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Mulinge M, Lemaire M, Servais JY, Rybicki A, Struck D, da Silva ES, Verhofstede C, Lie Y, Seguin-Devaux C, Schmit JC, Bercoff DP. HIV-1 tropism determination using a phenotypic Env recombinant viral assay highlights overestimation of CXCR4-usage by genotypic prediction algorithms for CRF01_AE and CRF02_AG [corrected]. PLoS One 2013; 8:e60566. [PMID: 23667426 PMCID: PMC3648519 DOI: 10.1371/journal.pone.0060566] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 02/28/2013] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Human Immunodeficiency virus type-1 (HIV) entry into target cells involves binding of the viral envelope (Env) to CD4 and a coreceptor, mainly CCR5 or CXCR4. The only currently licensed HIV entry inhibitor, maraviroc, targets CCR5, and the presence of CXCX4-using strains must be excluded prior to treatment. Co-receptor usage can be assessed by phenotypic assays or through genotypic prediction. Here we compared the performance of a phenotypic Env-Recombinant Viral Assay (RVA) to the two most widely used genotypic prediction algorithms, Geno2Pheno[coreceptor] and webPSSM. METHODS Co-receptor tropism of samples from 73 subtype B and 219 non-B infections was measured phenotypically using a luciferase-tagged, NL4-3-based, RVA targeting Env. In parallel, tropism was inferred genotypically from the corresponding V3-loop sequences using Geno2Pheno[coreceptor] (5-20% FPR) and webPSSM-R5X4. For discordant samples, phenotypic outcome was retested using co-receptor antagonists or the validated Trofile® Enhanced-Sensitivity-Tropism-Assay. RESULTS The lower detection limit of the RVA was 2.5% and 5% for X4 and R5 minority variants respectively. A phenotype/genotype result was obtained for 210 samples. Overall, concordance of phenotypic results with Geno2Pheno[coreceptor] was 85.2% and concordance with webPSSM was 79.5%. For subtype B, concordance with Geno2pheno[coreceptor] was 94.4% and concordance with webPSSM was 79.6%. High concordance of genotypic tools with phenotypic outcome was seen for subtype C (90% for both tools). Main discordances involved CRF01_AE and CRF02_AG for both algorithms (CRF01_AE: 35.9% discordances with Geno2Pheno[coreceptor] and 28.2% with webPSSM; CRF02_AG: 20.7% for both algorithms). Genotypic prediction overestimated CXCR4-usage for both CRFs. For webPSSM, 40% discordance was observed for subtype A. CONCLUSIONS Phenotypic assays remain the most accurate for most non-B subtypes and new subtype-specific rules should be developed for non-B subtypes, as research studies more and more draw conclusions from genotypically-inferred tropism, and to avoid unnecessarily precluding patients with limited treatment options from receiving maraviroc or other entry inhibitors.
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Affiliation(s)
- Martin Mulinge
- Laboratory of Retrovirology, Centre Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Morgane Lemaire
- Laboratory of Retrovirology, Centre Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Jean-Yves Servais
- Laboratory of Retrovirology, Centre Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Arkadiusz Rybicki
- Laboratory of Retrovirology, Centre Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Daniel Struck
- Laboratory of Retrovirology, Centre Recherche Public de la Santé, Luxembourg, Luxembourg
| | | | | | - Yolanda Lie
- Monogram Biosciences Inc., South San Francisco, California, United States of America
| | - Carole Seguin-Devaux
- Laboratory of Retrovirology, Centre Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Jean-Claude Schmit
- Laboratory of Retrovirology, Centre Recherche Public de la Santé, Luxembourg, Luxembourg
- Service National des Maladies Infectieuses, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
| | - Danielle Perez Bercoff
- Laboratory of Retrovirology, Centre Recherche Public de la Santé, Luxembourg, Luxembourg
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Lin NH, Becerril C, Giguel F, Novitsky V, Moyo S, Makhema J, Essex M, Lockman S, Kuritzkes DR, Sagar M. Env sequence determinants in CXCR4-using human immunodeficiency virus type-1 subtype C. Virology 2012; 433:296-307. [PMID: 22954962 DOI: 10.1016/j.virol.2012.08.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/12/2012] [Accepted: 08/01/2012] [Indexed: 02/09/2023]
Abstract
HIV-1 subtype C (HIV-1C) CXCR4-using virus is isolated infrequently and is poorly characterized. Understanding HIV-1C env characteristics has implications for the clinical use of antiretrovirals that target viral entry. A total of 209 env clones derived from 10 samples with mixed CCR5-(R5), CXCR4-using (X4) or dual-tropic HIV-1C were phenotyped for coreceptor usage. Intra-patient X4 and R5 variants generally formed distinct monophyletic phylogenetic clusters. X4 compared to R5 envs had significantly greater amino acid variability and insertions, higher net positive charge, fewer glycosylation sites and increased basic amino acid substitutions in the GPGQ crown. Basic amino acid substitution and/or insertion prior to the crown are highly sensitive characteristics for predicting X4 viruses. Chimeric env functional studies suggest that the V3 loop is necessary but often not sufficient to impart CXCR4 utilization. Our studies provide insights into the unique genotypic characteristics of X4 variants in HIV-1C.
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Affiliation(s)
- Nina H Lin
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
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3
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Musyoki A, Mothapo K, Rakgole J, Lukhwareni A, Bessong P, Selabe G, Bredell H, Williamson C, Mphahlele MJ. Genetic characterization of HIV before widespread testing of HIV vaccine candidates at a clinical trial site in Pretoria, South Africa. AIDS Res Hum Retroviruses 2012; 28:1131-8. [PMID: 22106990 DOI: 10.1089/aid.2011.0285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We studied 123 samples from adult chronic HIV patients initiating HAART from various centers around a newly established clinical trial site in Pretoria. Each sample was sequenced in at least one structural gene (pol, gag, and env) or functional gene (vif, vpr, and vpu). A subset of 25 samples was subjected to near full-genome analysis. All samples were HIV-1 subtype C. Highly conserved regions within the gene sequences were observed. Overall, the gag and vif sequences showed closer similarity followed by the env, vpr, pol, and vpu. The env gene was the most difficult to sequence, resulting in only 31 sequences from 40 samples; of these, 25 were predicted to be R5 coreceptor tropic, while 6 were X4 tropic. The study asserted the predominance of HIV-1 subtype C within the catchment population.
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Affiliation(s)
- Andrew Musyoki
- HIV and Hepatitis Research Unit, Department of Virology, Medunsa Campus, University of Limpopo/National Health Laboratory Service, Pretoria, South Africa
| | - Khutso Mothapo
- HIV and Hepatitis Research Unit, Department of Virology, Medunsa Campus, University of Limpopo/National Health Laboratory Service, Pretoria, South Africa
| | - Johnny Rakgole
- HIV and Hepatitis Research Unit, Department of Virology, Medunsa Campus, University of Limpopo/National Health Laboratory Service, Pretoria, South Africa
| | - Azwidowi Lukhwareni
- HIV and Hepatitis Research Unit, Department of Virology, Medunsa Campus, University of Limpopo/National Health Laboratory Service, Pretoria, South Africa
| | - Pascal Bessong
- AIDS Virus Research Laboratory, Department of Microbiology, University of Venda, Thohoyandou, South Africa
| | - Gloria Selabe
- HIV and Hepatitis Research Unit, Department of Virology, Medunsa Campus, University of Limpopo/National Health Laboratory Service, Pretoria, South Africa
| | - Helba Bredell
- Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town/National Health Laboratory Service, Cape Town, South Africa
| | - Carolyn Williamson
- Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town/National Health Laboratory Service, Cape Town, South Africa
| | - M. Jeffrey Mphahlele
- HIV and Hepatitis Research Unit, Department of Virology, Medunsa Campus, University of Limpopo/National Health Laboratory Service, Pretoria, South Africa
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Duri K, Soko W, Gumbo F, Kristiansen K, Mapingure M, Stray-Pedersen B, Muller, and the BHAMC Group F. Genotypic analysis of human immunodeficiency virus type 1 env V3 loop sequences: bioinformatics prediction of coreceptor usage among 28 infected mother-infant pairs in a drug-naive population. AIDS Res Hum Retroviruses 2011; 27:411-9. [PMID: 20969460 DOI: 10.1089/aid.2010.0142] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We sought to predict virus coreceptor utilization using a simple bioinformatics method based on genotypic analysis of human immunodeficiency virus types 1 (HIV-1) env V3 loop sequences of 28 infected but drug-naive women during pregnancy and their infected infants and to better understand coreceptor usage in vertical transmission dynamics. The HIV-1 env V3 loop was sequenced from plasma samples and analyzed for viral coreceptor usage and subtype in a cohort of HIV-1-infected pregnant women. Predicted maternal frequencies of the X4, R5X4, and R5 genotypes were 7%, 11%, and 82%, respectively. Antenatal plasma viral load was higher, with a mean log(10) (SD) of 4.8 (1.6) and 3.6 (1.2) for women with the X4 and R5 genotypes, respectively, p = 0.078. Amino acid substitution from the conserved V3 loop crown motif GPGQ to GPGR and lymphadenopathy were associated with the X4 genotype, p = 0.031 and 0.043, respectively. The maternal viral coreceptor genotype was generally preserved in vertical transmission and was predictive of the newborn's viral genotype. Infants born to mothers with X4 genotypes were more likely to have lower birth weights relative to those born to mothers with the R5 genotype, with a mean weight (SD) of 2870 (±332) and 3069 (±300) g, respectively. These data show that at least in HIV-1 subtype C, R5 coreceptor usage is the most predominant genotype, which is generally preserved following vertical transmission and is associated with the V3 GPGQ crown motif. Therefore, antiretroviral-naive pregnant women and their infants can benefit from ARV combination therapies that include R5 entry inhibitors following prediction of their coreceptor genotype using simple bioinformatics methods.
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Affiliation(s)
- Kerina Duri
- Department of Immunology, University of Zimbabwe, Harare, Zimbabwe
| | - White Soko
- Department of Immunology, National Institute of Health Research, Harare, Zimbabwe
| | - Felicity Gumbo
- Department of Paediatrics and Child Health, University of Zimbabwe, Harare, Zimbabwe
| | - Knut Kristiansen
- Department of Molecular Biology, University of Oslo, Oslo, Norway
| | | | - Babill Stray-Pedersen
- Department of Obstetrics and Gynaecology, University of Oslo and Rikshospitalet, Oslo, Norway
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Abstract
The identification of phenotypically distinct HIV-1 variants with different prevalence during the progression of the disease has been one of the earliest discoveries in HIV-1 biology, but its relevance to AIDS pathogenesis remains only partially understood. The physiological basis for the phenotypic variability of HIV-1 was elucidated with the discovery of distinct coreceptors employed by the virus to infect susceptible cells. The role of the viral phenotype in the variable clinical course and treatment outcome of HIV-1 infection has been extensively investigated over the past two decades. In this review, we summarize the major findings on the clinical significance of the HIV-1 coreceptor usage.
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Affiliation(s)
- Hanneke Schuitemaker
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.
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6
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Coetzer M, Nedellec R, Cilliers T, Meyers T, Morris L, Mosier DE. Extreme genetic divergence is required for coreceptor switching in HIV-1 subtype C. J Acquir Immune Defic Syndr 2011; 56:9-15. [PMID: 20921899 PMCID: PMC3006070 DOI: 10.1097/qai.0b013e3181f63906] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Coreceptor switching from CCR5 to CXCR4 is less common in subtype C HIV-1 infection than in subtype B for reasons that are unclear. We have examined sequential virus samples from a subtype C-infected child who had evidence of coreceptor switching. METHODS To examine HIV-1 envelope evolution towards CXCR4 usage, env sequences were correlated with phenotypic characteristics determined by entry assays, as well as the ability to use alternative coreceptors such as FPRL1, CCR3, CCR8 and others. The value of a phenotype predictor based on V3 sequences was also assessed. RESULTS Ninety-three sequences revealed 3 distinct coexistent virus lineages and only some members of one lineage evolved to use CXCR4. These lineages also had diverse alternative coreceptor patterns including the ability to use FPRL1, CCR3, CCR8, APJ, CMKLR1, RDC-1, CXCR6, CCR1, GPCR1, GPR15 and CCR6. Coreceptor switching was associated with extensive and rapid sequence divergence in the V1/V2 region in addition to V3 changes. Furthermore, interlineage recombination within the C2 region resulted in low predictability of a V3 sequence-based phenotype algorithm, and highlighted the importance of V1/V2 and V3 sequences in coreceptor usage. CONCLUSION These results suggest that the evolution to coreceptor switching in subtype C infection requires more mutations than other subtypes, and this contributes to the reduced incidence of R5X4 viruses.
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MESH Headings
- Child
- Cloning, Molecular
- HIV Infections/immunology
- HIV Infections/virology
- HIV-1/genetics
- HIV-1/immunology
- Humans
- Molecular Sequence Data
- Phenotype
- Phylogeny
- Receptors, CCR5/genetics
- Receptors, CCR5/immunology
- Receptors, CXCR4/genetics
- Receptors, CXCR4/immunology
- Receptors, Formyl Peptide/genetics
- Receptors, Formyl Peptide/immunology
- Receptors, Lipoxin/genetics
- Receptors, Lipoxin/immunology
- Recombination, Genetic/genetics
- env Gene Products, Human Immunodeficiency Virus/genetics
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Affiliation(s)
- Mia Coetzer
- Department of Immunology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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7
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Unusual five amino acid insert within subtype C HIV-1 envelope contributes to dual-tropism (X4R5). AIDS 2010; 24:1063-4. [PMID: 20299967 DOI: 10.1097/qad.0b013e328331f717] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
During the course of HIV infection, some HIV-1 viruses switch from using the CCR5 (R5) coreceptor to using CXCR4 (X4). Here, we describe two subtype C isolates from a Zimbabwean patient that switched from using R5 to using both R5 and X4 with an accompanying addition of five amino acids to the V3 loop region of envelope. The insert appears to be derived from the human genome rather than a duplication within HIV-1.
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8
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Jakobsen MR, Ellett A, Churchill MJ, Gorry PR. Viral tropism, fitness and pathogenicity of HIV-1 subtype C. Future Virol 2010. [DOI: 10.2217/fvl.09.77] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The majority of studies on HIV-1 pathogenesis have been conducted on subtype B HIV-1 (B-HIV) strains. However, B-HIV strains constitute the minority of HIV-1 cases worldwide, and are not common in regions that stand to benefit the most from advances in HIV-1 research such as southern Africa and Asia, where the HIV-1 pandemic is at its worst. The majority of individuals with HIV-1 are infected with subtype C HIV-1 (C-HIV) and reside in Southern Africa and Central Asia. Relatively little is known about C-HIV, but current evidence suggests the pathogenesis of C-HIV is distinct from B-HIV and other HIV-1 subtypes. This article summarizes what is currently known about the viral tropism, fitness and pathogenicity of C-HIV, and compares and contrasts these features to B-HIV. A thorough understanding of the molecular pathogenesis of C-HIV is important for a targeted approach to developing vaccines and novel drugs optimized for effectiveness in populations that are most in need.
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Affiliation(s)
- Martin R Jakobsen
- Centre for Virology, Burnet Institute, Melbourne, Victoria, Australia and Department of Infectious Diseases, Aarhus University Hospital, Skejby, Brendstrupgaardvej 100, 8200 Aarhus N, Denmark
| | - Anne Ellett
- Centre for Virology, Burnet Institute, Melbourne, Victoria, Australia
| | - Melissa J Churchill
- Centre for Virology, Burnet Institute, Melbourne, Victoria, Australia and Department of Medicine, Monash University, Melbourne, Victoria, Australia
| | - Paul R Gorry
- Centre for Virology, Burnet Institute, Melbourne, Victoria, Australia and Department of Medicine, Monash University, Melbourne, Victoria, Australia and Department of Microbiology & Immunology, University of Melbourne, Melbourne, Victoria, Australia
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9
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Abstract
OBJECTIVE To investigate the origins and evolutionary history of subtype C HIV-1 in Zimbabwe in a context of regional conflict and migration. DESIGN HIV-1C pol sequence datasets were generated from four sequential cohorts of antenatal women in Harare, Zimbabwe sampled over 15 years (1991-2006). METHODS One hundred and seventy-seven HIV-1C pol sequences were obtained from four successive cohorts in Zimbabwe. Maximum-likelihood methods were used to explore phylogenetic relationships between Zimbabwean HIV-1C sequences and subtype C strains from other regions. A Bayesian coalescent-based framework was used to estimate evolutionary parameters for HIV-1C in Zimbabwe, including origin and demographic growth patterns. RESULTS Zimbabwe HIV-1C pol demonstrated increasing sequence divergence over the 15-year period. Nearly all Zimbabwe sequences clustered phylogenetically with subtype C strains from neighboring countries. Bayesian evolutionary analysis indicated a most recent common ancestor date of 1973 with three epidemic growth phases: an initial, slow phase (1970s) followed by exponential growth (1980s), and a linearly expanding epidemic to the present. Bayesian trees provided evidence for multiple HIV-1C introductions into Zimbabwe during 1979-1981, corresponding with Zimbabwean national independence following a period of socio-political instability. CONCLUSION The Zimbabwean HIV-1C epidemic likely originated from multiple introductions in the late 1970s and grew exponentially during the 1980s, corresponding to changing political boundaries and rapid population influx from neighboring countries. The timing and phylogenetic clustering of the Zimbabwean sequences is consistent with an origin in southern Africa and subsequent expansion. HIV-1 sequence data contain important epidemiological information, which can help focus treatment and prevention strategies in light of more recent political volatility in Zimbabwe.
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Lynch RM, Shen T, Gnanakaran S, Derdeyn CA. Appreciating HIV type 1 diversity: subtype differences in Env. AIDS Res Hum Retroviruses 2009; 25:237-48. [PMID: 19327047 DOI: 10.1089/aid.2008.0219] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) group M is responsible for the current AIDS pandemic and exhibits exceedingly high levels of viral genetic diversity around the world, necessitating categorization of viruses into distinct lineages, or subtypes. These subtypes can differ by around 35% in the envelope (Env) glycoproteins of the virus, which are displayed on the surface of the virion and are targets for both neutralizing antibody and cell-mediated immune responses. This diversity reflects the remarkable ability of the virus to adapt to selective pressures, the bulk of which is applied by the host immune response, and represents a serious obstacle for developing an effective vaccine with broad coverage. Thus, it is important to understand the underlying biological consequences of intersubtype diversity. Recent studies have revealed that some of the HIV-1 subtypes exhibit phenotypic differences stemming from subtle changes in Env structure, particularly within the highly immunogenic V3 domain, which participates directly in viral entry. This review will therefore explore current research that describes subtype differences in Env at the genetic and phenotypic level, focusing in particular on V3, and highlighting recent discoveries about the unique features of subtype C Env, which is the most globally prevalent subtype.
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Affiliation(s)
- Rebecca M. Lynch
- Immunology and Molecular Pathogenesis Program, Emory University, Atlanta, Georgia 30329
| | - Tongye Shen
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - S. Gnanakaran
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Cynthia A. Derdeyn
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia 30329
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329
- Emory Vaccine Center, Emory University, Atlanta, Georgia 30329
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Campbell GR, Spector SA. CCL2 increases X4-tropic HIV-1 entry into resting CD4+ T cells. J Biol Chem 2008; 283:30745-53. [PMID: 18784079 DOI: 10.1074/jbc.m804112200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
During human immunodeficiency virus type 1 (HIV-1) infection, there is a strong positive correlation between CCL2 levels and HIV viral load. To determine whether CCL2 alters HIV-1 infection of resting CD4(+) T cells, we infected purified resting CD4(+) T cells after incubation with CCL2. We show that CCL2 up-regulates CXCR4 on resting CD4(+) T cells in a CCR2-dependent mechanism, and that this augmentation of CXCR4 expression by CCL2 increases the ability of these cells to be chemoattracted to CXCR4 using gp120 and renders them more permissive to X4-tropic HIV-1 infection. Thus, CCL2 has the capacity to render a large population of lymphocytes more susceptible to HIV-1 late in the course of infection.
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Affiliation(s)
- Grant R Campbell
- Department of Pediatrics, University of California San Diego, La Jolla, California 92093-0672, USA
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12
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Subtype-specific conformational differences within the V3 region of subtype B and subtype C human immunodeficiency virus type 1 Env proteins. J Virol 2007; 82:903-16. [PMID: 18003735 DOI: 10.1128/jvi.01444-07] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The V3 region of the human immunodeficiency virus type 1 gp120 Env protein is a key domain in Env due to its role in interacting with the coreceptors CCR5 and CXCR4. We examined potential subtype-specific V3 region differences by comparing patterns of amino acid variability and probing for subtype-specific structures using 11 anti-V3 monoclonal antibodies (V3 MAbs). Differences between the subtypes in patterns of variability were most evident in the stem and turn regions of V3 (positions 9 to 24), with the two subtypes being very similar in the base region. The characteristics of the binding of V3 MAbs to Env proteins of the subtype B virus JR-FL and the subtype C virus BR025 suggested three patterns, as each group of MAbs recognized a specific conformation- or sequence-based epitope. Viruses pseudotyped with Env from JR-FL and BR025 were resistant to neutralization by the V3 MAbs, although the replacement of the Env V3 region of the SF162 virus with the JR-FL V3 created a pseudotyped virus that was hypersensitive to neutralization. A single mutation in V3 (H13R) made this chimeric Env selectively resistant to one group of V3 MAbs, consistent with the mAb binding properties. We hypothesize that there are intrinsic differences in V3 conformation between subtype B and subtype C that are localized to the stem and turn regions and that these differences have two important biological consequences: first, subtype B and subtype C V3 regions can have subtype-specific epitopes that will inherently limit antibody cross-reactivity, and second, V3 conformational differences may potentiate the frequent evolution of R5- into X4-tropic variants of subtype B but limit subtype C virus from using the same mechanism to evolve X4-tropic variants as efficiently.
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Novitsky V, Wester CW, DeGruttola V, Bussmann H, Gaseitsiwe S, Thomas A, Moyo S, Musonda R, Van Widenfelt E, Marlink RG, Essex M. The reverse transcriptase 67N 70R 215Y genotype is the predominant TAM pathway associated with virologic failure among HIV type 1C-infected adults treated with ZDV/ddI-containing HAART in southern Africa. AIDS Res Hum Retroviruses 2007; 23:868-78. [PMID: 17678469 DOI: 10.1089/aid.2006.0298] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1C has become the dominant HIV-1 subtype in the global AIDS epidemic. Historically, the evolution of drug-resistant mutations was characterized primarily among antiretroviral (ARV)-treated HIV-1B infections. Whereas the non-B viruses are susceptible to the currently used ARVs, some differences between HIV-1 subtypes in response to ARV regimens have been reported. We analyzed the profile of ARV-associated mutations in HIV-1C infection treated with ZDV/ddI-containing regimens in an open-label, randomized 3 x 2 x 2 factorial study comparing ZDV/3TC vs. ZDV/ddI vs. d4T/3TC and EFV vs. NVP regimens in drug-naive adults in Botswana. The overall rate of virologic failure in the ZDV/ddI-containing arms was 14%. We addressed the development of NRTI-associated mutations in 23 virologically failed patients in the ZDV/ddI-containing arms. The 67N 70R 215Y genotype with wild-type amino acids at codon positions 41 and 210 was a dominant pattern of NRTI-associated mutations at the time of virologic failure. The mutation T215Y was the first step in the evolution of the 67N 70R 215Y genotype and was followed by mutations K70R and D67N. Representing a mixture of TAM-1 (41L/210W/215Y) and TAM-2 (67N/70R/215F /219Q) pathways, the 67N 70R 215Y genotype with wild-type amino acids at codon positions 41, 210, and 219 is a unique TAM pathway that is rarely seen in HIV-1B infection. Although limited by relatively small numbers, our data suggest that the 67N 70R 215Y genotype may be the HIV-1C-specific response to the first-line ZDV/ddI-containing regimen at the time of virologic failure. The presence of the 67N 70R 215Y genotype with wild-type amino acids at codon positions 41, 210, and 219 in HIV-1C infection suggests that the evolution of ARV-associated mutations and TAM pathways might be unique in non-B HIV-1 subtypes treated with particular ARV regimens.
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Affiliation(s)
- Vlad Novitsky
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, 02115, USA
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14
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Coetzer M, Cilliers T, Ping LH, Swanstrom R, Morris L. Genetic characteristics of the V3 region associated with CXCR4 usage in HIV-1 subtype C isolates. Virology 2006; 356:95-105. [PMID: 16942785 DOI: 10.1016/j.virol.2006.07.030] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Revised: 05/17/2006] [Accepted: 07/20/2006] [Indexed: 11/17/2022]
Abstract
CXCR4 coreceptor usage appears to occur less frequently among HIV-1 subtype C viruses. The aim of this study was to investigate the genetic determinants within the V3 region of subtype C isolates able to use CXCR4. Thirty-two subtype C isolates with known phenotypes (16 R5, 8 R5X4 and 8 X4 isolates) were assessed. A subtype C-specific V3 heteroduplex tracking assay (HTA) was used to determine sample complexity, and nucleotide sequencing analysis was used to compare characteristics associated with CCR5 and CXCR4-using isolates. There were sufficient genetic differences to discriminate between R5 viruses and those able to use CXCR4. In general, R5 isolates had an HTA mobility ratio >0.9 whereas CXCR4-using isolates were usually <0.9. Multiple bands were more frequently seen among the dualtropic isolates. Sequence analysis of the V3 region showed that CXCR4-using viruses were often associated with an increased positive amino acid charge, insertions and loss of a glycosylation site, similar to HIV-1 subtype B. In contrast, where subtype B consensus V3 has a GPGR crown motif irrespective of coreceptor usage, all 16 subtype C R5 viruses had a conserved GPGQ sequence at the tip of the loop, while 12 of the 16 (75%) CXCR4-using viruses had substitutions in this motif, most commonly arginine (R). These findings were confirmed using a larger published data set. We therefore suggest that changes within the crown motif of subtype C viruses might be an additional pathway to utilise CXCR4 and thus GPGQ may limit the potential for the development of X4 viruses.
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Affiliation(s)
- Mia Coetzer
- AIDS Virus Research Unit, National Institute for Communicable Diseases, Private Bag X4, Sandringham, Johannesburg, Gauteng 2131, South Africa
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Vidal N, Mulanga C, Bazepeo SE, Mwamba JK, Tshimpaka JW, Kashi M, Mama N, Laurent C, Lepira F, Delaporte E, Peeters M. Distribution of HIV-1 variants in the Democratic Republic of Congo suggests increase of subtype C in Kinshasa between 1997 and 2002. J Acquir Immune Defic Syndr 2006; 40:456-62. [PMID: 16280702 DOI: 10.1097/01.qai.0000159670.18326.94] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The Democratic Republic of Congo (DRC) is characterized by low and stable HIV prevalences and high HIV-1 genetic diversity and is most probably the epicenter of HIV-1 group M. Our major goal was to study the distribution of HIV-1 variants over a 5-year period against a background of political instability and civil war. A total of 288 HIV-1-positive samples collected in 2002 from sentinel population groups in an HIV serosurveillance study performed in 4 cities (Kinshasa [capital city], Mbuji-Mayi [south], Lubumbashi [southeast], and Kisangani [northeast]) were genetically characterized by sequencing and phylogenetic analysis of the V3-V5 env region. The results were compared with those obtained in 1997. Similarly, as in 1997, an extremely high genetic diversity of HIV-1 strains overall and a heterogeneous geographic distribution were seen in 2002. All subtypes and several circulating recombinant forms were present, high intrasubtype diversity was observed, and 5.6% of the samples could not be classified. In each geographic region of the DRC, the genetic diversity was significantly higher than in neighboring countries. Comparison of subtype distribution in similar population groups in Kinshasa in 1997 and 2002 revealed an overall increase of subtype C in Kinshasa from 2.1% to 9.7% and, more precisely, from 0% to 18.9% in female sex workers (P = 0.013). Genetic characterization of HIV-positive samples from sentinel surveys adds significant additional information on new trends in the HIV epidemic. These changes could have implications regarding the spread of HIV infection in the DRC as well on vaccine and/or treatment strategies.
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Affiliation(s)
- Nicole Vidal
- UR36, Institut de Recherche pour e Developement (IRD), Montpellier, France
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16
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Pérez-Alvarez L, Muñoz M, Delgado E, Miralles C, Ocampo A, García V, Thomson M, Contreras G, Nájera R. Isolation and biological characterization of HIV-1 BG intersubtype recombinants and other genetic forms circulating in Galicia, Spain. J Med Virol 2006; 78:1520-8. [PMID: 17063519 DOI: 10.1002/jmv.20734] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The biological characteristics of HIV-1 primary isolates of different recombinant forms (RFs) and non-B subtypes from Galicia, Spain, were investigated and the relationships between biological phenotype and evolution of infection were determined. Peripheral blood mononuclear cells (PBMCs) were obtained during the follow-up of 32 patients infected with HIV-1 non-subtype B genetic forms, characterized in partial sequences of pol (protease-reverse transcriptase) and env V3 region: 12 (37.5%) circulating RFs (CRFs), 9 (28.1%) unique RFs (URFs), and 11(34.4%) non-B subtypes. Primary isolates were obtained by coculture with donor PBMCs. Syncytium-inducing (SI) phenotype was examined in MT2 cell line and coreceptor use in GHOST and U87.CD4 cells. Fifty percent of tissue culture infective dose (TCID(50)) and viral phenotype based on V3 net charge and Geno2pheno(coreceptor) bioinformatic method were determined. Fifty-four HIV-1 primary isolates were obtained. CRF14_BG and BG URFs represented the largest group, being all SI/X4, independently of the CD4+ cell count, viral load, or the duration of infection. By contrast, 10 of 11 CRF02_AG viruses were NSI/R5. The prediction of co-receptor use was concordant with biological characterization in all NSI/R5 and in 23 of 26 SI/X4 isolates. The presence of SI/X4 or SI/X4,R5 isolates at early stages of the infection in addition to a decrease in CD4+ counts below 500 cells/microl between 2 and 6 years since diagnosis was observed in all patients infected with CRF14_BG and BG URFs. These data contrast with the usual progression in B subtype infections, in which SI/X4 viruses rarely predominate in the early years of HIV-1 infection.
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Affiliation(s)
- Lucía Pérez-Alvarez
- Area de Patogenia Viral, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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17
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Kalpana A, Srikanth T, Abhay J, Sushama J, Swarali K, Ramesh P. gp120 sequences from HIV type 1 subtype C early seroconverters in India. AIDS Res Hum Retroviruses 2004; 20:889-94. [PMID: 15320993 DOI: 10.1089/0889222041725217] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A limited number of full-length gp120 sequences are currently available for subtype C HIV-1 from India. Sequence data from HIV-1 subtype C in early seroconverter stage virus are also very limited. With the objective of identifying the sequence variation in early seroconverters, we compared Indian subtype C gp120 sequences obtained from six early seroconverters presented in this study with non-Indian subtype C sequences from other parts of the world obtained from the Los Alamos database and subtype C potential vaccine candidate sequences. All these samples were collected within a few weeks of seroconversion and hence they represent gp120 sequences of currently circulating viral strains in India. The phylogenetic tree indicated that the Indian sequences compared here clustered together within the C clade. The seroconverter sequences presented in the study would surely help in identifying the immunogenic epitopes and could be utilized further for developing effective prophylactic strategies against HIV-1 subtype C for India.
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Affiliation(s)
- Agnihotri Kalpana
- Department of Molecular Virology, National AIDS Research Institute, Pune, India
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18
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Sibanda EN, Stanczuk G, Kasolo F. HIV/AIDS in Central Africa: pathogenesis, immunological and medical issues. Int Arch Allergy Immunol 2004; 132:183-95. [PMID: 14646379 DOI: 10.1159/000074299] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The estimated worldwide prevalence of human immunodeficiency virus (HIV) infections topped 52.5 million in June 2003, a mere 20 years after the aetiological agent was shown to be a sexually transmissible virus with a predilection for CD4+ T lymphocytes. More than 22 million people have died of the acquired immunodeficiency syndrome (AIDS) and the condition has in one generation become the most devastating and persistent epidemics in recorded history. More than two thirds of the world total of HIV-infected people live in Sub-Saharan Africa. In Central and Southern Africa at least 20% of the adult population is infected. As these adults die, they leave increasing numbers of orphans. Life expectancy at birth declined by 10 years per decade since the late 1980s to 50 years in the late 1990s, and in Botswana it is estimated to be as low as 33 years by 2010. The epidemic is increasing unabated and prospects for a curative or protective vaccine remain remote. The impact on HIV in Africa has been so profound that it influences political, economic, agriculture/food security, social, education, defence, science and health considerations. The medical and in particular immunology communities in Central Africa have the invidious challenge of on the one hand diagnosing the condition, monitoring its impact and contributing to treatment and management efforts. The science and clinical practice of immunology is challenged to find answers to the epidemic, perhaps including a vaccine. In this review we address the peculiarities of the HIV epidemic in Africa, its epidemiology and immunopathogenesis. We address the effect of the epidemic on individual patients, in their homes, workplaces and the knock-on effects on families and friends of the infected. Respective specialists discuss special groups (women, children) that are predominantly seen in Africa. We also discuss the impact of the epidemic on the clinical practice of medicine in general and challenges faced in the introduction of antiretroviral medicines. We also discuss options available for the diagnosis, treatment and monitoring of HIV-infected patients in this region.
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Affiliation(s)
- Elopy Nimele Sibanda
- Department of Immunology, University of Zimbabwe College of Medicine, Harare, Zimbabwe.
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Moore JP, Kitchen SG, Pugach P, Zack JA. The CCR5 and CXCR4 coreceptors--central to understanding the transmission and pathogenesis of human immunodeficiency virus type 1 infection. AIDS Res Hum Retroviruses 2004; 20:111-26. [PMID: 15000703 DOI: 10.1089/088922204322749567] [Citation(s) in RCA: 327] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In this review, we will discuss what is known, what is suspected, and what still remains obscure about the central role played by coreceptor expression and usage in the transmission and pathogenic consequences of human immunodeficiency virus type 1 (HIV-1) infection. An emphasis will be on the HIV-1 phenotypic variants that are defined by their usage of the CCR5 or CXCR4 coreceptors, and how the different cellular tropism of these variants influences how and where HIV-1 replicates in vivo. We will also review what might happen when coreceptor antagonists are used clinically to treat HIV-1 infection.
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Affiliation(s)
- John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York 10021, USA.
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20
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21
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Papathanasopoulos MA, Hunt GM, Tiemessen CT. Evolution and diversity of HIV-1 in Africa--a review. Virus Genes 2003; 26:151-63. [PMID: 12803467 DOI: 10.1023/a:1023435429841] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The HIV/AIDS pandemic represents a major development crisis for the African continent, which is the worst affected region in the world. Currently, almost 30 of the 42 million people infected with HIV worldwide live in Africa. AIDS in humans is caused by two lentiviruses, HIV-1 and HIV-2, which entered the human population by zoonotic transmissions from at least two different African primate species. Extensive phylogenetic analyses of partial and full-length genome sequences have helped to gain insights into the evolutionary biology and population dynamics of HIV. One of the major characteristics of HIV is its rapid evolution, which has resulted in substantial genetic diversity amongst different isolates, the majority of which are represented in Africa. Genetic variability of HIV and any consequent phenotypic variation poses a significant challenge to disease control and surveillance in different geographic regions of Africa. This review focuses on the origins and evolution of HIV, current classification and diversity of HIV isolates in Africa and provides an extensive account of the geographic distribution of HIV types, groups, and subtypes in each of the 49 African countries. Numerous epidemiological studies have provided a picture of HIV distribution patterns in most countries in Africa, and these show increasing evidence of the importance of HIV-1 recombinants. In particular, this review highlights that our current understanding of HIV distribution in Africa is incomplete and inadequately represents the diversity of the virus, and underscores the need for ongoing surveillance.
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Affiliation(s)
- Maria A Papathanasopoulos
- AIDS Virus Research Unit, National Institute for Communicable Diseases, Department of Virology, University of the Witwatersrand, Johannesburg, South Africa.
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Nájera R, Delgado E, Pérez-Alvarez L, Thomson MM. Genetic recombination and its role in the development of the HIV-1 pandemic. AIDS 2003; 16 Suppl 4:S3-16. [PMID: 12698994 DOI: 10.1097/00002030-200216004-00002] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Rafael Nájera
- Department of Viral Patogénesis, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
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23
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Williamson C, Morris L, Maughan MF, Ping LH, Dryga SA, Thomas R, Reap EA, Cilliers T, van Harmelen J, Pascual A, Ramjee G, Gray G, Johnston R, Karim SA, Swanstrom R. Characterization and selection of HIV-1 subtype C isolates for use in vaccine development. AIDS Res Hum Retroviruses 2003; 19:133-44. [PMID: 12639249 DOI: 10.1089/088922203762688649] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
HIV-1 genetic diversity among circulating strains presents a major challenge for HIV-1 vaccine development, particularly for developing countries where less sequence information is available. To identify representative viruses for inclusion in candidate vaccines targeted for South Africa, we applied an efficient sequence survey strategy to samples from recently and chronically infected persons residing in potential vaccine trial sites. All 111 sequences were subtype C, including 30 partial gag, 26 partial pol, 27 V2-V3 env, and 28 V5-partial gp41 sequences. Of the 10 viruses cultured from recently infected individuals, 9 were R5 and 1 was R5X4. Two isolates, Du151 and Du422, collected within 2 months of infection, were selected as vaccine strains on the basis of their amino acid similarity to a derived South African consensus sequence The selection of recently transmitted R5 isolates for vaccine design may provide an advantage in a subtype C R5-dominant epidemic. The full-length Du422 gag and Du151 pol and env genes were cloned into the Venezuelan equine encephalitis (VEE) replicon particle (VRP) expression system. Du422 Gag protein expressed from the VRP accumulated to a high level and was immunogenic as demonstrated by cytotoxic T lymphocyte responses in mice vaccinated with gag-VRPs. Optimization of codon use for VRP expression in human cells did not enhance expression of the gag gene. The cloned Du151 env gene encoded a functional protein as demonstrated by fusion of VRP-infected cells with cells expressing CD4 and CCR5. Genes identified in this study have been incorporated into the VEE VRP candidate vaccines targeted for clinical trial in South Africa.
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Affiliation(s)
- Carolyn Williamson
- Division of Medical Virology, University of Cape Town, Observatory, Cape Town, South Africa 7925.
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Thomson MM, Pérez-Alvarez L, Nájera R. Molecular epidemiology of HIV-1 genetic forms and its significance for vaccine development and therapy. THE LANCET. INFECTIOUS DISEASES 2002; 2:461-71. [PMID: 12150845 DOI: 10.1016/s1473-3099(02)00343-2] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Since their initial expansion in human beings roughly seven decades ago in central Africa, the HIV-1 pandemic strains have diversified extensively through mutation and recombination. 24 circulating genetic forms of the main HIV-1 group are presently recognised, including 11 subtypes or sub-subtypes and 13 circulating recombinant forms. New genetic forms are being introduced in different areas of the world, changing the molecular epidemiology of the infection. It is generally agreed that the control of the HIV-1 pandemic requires the development of vaccines that efficiently protect against the range of HIV-1 genetic forms. The introduction of effective antiretroviral therapies in areas of high HIV-1 prevalence may also contribute to the control of the pandemic, as has been documented in developed countries. Efficient targeting of the extensive genetic diversity of HIV-1 constitutes one of the major challenges in present efforts against the pandemic, although the significance of HIV-1 genetic forms for vaccine development and therapy remains to be defined.
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Affiliation(s)
- Michael M Thomson
- Department of Viral Pathogenesis, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Ctra Majadahonda-Pozuelo, 28220, Madrid, Majadahonda, Spain
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25
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