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Kimberley Herard
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Heeyah Song
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Qianhong Qin
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | | | - Paul Farmer
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | | | - Jill Gilmour
- Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Susan Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | | | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | - Ling Yue
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
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Benureau Y, Colin P, Staropoli I, Gonzalez N, Garcia-Perez J, Alcami J, Arenzana-Seisdedos F, Lagane B. Guidelines for cloning, expression, purification and functional characterization of primary HIV-1 envelope glycoproteins. J Virol Methods 2016; 236:184-195. [PMID: 27451265 DOI: 10.1016/j.jviromet.2016.07.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/13/2016] [Accepted: 07/19/2016] [Indexed: 12/14/2022]
Abstract
The trimeric HIV-1 envelope (Env) glycoproteins gp120 and gp41 mediate virus entry into target cells by engaging CD4 and the coreceptors CCR5 or CXCR4 at the cell surface and driving membrane fusion. Receptor/gp120 interactions regulate the virus life cycle, HIV infection transmission and pathogenesis. Env is also the target of neutralizing antibodies. Efforts have thus been made to produce soluble HIV-1 glycoproteins to develop vaccines and study the role and mechanisms of HIV/receptor interactions. However, production and purification of Env glycoproteins and their functional assessment has to cope with multiple obstacles. These include difficulties in amplifying and cloning env sequences and setting up receptor binding assays that are suitable for studies on large collections of glycoproteins, flexible enough to adapt to Env and receptor structural heterogeneities, and allow recapitulating the receptor binding properties of virion-associated Env trimers. Here we identify these difficulties and present protocols to produce primary gp120 and determination of their binding properties to receptors. The receptor binding assays confirmed that the produced glycoproteins are competent for binding CD4 and undergo proper CD4-induced conformational changes required for interaction with CCR5. These assays may help elucidate the role of gp120/receptor interactions in the pathophysiology of HIV infection and develop HIV-1 entry inhibitors.
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Affiliation(s)
- Yann Benureau
- INSERM U1108, Institut Pasteur, 75015 Paris, France; Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, 75015 Paris, France.
| | - Philippe Colin
- INSERM U1108, Institut Pasteur, 75015 Paris, France; Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, 75015 Paris, France.
| | - Isabelle Staropoli
- INSERM U1108, Institut Pasteur, 75015 Paris, France; Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, 75015 Paris, France.
| | - Nuria Gonzalez
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain.
| | - Javier Garcia-Perez
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain.
| | - Jose Alcami
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain.
| | - Fernando Arenzana-Seisdedos
- INSERM U1108, Institut Pasteur, 75015 Paris, France; Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, 75015 Paris, France.
| | - Bernard Lagane
- INSERM U1108, Institut Pasteur, 75015 Paris, France; Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, 75015 Paris, France.
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Junttila N, Lévêque N, Magnius L, Kabue J, Muyembe-Tamfum JJ, Maslin J, Lina B, Norder H. Complete coding regions of the prototypes enterovirus B93 and C95: Phylogenetic analyses of the P1 and P3 regions of EV-B and EV-C strains. J Med Virol 2014; 87:485-97. [DOI: 10.1002/jmv.24062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2014] [Indexed: 01/30/2023]
Affiliation(s)
- N. Junttila
- MTC; Karolinska Institutet; Stockholm Sweden
| | - N. Lévêque
- Clinical and Molecular Virology Unit; University Hospital Faculty of Medicine; Reims France
- Laboratory of Virology, National Enterovirus Laboratory; Hospices Civils de Lyon; France
| | | | - J.P. Kabue
- National Institute of Biomedical Research; Kinshasa, Democratic Republic of the Congo
| | - J. J. Muyembe-Tamfum
- National Institute of Biomedical Research; Kinshasa, Democratic Republic of the Congo
| | - J. Maslin
- Department of Biology; Saint-Anne Military Hospital; Toulon France
| | - B. Lina
- Laboratory of Virology, National Enterovirus Laboratory; Hospices Civils de Lyon; France
| | - H. Norder
- MTC; Karolinska Institutet; Stockholm Sweden
- Department of Infectious Diseases/Section of Clinical Virology; Institute of Biomedicine; University of Gothenburg; Gothenburg Sweden
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Abstract
Objective The aim of this study was to examine the course of time-dependent evolution of HIV-1 subtype A on a global level, especially with respect to the dynamics of immunogenic HIV gag epitopes. Methods We used a total of 1,893 HIV-1 subtype A gag sequences representing a timeline from 1985 through 2010, and 19 different countries in Africa, Europe and Asia. The phylogenetic relationship of subtype A gag and its epidemic dynamics was analysed through a Maximum Likelihood tree and Bayesian Skyline plot, genomic variability was measured in terms of G→A substitutions and Shannon entropy, and the time-dependent evolution of HIV subtype A gag epitopes was examined. Finally, to confirm observations on globally reported HIV subtype A sequences, we analysed the gag epitope data from our Kenyan, Pakistani, and Afghan cohorts, where both cohort-specific gene epitope variability and HLA restriction profiles of gag epitopes were examined. Results The most recent common ancestor of the HIV subtype A epidemic was estimated to be 1956±1. A period of exponential growth began about 1980 and lasted for approximately 7 years, stabilized for 15 years, declined for 2–3 years, then stabilized again from about 2004. During the course of evolution, a gradual increase in genomic variability was observed that peaked in 2005–2010. We observed that the number of point mutations and novel epitopes in gag also peaked concurrently during 2005–2010. Conclusion It appears that as the HIV subtype A epidemic spread globally, changing population immunogenetic pressures may have played a role in steering immune-evolution of this subtype in new directions. This trend is apparent in the genomic variability and epitope diversity of HIV-1 subtype A gag sequences.
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Abidi SH, Shahid A, Lakhani LS, Khanani MR, Ojwang P, Okinda N, Shah R, Abbas F, Rowland-Jones S, Ali S. Population-specific evolution of HIV Gag epitopes in genetically diverged patients. INFECTION GENETICS AND EVOLUTION 2013; 16:78-86. [PMID: 23403357 DOI: 10.1016/j.meegid.2013.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 01/30/2013] [Accepted: 02/03/2013] [Indexed: 10/27/2022]
Abstract
BACKGROUND Under the host selection pressure HIV evolves rapidly to override crucial steps in the antigen presentation pathway. This allows the virus to escape binding and recognition by cytotoxic T lymphocytes. Selection pressures on HIV can be unique depending on the immunogenetics of host populations. It is therefore logical to hypothesize that the virus evolving in a given population will carry signature mutations that will allow it to survive in that particular host milieu. OBJECTIVES The aim of this study was to perform a comparative analysis of HIV-1 Gag subtype A sequences from two genetically diverged populations, namely, Kenyan and Pakistani. We analyzed unique mutations that could intercept the antigen processing pathway and potentially change the repertoire of Gag epitopes in each study group. METHODS Twenty-nine Kenyan and 56 Pakistani samples from HIV-1 subtype A-infected patients were used in this study. The HIV-1 gag region p24 and p2p7p1p6 was sequenced and mutations affecting proteasomal degradation, TAP binding, HLA binding and CTL epitope generation, were analyzed using the in silico softwares NetChop and MAPPP, TAPPred, nHLAPred and CTLPred, respectively. RESULTS Certain mutations unique to either Pakistani or Kenyan patients were observed to affect sites for proteasomal degradation, TAP binding, and HLA binding. As a consequence of these mutations, epitope pattern in these populations was altered. CONCLUSION Unique selection pressures can steer the direction of viral epitope evolution in the host populations. Population-specific HIV epitopes have to be taken into account while designing treatment as well as vaccine for HIV.
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Affiliation(s)
- Syed H Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
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Goldstein G, Damiano E, Donikyan M, Pasha M, Beckwith E, Chicca J. HIV-1 Tat B-cell epitope vaccination was ineffectual in preventing viral rebound after ART cessation: HIV rebound with current ART appears to be due to infection with new endogenous founder virus and not to resurgence of pre-existing Tat-dependent viremia. Hum Vaccin Immunother 2012; 8:1425-30. [PMID: 23095869 DOI: 10.4161/hv.21616] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
CD4 T cell activation, essential for productive HIV infection, is provided initially in acute HIV infection by innate immune system secretion of activating cytokines. This cytokine response wanes with time and long-term activation of CD4 cells is maintained by HIV Tat protein secreted by HIV infected cells. Structured treatment interruption (STI) in well-controlled antiretroviral-treated (ART) subjects was explored a decade ago with a consensus finding that, in most subjects, HIV levels rebounded within four weeks to pre-ART levels. Based on these observations we initiated a randomized placebo-controlled study of a universal anti-Tat epitope vaccine, TUTI-16, to determine if immunological blockade of Tat would prevent HIV rebound after ART cessation. TUTI-16 immunization was safe, with predominantly mild local and systemic injection-related adverse reactions. TUTI-16 was also immunogenic, with high levels of anti-Tat antibodies compared with levels previously shown to reduce HIV replication in vivo. Of 21 subjects analyzed, 13 (62%) had HIV rebounds vs. 8 (38%) that remained aviremia, but this distribution was not vaccine-related (p = 0.61 log-rank (Mantel-Cox) test), nullifying our hypothesis that anti-Tat antibodies would block rebound of Tat-dependent set-point HIV viremia after ART cessation. Our present findings are consistent with recent molecular findings that rebounding virus following STI is homogeneous and unrelated to previous circulating HIV, suggesting that rebounding HIV represents new founder virus, akin to the original acute HIV infection. We propose, therefore, that STI may have potential as a practical and economical approach to testing the safety and efficacy of candidate prophylactic HIV vaccines.
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Intersubtype differences in the effect of a rare p24 gag mutation on HIV-1 replicative fitness. J Virol 2012; 86:13423-33. [PMID: 23015721 DOI: 10.1128/jvi.02171-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Certain immune-driven mutations in HIV-1, such as those arising in p24(Gag), decrease viral replicative capacity. However, the intersubtype differences in the replicative consequences of such mutations have not been explored. In HIV-1 subtype B, the p24(Gag) M250I mutation is a rare variant (0.6%) that is enriched among elite controllers (7.2%) (P = 0.0005) and appears to be a rare escape variant selected by HLA-B58 supertype alleles (P < 0.01). In contrast, in subtype C, it is a relatively common minor polymorphic variant (10 to 15%) whose appearance is not associated with a particular HLA allele. Using site-directed mutant viruses, we demonstrate that M250I reduces in vitro viral replicative capacity in both subtype B and subtype C sequences. However, whereas in subtype C downstream compensatory mutations at p24(Gag) codons 252 and 260 reduce the adverse effects of M250I, fitness costs in subtype B appear difficult to restore. Indeed, patient-derived subtype B sequences harboring M250I exhibited in vitro replicative defects, while those from subtype C did not. The structural implications of M250I were predicted by protein modeling to be greater in subtype B versus C, providing a potential explanation for its lower frequency and enhanced replicative defects in subtype B. In addition to accounting for genetic differences between HIV-1 subtypes, the design of cytotoxic-T-lymphocyte-based vaccines may need to account for differential effects of host-driven viral evolution on viral fitness.
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Goldstein G, Chicca JJ. Exploratory clinical studies of a synthetic HIV-1 Tat epitope vaccine in asymptomatic treatment-naïve and antiretroviral-controlled HIV-1 infected subjects plus healthy uninfected subjects. Hum Vaccin Immunother 2012; 8:479-85. [PMID: 22336878 DOI: 10.4161/hv.19184] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
TUTI-16 is a synthetic universal HIV-1 Tat epitope vaccine, designed to induce anti-Tat antibodies that block the function of circulating Tat, an HIV encoded protein secreted by HIV-1 infected cells. Circulating Tat activates CD4 T cells, permitting HIV replication and sustained viremia. Safety, immunogenicity and antiretroviral potential of TUTI-16 were explored in a randomized double-blind dose-escalating study in asymptomatic treatment-naïve HIV-1 infected subjects. TUTI-16 was safe, with mild local and systemic injection-related adverse reactions, but the antibody response was barely detectable. Surprisingly, a highly statistically significant reduction of HIV-1 viral load was found in the lowest 30 μg vaccine dose group (p < 0.01) but not at the higher doses. We posited that an anti-Tat antibody response below the limit of detection inhibited HIV viral load at this dose, an effect nullified at higher vaccine doses by activating cytokines induced by adjuvant components in TUTI-16. To clarify this immunogenicity/activation conundrum open label immunogenicity studies were performed in healthy HIV uninfected and aviremic ART-controlled HIV-infected subjects. These established that (1) healthy HIV negative subjects had robust antibody responses, maximal with 1 mg TUTI-16, (2) ART-controlled aviremic HIV infected subjects had similarly robust antibody responses, and (3) adjuvant-induced increases of HIV viral load did not occur in the presence of ART. These studies provided us a basis for the design of a protocol to explore the therapeutic potential of TUTI-16 vaccination to provide drug free control of HIV-1 viremia.
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Nonacs P, Kapheim KM. Modeling Disease Evolution with Multilevel Selection: HIV as a Quasispecies Social Genome. ACTA ACUST UNITED AC 2012. [DOI: 10.4303/jem/235553] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Lazaro E, Thu Tram L, Bellecave P, Guidicelli GL, Anies G, Hoang Khanh Thu H, Pillot Debelleix M, Vray M, Recordon-Pinson P, Taupin JL, Thi Xuan Lien T, Fleury H. Molecular characterization of HIV-1 CRF01_AE in Mekong Delta, Vietnam, and impact of T-cell epitope mutations on HLA recognition (ANRS 12159). PLoS One 2011; 6:e26244. [PMID: 22039450 PMCID: PMC3198469 DOI: 10.1371/journal.pone.0026244] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 09/23/2011] [Indexed: 12/02/2022] Open
Abstract
Background To date, 11 HIV-1 subtypes and 48 circulating recombinant forms have been described worldwide. The underlying reason why their distribution is so heterogeneous is not clear. Host genetic factors could partly explain this distribution. The aim of this study was to describe HIV-1 strains circulating in an unexplored area of Mekong Delta, Vietnam, and to assess the impact of optimal epitope mutations on HLA binding. Methods We recruited 125 chronically antiretroviral-naive HIV-1-infected subjects from five cities in the Mekong Delta. We performed high-resolution DNA typing of HLA class I alleles, sequencing of Gag and RT-Prot genes and phylogenetic analysis of the strains. Epitope mutations were analyzed in patients bearing the HLA allele restricting the studied epitope. Optimal wild-type epitopes from the Los Alamos database were used as reference. T-cell epitope recognition was predicted using the immune epitope database tool according to three different scores involved in antigen processing (TAP and proteasome scores) and HLA binding (MHC score). Results All sequences clustered with CRF01_AE. HLA class I genotyping showed the predominance of Asian alleles as A*11:01 and B*46:01 with a Vietnamese specificity held by two different haplotypes. The percentage of homology between Mekong and B consensus HIV-1 sequences was above 85%. Divergent epitopes had TAP and proteasome scores comparable with wild-type epitopes. MHC scores were significantly lower in divergent epitopes with a mean of 2.4 (±0.9) versus 2 (±0.7) in non-divergent ones (p<0.0001). Conclusions Our study confirms the wide predominance of CRF01_AE in the Mekong Delta where patients harbor a specific HLA pattern. Moreover, it demonstrates the lower MHC binding affinity among divergent epitopes. This weak immune pressure combined with a narrow genetic diversity favors immune escape and could explain why CRF01_AE is still predominant in Vietnam, particularly in the Mekong area.
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Affiliation(s)
- Estibaliz Lazaro
- Laboratoire de Virologie, CHU de Bordeaux et CNRS-UMR 5234, Université Victor Segalen-Bordeaux 2, Bordeaux, France
| | | | - Pantxika Bellecave
- Laboratoire de Virologie, CHU de Bordeaux et CNRS-UMR 5234, Université Victor Segalen-Bordeaux 2, Bordeaux, France
| | | | - Guerric Anies
- Laboratoire d'immunologie et immunogénétique, CHU de Bordeaux, Bordeaux, France
- CNRS-UMR 5164, Université Victor Segalen-Bordeaux 2, Bordeaux, France
| | | | - Marie Pillot Debelleix
- Laboratoire de Virologie, CHU de Bordeaux et CNRS-UMR 5234, Université Victor Segalen-Bordeaux 2, Bordeaux, France
| | | | - Patricia Recordon-Pinson
- Laboratoire de Virologie, CHU de Bordeaux et CNRS-UMR 5234, Université Victor Segalen-Bordeaux 2, Bordeaux, France
| | - Jean-Luc Taupin
- Laboratoire d'immunologie et immunogénétique, CHU de Bordeaux, Bordeaux, France
- CNRS-UMR 5164, Université Victor Segalen-Bordeaux 2, Bordeaux, France
| | | | - Herve Fleury
- Laboratoire de Virologie, CHU de Bordeaux et CNRS-UMR 5234, Université Victor Segalen-Bordeaux 2, Bordeaux, France
- * E-mail:
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O'Connor SL, Lhost JJ, Becker EA, Detmer AM, Johnson RC, MacNair CE, Wiseman RW, Karl JA, Greene JM, Burwitz BJ, Bimber BN, Lank SM, Tuscher JJ, Mee ET, Rose NJ, Desrosiers RC, Hughes AL, Friedrich TC, Carrington M, O'Connor DH. MHC heterozygote advantage in simian immunodeficiency virus-infected Mauritian cynomolgus macaques. Sci Transl Med 2010; 2:22ra18. [PMID: 20375000 PMCID: PMC2865159 DOI: 10.1126/scitranslmed.3000524] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The importance of a broad CD8 T lymphocyte (CD8-TL) immune response to HIV is unknown. Ex vivo measurements of immunological activity directed at a limited number of defined epitopes provide an incomplete portrait of the actual immune response. We examined viral loads in simian immunodeficiency virus (SIV)-infected major histocompatibility complex (MHC)-homozygous and MHC-heterozygous Mauritian cynomolgus macaques. Chronic viremia in MHC-homozygous macaques was 80 times that in MHC-heterozygous macaques. Virus from MHC-homozygous macaques accumulated 11 to 14 variants, consistent with escape from CD8-TL responses after 1 year of SIV infection. The pattern of mutations detected in MHC-heterozygous macaques suggests that their epitope-specific CD8-TL responses are a composite of those present in their MHC-homozygous counterparts. These results provide the clearest example of MHC heterozygote advantage among individuals infected with the same immunodeficiency virus strain, suggesting that broad recognition of multiple CD8-TL epitopes should be a key feature of HIV vaccines.
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Affiliation(s)
- Shelby L. O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Jennifer J. Lhost
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Ericka A. Becker
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Ann M. Detmer
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Randall C. Johnson
- Laboratory of Genomic Diversity, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702
- Chaire de Bioinformatique, Conservatoire National des Arts et Metiers, 75003, Paris, France
| | - Caitlin E. MacNair
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Roger W. Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Julie A. Karl
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Justin M. Greene
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Benjamin J. Burwitz
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Benjamin N. Bimber
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Simon M. Lank
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Jennifer J. Tuscher
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Edward T. Mee
- Division of Retrovirology, National Institute for Biological Standards and Control, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Nicola J. Rose
- Division of Retrovirology, National Institute for Biological Standards and Control, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Ronald C. Desrosiers
- New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts 01772
| | - Austin L. Hughes
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208
| | - Thomas C. Friedrich
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Mary Carrington
- Cancer and Inflammation Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702 and Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts 02114
| | - David H. O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
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Goldstein G, Chicca JJ. A universal anti-HIV-1 Tat epitope vaccine that is fully synthetic and self-adjuvanting. Vaccine 2009; 28:1008-14. [PMID: 19931501 DOI: 10.1016/j.vaccine.2009.10.129] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 10/27/2009] [Accepted: 10/28/2009] [Indexed: 10/20/2022]
Abstract
Circulating HIV-1 Tat protein is essential for maintenance of the chronic HIV replication that predicates both HIV transmission and clinical progression to AIDS/death. A synthetic anti-Tat epitope vaccine (TUTI-16) was designed to induce neutralizing antibodies to Tat and, hopefully, provide immunological control of HIV replication. TUTI-16 is composed of (1) a conserved Tat B cell epitope (Tat 4-12), rendered universal by introducing known variant amino acids at variable positions 7, 9 and 12 during solid phase synthesis, (2) a promiscuous T helper sequence and (3) a lipopeptide toll-like receptor 2 (TLR2) agonist. TUTI-16 induced high titer antibodies against all 8 known variants of the Tat epitope.
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Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection. PLoS One 2009; 4:e7727. [PMID: 19890401 PMCID: PMC2768328 DOI: 10.1371/journal.pone.0007727] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Accepted: 09/18/2009] [Indexed: 11/19/2022] Open
Abstract
Background Aiming to answer the broad question “When does mutation occur?” this study examined the time of appearance, dominance, and completeness of in vivo Gag mutations in primary HIV-1 subtype C infection. Methods A primary HIV-1C infection cohort comprised of 8 acutely and 34 recently infected subjects were followed frequently up to 500 days post-seroconversion (p/s). Gag mutations were analyzed by employing single-genome amplification and direct sequencing. Gag mutations were determined in relation to the estimated time of seroconversion. Time of appearance, dominance, and completeness was compared for different types of in vivo Gag mutations. Results Reverse mutations to the wild type appeared at a median (IQR) of 62 (44;139) days p/s, while escape mutations from the wild type appeared at 234 (169;326) days p/s (p<0.001). Within the subset of mutations that became dominant, reverse and escape mutations appeared at 54 (30;78) days p/s and 104 (47;198) days p/s, respectively (p<0.001). Among the mutations that reached completeness, reverse and escape mutations appeared at 54 (30;78) days p/s and 90 (44;196) days p/s, respectively (p = 0.006). Time of dominance for reverse mutations to and escape mutations from the wild type was 58 (44;105) days p/s and 219 (90;326) days p/s, respectively (p<0.001). Time of completeness for reverse and escape mutations was 152 (100;176) days p/s and 243 (101;370) days p/s, respectively (p = 0.001). Fitting a Cox proportional hazards model with frailties confirmed a significantly earlier time of appearance (hazard ratio (HR): 2.6; 95% CI: 2.3–3.0), dominance (4.8 (3.4–6.8)), and completeness (3.6 (2.3–5.5)) of reverse mutations to the wild type Gag than escape mutations from the wild type. Some complex mutational pathways in Gag included sequential series of reversions and escapes. Conclusions The study identified the timing of different types of in vivo Gag mutations in primary HIV-1 subtype C infection in relation to the estimated time of seroconversion. Overall, the in vivo reverse mutations to the wild type occurred significantly earlier than escape mutations from the wild type. This shorter time to incidence of reverse mutations remained in the subsets of in vivo Gag mutations that reached dominance or completeness.
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David R. Selective pressure. Nat Rev Immunol 2009. [DOI: 10.1038/nri2595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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