501
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Bansal A, Gough E, Ritter D, Wilson C, Mulenga J, Allen S, Goepfert PA. Group M-based HIV-1 Gag peptides are frequently targeted by T cells in chronically infected US and Zambian patients. AIDS 2006; 20:353-60. [PMID: 16439868 DOI: 10.1097/01.aids.0000206501.16783.67] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The enormous sequence diversity of HIV-1 has been a major obstacle in the development of a globally useful vaccine for AIDS. The consensus and ancestral sequence-based immunogens minimize the genetic distance between contemporary isolates and vaccine strains. Hence these sequences may be promising candidates for HIV vaccines or serve as a universal reagent set for evaluating Gag-specific responses. METHODS In this study, we measured the T-cell reactivity to consensus (subtype A, B, C and group M), ancestral (group M and subtype B) and HXB2 Gag peptides (15-mers overlapping by 11) in HIV-1-infected subjects from two reference populations. We evaluated the Gag-specific T-cell responses in 43 chronically infected US (subtype B) and 13 Zambian (subtype C) subjects using an interferon-gamma enzyme-linked immunosorbent spot assay. RESULTS Our findings demonstrate a broad cross-reactivity of nearly 70% among all the seven Gag immunogens evaluated. Consensus M sequences elicited similar levels of responses as did the consensus B, ancestral subtype B and HXB2 peptides in subtype B-infected US patients. In subtype C-infected Zambian subjects, responses of similar breadth and magnitude were elicited by consensus C, consensus M and ancestral M peptides. CONCLUSION Our data demonstrate that peptide pools based on consensus or ancestral M-based sequences can be used to evaluate Gag-specific responses elicited by subtype B or subtype C-based immunogens.
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Affiliation(s)
- Anju Bansal
- Department of Medicine, Emory University, Atlanta, Georgia, USA
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502
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Nathanson N. Virus perpetuation in populations: biological variables that determine persistence or eradication. ARCHIVES OF VIROLOGY. SUPPLEMENTUM 2006:3-15. [PMID: 16355865 PMCID: PMC7121194 DOI: 10.1007/3-211-29981-5_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In this review, I use the term “perpetuation” for persistence of a virus in a population, since this is a different phenomenon from persistence of a virus in an infected host. Important variables that influence perpetuation differ in small (<1,000 individuals) and large (>10,000) populations: in small populations, two important variables are persistence in individuals, and turnover of the population, while in large populations important variables are transmissibility, generation time, and seasonality. In small populations, viruses such as poliovirus that cause acute infections cannot readily be perpetuated, in contrast to viruses such as hepatitis B virus, that cause persistent infections. However, small animal populations can turnover significantly each year, permitting the perpetuation of some viruses that cause acute infections. Large populations of humans are necessary for the perpetuation of acute viruses; for instance, measles required a population of 500,000 for perpetuation in the pre-measles vaccine era. Furthermore, if an acute virus, such as poliovirus, exhibits marked seasonality in large populations, then it may disappear during the seasonal trough, even in the presence of a large number of susceptible persons. Eradication is the converse of perpetuation and can be used as a definitive approach to the control of a viral disease, as in the instance of smallpox. Therefore, the requirements for perpetuation have significant implications for practical public health goals.
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Affiliation(s)
- N Nathanson
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA.
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503
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Brown SA, Slobod KS, Surman S, Zirkel A, Zhan X, Hurwitz JL. Individual HIV type 1 envelope-specific T cell responses and epitopes do not segregate by virus subtype. AIDS Res Hum Retroviruses 2006; 22:188-94. [PMID: 16478402 DOI: 10.1089/aid.2006.22.188] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 vaccines are often designed to target one or several virus subtype(s). They therefore include antigens (e.g., env or env/gag/pol) from each targeted subtype to elicit subtype-directed immunity. To determine if individual T cells respond to HIV-1 antigens in a subtype-directed manner, we selected four T cell hybridomas, each representative of a different immunodominant response toward a subtype B envelope. Hybridomas were tested for responses toward 20 subtype B envelope proteins and one protein each from subtypes A, C, and D. None of the hybridomas cross-reacted with all subtype B envelopes, yet three responded to a non-B protein. Core epitopes and flanking regions affected responsiveness. This lack of subtype-directed activity was corroborated by analyses of the Los Alamos database; like immune responses, epitope distributions were not dictated by subtype. Results highlight the difficulty of predicting immune responses based on subtype alone and encourage considerations of antigenic disparity in addition to subtype disparity during HIV-1 vaccine design.
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Affiliation(s)
- S A Brown
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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504
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Tomaras GD, Shen X, Greenberg ML. Antibody responses and virus escape: implications for HIV-1 vaccine and therapeutic design. Future Virol 2006. [DOI: 10.2217/17460794.1.1.79] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
HIV-1 can escape from neutralizing antibodies rapidly during natural infection. Evolution of antibody escape is an important consideration for both vaccine and therapeutic development. Recent studies highlight both the potential strength of specific monoclonal antibody therapies for decreasing viral load and the need to understand virus escape in this setting. For envelope-based vaccine strategies, a greater understanding of both type- specific and more conserved neutralizing epitopes in addition to the evolution of these epitopes and the HIV envelope in response to selective pressure is critical in understanding and predicting vaccine efficacy. The pattern of virus envelope evolution, as a result of escape from antibody pressure, may be used ultimately to decipher the antibody specificities responsible for virus suppression and determine if a particular vaccine design or therapeutic regimen is potentially detrimental or highly beneficial to host survival. Integrative approaches using both traditional experimental methods and computational immunology for detailed mapping of virus envelope evolution in response to selective pressure may drive future innovations in HIV vaccines and therapeutic interventions.
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Affiliation(s)
- Georgia D Tomaras
- Duke University Medical Center, BOX 2926 Departments of Surgery and Immunology, Centers for AIDS Research (CFAR) and Virology, Rm 205 SORF, LaSalle Street Ext., Durham, NC 27710, USA
| | - Xiaoying Shen
- Duke University Medical Center, Department of Surgery, Center for AIDS Research (CFAR), Durham, NC 27710, USA
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505
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McKinnon LR, Ball TB, Kimani J, Wachihi C, Matu L, Luo M, Embree J, Fowke KR, Plummer FA. Cross-clade CD8(+) T-cell responses with a preference for the predominant circulating clade. J Acquir Immune Defic Syndr 2005; 40:245-9. [PMID: 16249696 DOI: 10.1097/01.qai.0000184858.16447.04] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Human immunodeficiency virus (HIV) genetic diversity is a major impediment to the design of a successful vaccine. Even if an HIV vaccine is proven effective, it remains to be seen whether this protection will extend to inter-clade, intra-clade, and recombinant strains. We used recombinant vaccinia-based interferon gamma (IFN) Elispot assays to test the inter-clade crossreactivity of clades A, B, C, and D HIV Env in two cohorts of HIV-infected Kenyans. Despite the tremendous diversity in this HIV protein, a substantial proportion of multi-clade responses were observed. Although these multi-clade responses correlated well with each other in regression analyses, clade A responses were seen at a higher frequency and at greater relative magnitudes in a proportion of these patients, when compared to the other three clades. Epitope mapping indicates CD8(+) T cell recognition of conserved regions of Env, accounting for the high degree of cross-reactivity but not the clade A preference. A better understanding of cross-clade CD8(+) T cell responses to HIV may help to predict whether a successful vaccine could be used to stop geographically and genetically distinct HIV epidemics.
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Affiliation(s)
- Lyle R McKinnon
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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506
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Gupta RM, Prasad VVSP, Rai A, Seth P. Analysis of HIV type 1 subtype C full-length gag gene sequences from India: novel observations and plausible implications. AIDS Res Hum Retroviruses 2005; 21:1066-72. [PMID: 16379612 DOI: 10.1089/aid.2005.21.1066] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Twenty-four HIV-1 gag genes from patients in India were sequenced and analyzed. All measured 1476-1491 nucleotides with an average of 1483 nucleotides in length. Phylogenetic analysis revealed a homogeneous epidemic of HIV-1 subtype C. Intragenotypic divergence of up to 6.6% was present. Fourteen novel conserved signature pattern residues were delineated for HIV-1 subtype C strains. Each of the 15 nucleocapsid (NC) basic residues was highly conserved p6 gag LXSLFG and PT/SAPP motifs were highly conserved except for PTVPT in three and PTAPT in two strains. Zinc finger motifs were conserved in all. Documented HIV-1 subtype C gag immunodominant CTL epitopes were conserved. The evolving predominance and the change in nature of the epidemic from Thai B to that of subtype C in the Northeastern regions of India were observed. Tracking the evolution of the Indian epidemic has implications for developing a vaccine.
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Affiliation(s)
- R M Gupta
- Department of Microbiology, Armed Forces Medical College, Pune, India
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507
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Affiliation(s)
- Robert C Gallo
- Institute of Human Virology, University of Maryland Biotechnology Institute, University of Maryland Baltimore, Baltimore, MD, USA.
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508
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Allen TM, Altfeld M, Geer SC, Kalife ET, Moore C, O'sullivan KM, Desouza I, Feeney ME, Eldridge RL, Maier EL, Kaufmann DE, Lahaie MP, Reyor L, Tanzi G, Johnston MN, Brander C, Draenert R, Rockstroh JK, Jessen H, Rosenberg ES, Mallal SA, Walker BD. Selective escape from CD8+ T-cell responses represents a major driving force of human immunodeficiency virus type 1 (HIV-1) sequence diversity and reveals constraints on HIV-1 evolution. J Virol 2005; 79:13239-49. [PMID: 16227247 PMCID: PMC1262562 DOI: 10.1128/jvi.79.21.13239-13249.2005] [Citation(s) in RCA: 280] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The sequence diversity of human immunodeficiency virus type 1 (HIV-1) represents a major obstacle to the development of an effective vaccine, yet the forces impacting the evolution of this pathogen remain unclear. To address this issue we assessed the relationship between genome-wide viral evolution and adaptive CD8+ T-cell responses in four clade B virus-infected patients studied longitudinally for as long as 5 years after acute infection. Of the 98 amino acid mutations identified in nonenvelope antigens, 53% were associated with detectable CD8+ T-cell responses, indicative of positive selective immune pressures. An additional 18% of amino acid mutations represented substitutions toward common clade B consensus sequence residues, nine of which were strongly associated with HLA class I alleles not expressed by the subjects and thus indicative of reversions of transmitted CD8 escape mutations. Thus, nearly two-thirds of all mutations were attributable to CD8+ T-cell selective pressures. A closer examination of CD8 escape mutations in additional persons with chronic disease indicated that not only did immune pressures frequently result in selection of identical amino acid substitutions in mutating epitopes, but mutating residues also correlated with highly polymorphic sites in both clade B and C viruses. These data indicate a dominant role for cellular immune selective pressures in driving both individual and global HIV-1 evolution. The stereotypic nature of acquired mutations provides support for biochemical constraints limiting HIV-1 evolution and for the impact of CD8 escape mutations on viral fitness.
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Affiliation(s)
- Todd M Allen
- Howard Hughes Medical Institute, Partners AIDS Research Center, and Infectious Disease Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
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509
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Lian Y, Srivastava I, Gómez-Román VR, Zur Megede J, Sun Y, Kan E, Hilt S, Engelbrecht S, Himathongkham S, Luciw PA, Otten G, Ulmer JB, Donnelly JJ, Rabussay D, Montefiori D, van Rensburg EJ, Barnett SW. Evaluation of envelope vaccines derived from the South African subtype C human immunodeficiency virus type 1 TV1 strain. J Virol 2005; 79:13338-49. [PMID: 16227256 PMCID: PMC1262580 DOI: 10.1128/jvi.79.21.13338-13349.2005] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Accepted: 07/27/2005] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) subtype C infections are on the rise in Sub-Saharan Africa and Asia. Therefore, there is a need to develop an HIV vaccine capable of eliciting broadly reactive immune responses against members of this subtype. We show here that modified HIV envelope (env) DNA vaccines derived from the South African subtype C TV1 strain are able to prime for humoral responses in rabbits and rhesus macaques. Priming rabbits with DNA plasmids encoding V2-deleted TV1 gp140 (gp140TV1DeltaV2), followed by boosting with oligomeric protein (o-gp140TV1DeltaV2) in MF59 adjuvant, elicited higher titers of env-binding and autologous neutralizing antibodies than priming with DNA vaccines encoding the full-length TV1 env (gp160) or the intact TV1 gp140. Immunization with V2-deleted subtype B SF162 env and V2-deleted TV1 env together using a multivalent vaccine approach induced high titers of oligomeric env-binding antibodies and autologous neutralizing antibodies against both the subtypes B and C vaccine strains, HIV-1 SF162 and TV1, respectively. Low-level neutralizing activity against the heterologous South African subtype C TV2 strain, as well as a small subset of viruses in a panel of 13 heterologous primary isolates, was observed in some rabbits immunized with the V2-deleted vaccines. Immunization of rhesus macaques with the V2-deleted TV1 DNA prime/protein boost also elicited high titers of env-binding antibodies and moderate titers of autologous TV1 neutralizing antibodies. The pilot-scale production of the various TV1 DNA vaccine constructs and env proteins described here should provide an initial platform upon which to improve the immunogenicity of these subtype C HIV envelope vaccines.
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Affiliation(s)
- Ying Lian
- Chiron Corp., 4560 Horton St., 4.3, Emeryville, CA 94608.
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510
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Derdeyn CA, Silvestri G. Viral and host factors in the pathogenesis of HIV infection. Curr Opin Immunol 2005; 17:366-73. [PMID: 15955686 DOI: 10.1016/j.coi.2005.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Accepted: 06/01/2005] [Indexed: 01/02/2023]
Abstract
Recent studies suggest that the pathogenesis of HIV infection and AIDS involves two distinct phases. During acute infection, massive depletion of CD4+CCR5+ memory T cells within the mucosal-associated lymphoid tissue leads to major and potentially irreversible damage to CD4+ T-cell-mediated immune functions. The emergence of potent, but ultimately ineffective, cell-mediated and humoral responses to HIV leads to the chronic phase of infection, which is characterized by partial control of viral replication, chronic immune activation, progressive decline of the naïve and memory T-cell pool, and systemic CD4+ T-cell depletion. The identification of these two pathogenic phases of HIV infection could have important implications in terms of HIV therapy and vaccine development.
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Affiliation(s)
- Cynthia A Derdeyn
- Division of Infectious Diseases, Department of Pathology, and Emory Vaccine Center, Emory University, 954 Gatewood Road NE, Atlanta, Georgia 30329, USA
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511
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Thomson SA, Jaramillo AB, Shoobridge M, Dunstan KJ, Everett B, Ranasinghe C, Kent SJ, Gao K, Medveckzy J, Ffrench RA, Ramshaw IA. Development of a synthetic consensus sequence scrambled antigen HIV-1 vaccine designed for global use. Vaccine 2005; 23:4647-57. [PMID: 15964105 DOI: 10.1016/j.vaccine.2005.04.045] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2005] [Revised: 03/18/2005] [Accepted: 04/28/2005] [Indexed: 10/25/2022]
Abstract
Induction of high levels of broadly reactive cytotoxic T lymphocytes (CTL) remains a promising approach for an effective HIV-1 vaccine. We have developed a novel genetic-based vaccine strategy that encodes consensus overlapping peptide sets from all HIV-1 proteins scrambled together. This synthetic scrambled antigen vaccine (SAVINE) strategy has significant advantages, e.g. capacity to encode more antigens safely and is very flexible compared to traditional isolate-based strategies. The SAVINE vaccine strategy is clearly immunogenic, being able to restimulate a range of human HIV-1 specific responses in vitro and induce HIV-1 specific immunity in vivo in mice. Interestingly, different in vivo delivery strategies affected the resulting immunity and immunodominance pattern in mice. This platform strategy could be used for other infections and cancers where T cell responses are important for protection.
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Affiliation(s)
- Scott A Thomson
- Division of Immunology and Genetics, John Curtin School of Medical Research (JCSMR), Australian National University, P.O. Box 334, Canberra, ACT 2601, Australia.
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512
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Tetteh KKA, Cavanagh DR, Corran P, Musonda R, McBride JS, Conway DJ. Extensive antigenic polymorphism within the repeat sequence of the Plasmodium falciparum merozoite surface protein 1 block 2 is incorporated in a minimal polyvalent immunogen. Infect Immun 2005; 73:5928-35. [PMID: 16113313 PMCID: PMC1231057 DOI: 10.1128/iai.73.9.5928-5935.2005] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polymorphism in pathogen antigens presents a complex challenge for vaccine design. A prime example is the N-terminal block 2 region of the Plasmodium falciparum merozoite surface protein 1 (MSP1), to which allele-specific antibodies have been associated with protection from malaria. In a Zambian population studied here, 49 of 91 alleles sampled were of the K1-like type (the most common of three block 2 types in all African populations), and most of these had unique sequences due to variation in tri- and hexapeptide repetitive motifs. There were significant negative correlations between allelic sequence lengths of different regions of the repeats, so the complete repeat sequence had less length variation than its component parts, suggesting a constraint on overall length. Diverse epitopes recognized by three murine monoclonal antibodies and 24 individual human sera were then mapped by using a comprehensive panel of synthetic peptides, revealing epitopes in all regions of the repeats. To incorporate these different epitopes in a single molecule, a composite sequence of minimal overall length (78 amino acids) was then designed and expressed as a recombinant antigen. More human immune sera reacted with this "K1-like Super Repeat" antigen than with proteins consisting of single natural allelic sequences, and immunization of mice elicited antibodies that recognized a range of five cultured parasite lines with diverse K1-like MSP1 block 2 repeat sequences. Thus, complex allelic polymorphism was deconstructed and a minimal composite polyvalent antigen was engineered, delivering a designed candidate sequence for inclusion in a malaria vaccine.
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Affiliation(s)
- Kevin K A Tetteh
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St., London WC1E 7HT, United Kingdom.
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513
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Akouamba BS, Viel J, Charest H, Merindol N, Samson J, Lapointe N, Brenner BG, Lalonde R, Harrigan PR, Boucher M, Soudeyns H. HIV-1 genetic diversity in antenatal cohort, Canada. Emerg Infect Dis 2005; 11:1230-4. [PMID: 16102312 PMCID: PMC3320510 DOI: 10.3201/eid1108.040877] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We studied HIV genetic diversity in a cohort of 127 pregnant, HIV-infected women who received prenatal care at Sainte-Justine Hospital in Montreal, Canada, between 1999 and 2003. Clade assignments were derived by phylogenetic analysis of amplified pol sequences. Genotyping was successful in 103 of 127 women, 59 (57.3%) of whom were infected with clade B HIV-1, and 44 (42.7%) with nonclade B viruses, including subtypes A, C, D, F, G, and H. Four sequences remained unassigned. Forty-three of 44 women infected with non-clade B viruses were newcomers from sub-Saharan Africa, and subtype identity was consistent with those circulating in their countries of origin. These results highlight the epidemiologic importance of non-B HIV-1 in antenatal populations in a large North American urban center, underscore the influence of population movements on clade intermixing, and identify a group of patients who could be targeted for surveillance and drug therapy followup.
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Affiliation(s)
- Bertine S. Akouamba
- Hôpital Sainte-Justine, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Janique Viel
- Hôpital Sainte-Justine, Montreal, Quebec, Canada
| | - Hugues Charest
- Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Natacha Merindol
- Hôpital Sainte-Justine, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | | | - Normand Lapointe
- Hôpital Sainte-Justine, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Bluma G. Brenner
- Lady Davis Institute for Medical Research, Montreal, Quebec, Canada
| | | | - P. Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Marc Boucher
- Hôpital Sainte-Justine, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Hugo Soudeyns
- Hôpital Sainte-Justine, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
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514
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Doria-Rose NA, Learn GH, Rodrigo AG, Nickle DC, Li F, Mahalanabis M, Hensel MT, McLaughlin S, Edmonson PF, Montefiori D, Barnett SW, Haigwood NL, Mullins JI. Human immunodeficiency virus type 1 subtype B ancestral envelope protein is functional and elicits neutralizing antibodies in rabbits similar to those elicited by a circulating subtype B envelope. J Virol 2005; 79:11214-24. [PMID: 16103173 PMCID: PMC1193599 DOI: 10.1128/jvi.79.17.11214-11224.2005] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Accepted: 06/07/2005] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) is a difficult target for vaccine development, in part because of its ever-expanding genetic diversity and attendant capacity to escape immunologic recognition. Vaccine efficacy might be improved by maximizing immunogen antigenic similarity to viruses likely to be encountered by vaccinees. To this end, we designed a prototype HIV-1 envelope vaccine using a deduced ancestral state for the env gene. The ancestral state reconstruction method was shown to be >95% accurate by computer simulation and 99.8% accurate when estimating the known inoculum used in an experimental infection study in rhesus macaques. Furthermore, the deduced ancestor gene differed from the set of sequences used to derive the ancestor by an average of 12.3%, while these latter sequences were an average of 17.3% different from each other. A full-length ancestral subtype B HIV-1 env gene was constructed and shown to produce a glycoprotein of 160 kDa that bound and fused with cells expressing the HIV-1 coreceptor CCR5. This Env was also functional in a virus pseudotype assay. When either gp160- or gp140-expressing plasmids and recombinant gp120 were used to immunize rabbits in a DNA prime-protein boost regimen, the artificial gene induced immunoglobulin G antibodies capable of weakly neutralizing heterologous primary HIV-1 strains. The results were similar for rabbits immunized in parallel with a natural isolate, HIV-1 SF162. Further design efforts to better present conserved neutralization determinants are warranted.
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515
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Ray SC, Fanning L, Wang XH, Netski DM, Kenny-Walsh E, Thomas DL. Divergent and convergent evolution after a common-source outbreak of hepatitis C virus. ACTA ACUST UNITED AC 2005; 201:1753-9. [PMID: 15939791 PMCID: PMC2213258 DOI: 10.1084/jem.20050122] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The genomic sequences of viruses that are highly mutable and cause chronic infection tend to diverge over time. We report that these changes represent both immune-driven selection and, in the absence of immune pressure, reversion toward an ancestral consensus. Sequence changes in hepatitis C virus (HCV) structural and nonstructural genes were studied in a cohort of women accidentally infected with HCV in a rare common-source outbreak. We compared sequences present in serum obtained 18–22 yr after infection to sequences present in the shared inoculum and found that HCV evolved along a distinct path in each woman. Amino acid substitutions in known epitopes were directed away from consensus in persons having the HLA allele associated with that epitope (immune selection), and toward consensus in those lacking the allele (reversion). These data suggest that vaccines for genetically diverse viruses may be more effective if they represent consensus sequence, rather than a human isolate.
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Affiliation(s)
- Stuart C Ray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.
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516
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Li M, Gao F, Mascola JR, Stamatatos L, Polonis VR, Koutsoukos M, Voss G, Goepfert P, Gilbert P, Greene KM, Bilska M, Kothe DL, Salazar-Gonzalez JF, Wei X, Decker JM, Hahn BH, Montefiori DC. Human immunodeficiency virus type 1 env clones from acute and early subtype B infections for standardized assessments of vaccine-elicited neutralizing antibodies. J Virol 2005; 79:10108-25. [PMID: 16051804 PMCID: PMC1182643 DOI: 10.1128/jvi.79.16.10108-10125.2005] [Citation(s) in RCA: 946] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Accepted: 05/09/2005] [Indexed: 01/16/2023] Open
Abstract
Induction of broadly cross-reactive neutralizing antibodies is a high priority for AIDS vaccine development but one that has proven difficult to be achieved. While most immunogens generate antibodies that neutralize a subset of T-cell-line-adapted strains of human immunodeficiency virus type 1 (HIV-1), none so far have generated a potent, broadly cross-reactive response against primary isolates of the virus. Even small increments in immunogen improvement leading to increases in neutralizing antibody titers and cross-neutralizing activity would accelerate vaccine development; however, a lack of uniformity in target strains used by different investigators to assess cross-neutralization has made the comparison of vaccine-induced antibody responses difficult. Thus, there is an urgent need to establish standard panels of HIV-1 reference strains for wide distribution. To facilitate this, full-length gp160 genes were cloned from acute and early subtype B infections and characterized for use as reference reagents to assess neutralizing antibodies against clade B HIV-1. Individual gp160 clones were screened for infectivity as Env-pseudotyped viruses in a luciferase reporter gene assay in JC53-BL (TZM-bl) cells. Functional env clones were sequenced and their neutralization phenotypes characterized by using soluble CD4, monoclonal antibodies, and serum samples from infected individuals and noninfected recipients of a recombinant gp120 vaccine. Env clones from 12 R5 primary HIV-1 isolates were selected that were not unusually sensitive or resistant to neutralization and comprised a wide spectrum of genetic, antigenic, and geographic diversity. These reference reagents will facilitate proficiency testing and other validation efforts aimed at improving assay performance across laboratories and can be used for standardized assessments of vaccine-elicited neutralizing antibodies.
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Affiliation(s)
- Ming Li
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
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517
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Abstract
OBJECTIVE To review the past 10 years of published research on human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) in the United States, including psychosocial and psychiatric risk factors, epidemiology, biology, neurocognitive and psychiatric sequelae, disclosure issues, prevention strategies, and biological and behavioral treatments. METHOD Researchers reviewed the English-language literature with a focus on child and adolescent risk factors associated with HIV/AIDS, prevention, and treatment. RESULTS Substantial scientific advances have occurred over the past two decades leading to decreased morbidity and mortality in the United States from AIDS-related opportunistic infections. At the same time, rates of HIV infection are increasing in teenagers, young women, and minorities, and growing numbers of youths are living with an infected family member. Understanding HIV risk behavior requires a broad theoretical framework. Comprehensive HIV prevention programs have led to reduced risk behavior among HIV-affected youths and teens at risk of infection. Biological and behavioral treatments of HIV infection continue to evolve and have led to longer life span, improved quality of life, and fewer psychiatric problems. CONCLUSIONS HIV/AIDS has significant mental health implications, and psychiatry can play a critical role in curbing the epidemic. With minimal effort, mental health professionals can adapt and apply the strategies that they use to treat psychiatric symptoms to prevent HIV transmission behaviors.
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518
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Boggiano C, Moya R, Pinilla C, Bihl F, Brander C, Sidney J, Sette A, Blondelle SE. Discovery and characterization of highly immunogenic and broadly recognized mimics of the HIV-1 CTL epitope Gag77-85. Eur J Immunol 2005; 35:1428-37. [PMID: 15789356 DOI: 10.1002/eji.200425903] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human immunodeficiency virus (HIV)-specific cytotoxic T lymphocytes (CTL) play an important role in HIV infection. Given the viral genetic diversity, the selection of suitable antigens and epitope variants will be important in the design of an effective vaccine. We have previously shown that combinatorial libraries are useful tools to identify epitope mimics as well as potentially cross-reactive natural sequences in protein databases. We have applied this approach to the HIV Gag p17-derived epitope SL9 (SLYNTVATL) to identify broadly recognized SL9 mimics and to assess the cross-recognition of naturally occurring SL9 variants. Nine nonapeptides were identified that were up to one order of magnitude more effective than SL9 in stimulating CTL responses in PBMC from HIV-infected subjects. Using transgenic mice, we demonstrate that a number of these epitope mimics were able to generate de novo T cell responses that cross-reacted with the original SL9 sequence. Particularly, mimics with changes at the relatively conserved F-pocket anchor residue were frequently cross-recognized. This approach may lead to vaccine candidates with higher in vivo immunogenicity and increased potential for cross-recognition of naturally occurring SL9 variants.
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Affiliation(s)
- César Boggiano
- Torrey Pines Institute for Molecular Studies, San Diego, USA
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519
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Altfeld M, Allen TM, Kalife ET, Frahm N, Addo MM, Mothe BR, Rathod A, Reyor LL, Harlow J, Yu XG, Perkins B, Robinson LK, Sidney J, Alter G, Lichterfeld M, Sette A, Rosenberg ES, Goulder PJR, Brander C, Walker BD. The majority of currently circulating human immunodeficiency virus type 1 clade B viruses fail to prime cytotoxic T-lymphocyte responses against an otherwise immunodominant HLA-A2-restricted epitope: implications for vaccine design. J Virol 2005; 79:5000-5. [PMID: 15795285 PMCID: PMC1069570 DOI: 10.1128/jvi.79.8.5000-5005.2005] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) mutates to escape immune selection pressure, but there is little evidence of selection mediated through HLA-A2, the dominant class I allele in persons infected with clade B virus. Moreover, HLA-A2-restricted responses are largely absent in the acute phase of infection as the viral load is being reduced, suggesting that circulating viruses may lack immunodominant epitopes targeted through HLA-A2. Here we demonstrate an A2-restricted epitope within Vpr (Vpr59-67) that is targeted by acute-phase HIV-1-specific CD8+ T cells, but only in a subset of persons expressing HLA-A2. Individuals in the acute stage of infection with viruses containing the most common current sequence within this epitope (consensus sequence) were unable to mount epitope-specific T-cell responses, whereas subjects infected with the less frequent I60L variant all developed these responses. The I60L variant epitope was a stronger binder to HLA-A2 and was recognized by epitope-specific T cells at lower peptide concentrations than the consensus sequence epitope. These data demonstrate that HLA-A2 is capable of contributing to the acute-phase cytotoxic T-lymphocyte response in infected subjects, but that most currently circulating viruses lack a dominant immunogenic epitope presented by this allele, and suggest that immunodominant epitopes restricted by common HLA alleles may be lost as the epidemic matures.
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Affiliation(s)
- Marcus Altfeld
- Partners AIDS Research Center, Massachusetts General Hospital, 149 13th St., Boston, MA 02129, USA.
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520
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Ferreira MU, da Silva Nunes M, Wunderlich G. Antigenic diversity and immune evasion by malaria parasites. CLINICAL AND DIAGNOSTIC LABORATORY IMMUNOLOGY 2005; 11:987-95. [PMID: 15539495 PMCID: PMC524792 DOI: 10.1128/cdli.11.6.987-995.2004] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, 05508-900 São Paulo (SP), Brazil.
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521
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Slobod KS, Coleclough C, Brown SA, Stambas J, Zhan X, Surman S, Jones BG, Zirkel A, Freiden PJ, Brown B, Sealy R, Bonsignori M, Hurwitz JL. Clade, Country and Region-specific HIV-1 Vaccines: Are they necessary? AIDS Res Ther 2005; 2:3. [PMID: 15860130 PMCID: PMC1112584 DOI: 10.1186/1742-6405-2-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Accepted: 04/28/2005] [Indexed: 11/22/2022] Open
Abstract
Today, scientists are often encouraged to custom-design vaccines based on a particular country or clade. Here, we review the scientific literature and then suggest that the overwhelming endeavor to produce a unique vaccine for every world region or virus subtype may not be necessary.
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Affiliation(s)
- Karen S Slobod
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
- Department of Pediatrics, College of Medicine, 899 Madison Ave., University of Tennessee, Memphis, TN 38163 USA
| | - Chris Coleclough
- Department of Immunology, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
- Department of Pathology, College of Medicine, 899 Madison Ave., University of Tennessee, Memphis, TN 38163 USA
| | - Scott A Brown
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
| | - John Stambas
- Department of Microbiology and Immunology, University of Melbourne, Vic 3010, Australia
| | - Xiaoyan Zhan
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
| | - Sherri Surman
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
| | - Bart G Jones
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
| | - Amy Zirkel
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
| | - Pamela J Freiden
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
| | - Brita Brown
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
| | - Robert Sealy
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
| | - Mattia Bonsignori
- Department of Immunology, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
- Department of Clinical and Biological Sciences, University of Insubria, Varese, 21100, Italy
| | - Julia L Hurwitz
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
- Department of Pathology, College of Medicine, 899 Madison Ave., University of Tennessee, Memphis, TN 38163 USA
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522
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Bolesta E, Gzyl J, Wierzbicki A, Kmieciak D, Kowalczyk A, Kaneko Y, Srinivasan A, Kozbor D. Clustered epitopes within the Gag-Pol fusion protein DNA vaccine enhance immune responses and protection against challenge with recombinant vaccinia viruses expressing HIV-1 Gag and Pol antigens. Virology 2005; 332:467-79. [PMID: 15680412 DOI: 10.1016/j.virol.2004.09.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2003] [Accepted: 09/02/2004] [Indexed: 11/19/2022]
Abstract
We have generated a codon-optimized hGagp17p24-Polp51 plasmid DNA expressing the human immunodeficiency virus type 1 (HIV-1) Gag-Pol fusion protein that consists of clusters of highly conserved cytotoxic T lymphocyte (CTL) epitopes presented by multiple MHC class I alleles. In the hGagp17p24-Polp51 construct, the ribosomal frameshift site had been deleted together with the potentially immunosuppressive Gag nucleocapsid (p15) as well as Pol protease (p10) and integrase (p31). Analyses of the magnitude and breadth of cellular responses demonstrated that immunization of HLA-A2/K(b) transgenic mice with the hGagp17p24-Polp51 construct induced 2- to 5-fold higher CD8+ T-cell responses to Gag p17-, p24-, and Pol reverse transcriptase (RT)-specific CTL epitopes than the full-length hGag-PolDeltaFsDeltaPr counterpart. The increases were correlated with higher protection against challenge with recombinant vaccinia viruses (rVVs) expressing gag and pol gene products. Consistent with the profile of Gag- and Pol-specific CD8+ T cell responses, an elevated level of type 1 cytokine production was noted in p24- and RT-stimulated splenocyte cultures established from hGagp17p24-Polp51-immunized mice compared to responses induced with the hGag-PolDeltaFsDeltaPr vaccine. Sera of mice immunized with the hGagp17p24-Polp51 vaccine also exhibited an increased titer of p24- and RT-specific IgG2 antibody responses. The results from our studies provide insights into approaches for boosting the breadth of Gag- and Pol-specific immune responses.
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Affiliation(s)
- Elizabeth Bolesta
- Department of Immunology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
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523
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Melchionda F, Fry TJ, Milliron MJ, McKirdy MA, Tagaya Y, Mackall CL. Adjuvant IL-7 or IL-15 overcomes immunodominance and improves survival of the CD8+ memory cell pool. J Clin Invest 2005. [DOI: 10.1172/jci200523134] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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524
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Melchionda F, Fry TJ, Milliron MJ, McKirdy MA, Tagaya Y, Mackall CL. Adjuvant IL-7 or IL-15 overcomes immunodominance and improves survival of the CD8+ memory cell pool. J Clin Invest 2005; 115:1177-87. [PMID: 15841203 PMCID: PMC1074679 DOI: 10.1172/jci23134] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2004] [Accepted: 02/08/2005] [Indexed: 12/18/2022] Open
Abstract
Current models of T cell memory implicate a critical role for IL-7 in the effector-to-memory transition, raising the possibility that IL-7 therapy might enhance vaccine responses. IL-7 has not been studied, to our knowledge, before now for adjuvant activity. We administered recombinant human IL-7 (rhIL-7) to mice during immunization against the male antigen HY and compared these results with those obtained from mice immunized with rhIL-2 and rhIL-15. Administration of rhIL-7 or rhIL-15, but not rhIL-2, increased effector cells directed against these dominant antigens and dramatically enhanced CD8(+) effectors to subdominant antigens. The mechanisms by which the cytokines augmented effector pool generation were multifactorial and included rhIL-7-mediated costimulation and rhIL-15-mediated augmentation of the proliferative burst. The contraction phase of the antigen-specific response was exaggerated in cytokine-treated mice; however, CD8(+) memory pools in rhIL-7- or rhIL-15-treated groups demonstrated superior long-term survival resulting in quantitative advantages that remained long after the cytokines were discontinued, as demonstrated by improved survival after challenge with an HY-expressing tumor undertaken several weeks after cytokine cessation. These results confirm the adjuvant activity of rhIL-15 and demonstrate that rhIL-7 also serves as a potent vaccine adjuvant that broadens immunity by augmenting responses to subdominant antigens and improving the survival of the CD8(+) T cell memory pool.
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Affiliation(s)
- Fraia Melchionda
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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525
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Meintjes PL, Rodrigo AG. Evolution of relative synonymous codon usage in Human Immunodeficiency Virus type-1. J Bioinform Comput Biol 2005; 3:157-68. [PMID: 15751118 DOI: 10.1142/s0219720005000953] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2004] [Revised: 06/25/2004] [Accepted: 07/10/2004] [Indexed: 11/18/2022]
Abstract
Mutation in Human Immunodeficiency Virus type-1 (HIV-1) is extremely rapid, a consequence of a low-fidelity viral reverse transcription process. The envelope gene has been shown to accumulate substitutions at a rate of approximately 1% per year and can frequently spend a long time in the host (approximately 10 years). The relative synonymous codon usage (RSCU) in HIV-1 is known to be different from that of the human host. However, by reengineering the protein coding sequences of HIV-1 to reflect the RSCU patterns observed in humans, a large increase in protein expression is observed. It is reasonable to suggest that within a host there may be a selective drive for change in the RSCU of HIV-1 towards human RSCU. To test this hypothesis we analyzed HIV-1 partial envelope sequences from eight patients sampled serially in time. For each sequence, an RSCU table was constructed. Sequences were labelled as "early" or "late" depending on whether they were sampled before or after the mid-point of the study. Using the RSCU values as descriptor variables, a Principal Components Analysis (PCA) was performed. The first three components clearly discriminated between early and late sequences. We also constructed pooled groupwise RSCU tables for early and late sequences. The viral RSCU values of each of the groups were correlated with human RSCU. If there is selection for host-adaptation in RSCU, we expect that "late" viral RSCUs would tend to be more highly correlated with human RSCU than "early" viral RSCUs. In fact, tests of significance suggest that this is the case. However, closer examination of the data revealed that the apparent trend towards human RSCU can be attributed to the homogenization of the codon usage by mutation pressure rather than host adaptation.
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Affiliation(s)
- Peter L Meintjes
- Bioinformatics Institute and Computational and Evolutionary Biology Lab, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.
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526
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Pamungkas J, De Rose R, Iskandriati D, Noviana R, Paramastri Y, Dale CJ, Shoobridge M, Medveczky CJ, Ramshaw IA, Thomson S, Kent SJ. Comparison of whole gene and whole virus scrambled antigen approaches for DNA prime and fowlpox virus boost HIV type 1 vaccine regimens in macaques. AIDS Res Hum Retroviruses 2005; 21:292-300. [PMID: 15943571 DOI: 10.1089/aid.2005.21.292] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
T cell immunity plays a critical role in controlling HIV-1 viremia, and encoding a limited set of HIV-1 genes within DNA and poxvirus vectors can, when used sequentially, induce high levels of T cell immunity in primates. However, a limited breadth of T cell immunity exposes the host to potential infection with either genetically diverse HIV-1 strains or T cell escape variants of HIV-1. In an attempt to induce maximally broad immunity, we examined DNA and recombinant fowlpox virus (rFPV) vaccines encoding all HIV-1 genes derived from a global HIV-1 consensus sequence, but expressed as multiple overlapping scrambled 30-amino acid segments (scrambled antigen vaccines, or SAVINEs). Three groups of seven pigtail macaques were immunized with sets of DNA and rFPV expressing Gag/Pol antigens only, the whole genome SAVINE antigens, or no HIV-1 antigens and T cell immunity was monitored by ELISpot and intracellular cytokine staining. High levels of cross-subtype HIV-specific T cell immunity to Gag were consistently induced in the seven macaques primed with DNA and rFPV vaccines expressing Gag/Pol as intact proteins. It was, however, difficult to repeatedly boost immunity with further rFPV immunizations, presumably reflecting high levels of anti- FPV immunity. Unfortunately, this vaccine study did not consistently achieve a broadened level of T cell immunity to multiple HIV genes utilizing the novel whole-virus SAVINE approach, with only one of seven immunized animals generating broad T cell immunity to multiple HIV-1 proteins. Further refinements are planned with alternative vector strategies to evaluate the potential of the SAVINE technology.
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Affiliation(s)
- Joko Pamungkas
- Primate Research Center, Bogor Agricultural University, PSSP-IPB, Bogor, Indonesia 16151
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527
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Seaman MS, Xu L, Beaudry K, Martin KL, Beddall MH, Miura A, Sambor A, Chakrabarti BK, Huang Y, Bailer R, Koup RA, Mascola JR, Nabel GJ, Letvin NL. Multiclade human immunodeficiency virus type 1 envelope immunogens elicit broad cellular and humoral immunity in rhesus monkeys. J Virol 2005; 79:2956-63. [PMID: 15709015 PMCID: PMC548456 DOI: 10.1128/jvi.79.5.2956-2963.2005] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The development of a human immunodeficiency virus type 1 (HIV-1) vaccine that elicits potent cellular and humoral immune responses recognizing divergent strains of HIV-1 will be critical for combating the global AIDS epidemic. The present studies were initiated to examine the magnitude and breadth of envelope (Env)-specific T-lymphocyte and antibody responses generated by vaccines containing either a single or multiple genetically distant HIV-1 Env immunogens. Rhesus monkeys were immunized with DNA prime-recombinant adenovirus boost vaccines encoding a Gag-Pol-Nef polyprotein in combination with either a single Env or a mixture of clade-A, clade-B, and clade-C Envs. Monkeys receiving the multiclade Env immunization developed robust immune responses to all vaccine antigens and, importantly, a greater breadth of Env recognition than monkeys immunized with vaccines including a single Env immunogen. All groups of vaccinated monkeys demonstrated equivalent immune protection following challenge with the pathogenic simian-human immunodeficiency virus 89.6P. These data suggest that a multicomponent vaccine encoding Env proteins from multiple clades of HIV-1 can generate broad Env-specific T-lymphocyte and antibody responses without antigenic interference. This study demonstrates that it is possible to generate protective immune responses by vaccination with genetically diverse isolates of HIV-1.
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Affiliation(s)
- Michael S Seaman
- Beth Israel Deaconess Medical Center, Division of Viral Pathogenesis, 330 Brookline Ave./RE-113, Boston, MA 02215, USA
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528
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de Oliveira T, Salemi M, Gordon M, Vandamme AM, van Rensburg EJ, Engelbrecht S, Coovadia HM, Cassol S. Mapping sites of positive selection and amino acid diversification in the HIV genome: an alternative approach to vaccine design? Genetics 2005; 167:1047-58. [PMID: 15280222 PMCID: PMC1470929 DOI: 10.1534/genetics.103.018135] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A safe and effective HIV-1 vaccine is urgently needed to control the worldwide AIDS epidemic. Traditional methods of vaccine development have been frustratingly slow, and it is becoming increasingly apparent that radical new approaches may be required. Computational and mathematical approaches, combined with evolutionary reasoning, may provide new insights for the design of an efficacious AIDS vaccine. Here, we used codon-based substitution models and maximum-likelihood (ML) methods to identify positively selected sites that are likely to be involved in the immune control of HIV-1. Analysis of subtypes B and C revealed widespread adaptive evolution. Positively selected amino acids were detected in all nine HIV-1 proteins, including Env. Of particular interest was the high level of positive selection within the C-terminal regions of the immediate-early regulatory proteins, Tat and Rev. Many of the amino acid replacements were associated with the emergence of novel (or alternative) myristylation and casein kinase II (CKII) phosphorylation sites. The impact of these changes on the conformation and antigenicity of Tat and Rev remains to be established. In rhesus macaques, a single CTL-associated amino substitution in Tat has been linked to escape from acute SIV infection. Understanding the relationship between host-driven positive selection and antigenic variation may lead to the development of novel vaccine strategies that preempt the escape process.
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Affiliation(s)
- Tulio de Oliveira
- HIV Molecular Virology and Bioinformatics Laboratory, Africa Centre for Health and Population Studies, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4013, South Africa
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529
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Abstract
The third variable region, V3, of the gp120 surface envelope glycoprotein is an approximately 35-residue-long, frequently glycosylated, highly variable, disulfide-bonded structure that has a major influence on HIV-1 tropism. Thus the sequence of V3, directly or indirectly, can determine which coreceptor (CCR5 or CXCR4) is used to trigger the fusion potential of the Env complex, and hence which cells the virus can infect. V3 also influences HIV-1's sensitivity to, and ability to escape from, entry inhibitors that are being developed as antiviral drugs. For some strains, V3 is a prominent target for HIV-1 neutralizing antibodies (NAbs); indeed, for many years it was considered to be the "principal neutralization determinant" (PND). Some efforts to use V3 as a vaccine target continue to this day, despite disappointing progress over more than a decade. Recent findings on the structure, function, antigenicity, and immunogenicity of V3 cast new doubts on the value of this vaccine approach. Here, we review recent advances in the understanding of V3 as a determinant of viral tropism, and discuss how this new knowledge may inform the development of HIV-1 drugs and vaccines.
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Affiliation(s)
- Oliver Hartley
- Department of Structural Biology and Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland
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530
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Gao F, Weaver EA, Lu Z, Li Y, Liao HX, Ma B, Alam SM, Scearce RM, Sutherland LL, Yu JS, Decker JM, Shaw GM, Montefiori DC, Korber BT, Hahn BH, Haynes BF. Antigenicity and immunogenicity of a synthetic human immunodeficiency virus type 1 group m consensus envelope glycoprotein. J Virol 2005; 79:1154-63. [PMID: 15613343 PMCID: PMC538535 DOI: 10.1128/jvi.79.2.1154-1163.2005] [Citation(s) in RCA: 168] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genetic variation of human immunodeficiency virus (HIV-1) represents a major obstacle for AIDS vaccine development. To decrease the genetic distances between candidate immunogens and field virus strains, we have designed and synthesized an artificial group M consensus env gene (CON6 gene) to be equidistant from contemporary HIV-1 subtypes and recombinants. This novel envelope gene expresses a glycoprotein that binds soluble CD4, utilizes CCR5 but not CXCR4 as a coreceptor, and mediates HIV-1 entry. Key linear, conformational, and glycan-dependent monoclonal antibody epitopes are preserved in CON6, and the glycoprotein is recognized equally well by sera from individuals infected with different HIV-1 subtypes. When used as a DNA vaccine followed by a recombinant vaccinia virus boost in BALB/c mice, CON6 env gp120 and gp140CF elicited gamma interferon-producing T-cell responses that recognized epitopes within overlapping peptide pools from three HIV-1 Env proteins, CON6, MN (subtype B), and Chn19 (subtype C). Sera from guinea pigs immunized with recombinant CON6 Env gp120 and gp140CF glycoproteins weakly neutralized selected HIV-1 primary isolates. Thus, the computer-generated "consensus" env genes are capable of expressing envelope glycoproteins that retain the structural, functional, and immunogenic properties of wild-type HIV-1 envelopes.
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Affiliation(s)
- Feng Gao
- Department of Medicine, Duke University Medical Center, 112 Research Park III, Research Dr., Box 3347, Durham, NC 27710, USA.
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531
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Gao F, Korber BT, Weaver E, Liao HX, Hahn BH, Haynes BF. Centralized immunogens as a vaccine strategy to overcome HIV-1 diversity. Expert Rev Vaccines 2005; 3:S161-8. [PMID: 15285714 DOI: 10.1586/14760584.3.4.s161] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genetic variation of HIV-1 represents a major obstacle for AIDS vaccine development. With the amino acid sequence divergence as high as 30% in envelopes between different subtypes among HIV-1 group M viruses, it is unlikely that cross-subtype protection will occur equally well among all subtypes. Computer programs have been used to generate 'centralized' HIV gene sequences: consensus, ancestor or center of the tree. These sequences can decrease the genetic distances between the 'centralized' and wild-type gene immunogens to half of those between any wild-type immuongens to each other. Recent studies demonstrated that an artificial group M consensus env gene is equidistant from any subtype and recombinants. It is biologically functional and preserves antigenicity similar to contemporary Env proteins. Most importantly, the group M consensus Env immunogen can elicit both T- and B-cell responses to wild-type HIV-1 isolates.
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Affiliation(s)
- Feng Gao
- The Duke Human Vaccine Institute, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
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532
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Mullins JI, Nickle DC, Heath L, Rodrigo AG, Learn GH. Immunogen sequence: the fourth tier of AIDS vaccine design. Expert Rev Vaccines 2005; 3:S151-9. [PMID: 15285713 DOI: 10.1586/14760584.3.4.s151] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
While worldwide efforts to develop an effective HIV-1 vaccine are underway, the virus continues to spread, particularly in developing countries where the delivery of antiviral therapies presents formidable challenges. Vaccine research has largely focused on three general aspects: vectors, adjuvants, and immunization schedules. Our group favor the use of computational methods to design potential immunogens that capture the genetic and biological features of circulating viruses. These methods allow researchers to predict, in silico, the presence of potential glycosylation sites, humoral immune responses, and epitope coverage. This review shall compare three computational approaches for immunogen design: the consensus sequence, which has at each site the modal nucleotide or amino acid residue across a sequence alignment; the most recent common ancestor, the sequence estimated at the basal node of the clades seen in the HIV-1 phylogeny; and the center of tree method, which minimizes the evolutionary distance to all sequences in the data set.
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Affiliation(s)
- James I Mullins
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98109-8070, USA.
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533
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Mbisa JL, Nikolenko GN, Pathak VK. Mutations in the RNase H primer grip domain of murine leukemia virus reverse transcriptase decrease efficiency and accuracy of plus-strand DNA transfer. J Virol 2005; 79:419-27. [PMID: 15596835 PMCID: PMC538714 DOI: 10.1128/jvi.79.1.419-427.2005] [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: 11/20/2022] Open
Abstract
The RNase H primer grip of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) contacts the DNA primer strand and positions the template strand near the RNase H active site, influencing RNase H cleavage efficiency and specificity. Sequence alignments show that 6 of the 11 residues that constitute the RNase H primer grip have functional equivalents in murine leukemia virus (MLV) RT. We previously showed that a Y586F substitution in the MLV RNase H primer grip resulted in a 17-fold increase in substitutions within 18 nucleotides of adenine-thymine tracts, which are associated with a bent DNA conformation. To further determine the effects of the MLV RNase H primer grip on replication fidelity and viral replication, we performed additional mutational analysis. Using either beta-galactosidase (lacZ) or green fluorescent protein (GFP) reporter genes, we found that S557A, A558V, and Q559L substitutions resulted in statistically significant increases in viral mutation rates, ranging from 2.1- to 3.8-fold. DNA sequencing analysis of nonfluorescent GFP clones indicated that the mutations in RNase H primer grip significantly increased the frequency of deletions between the primer-binding site (PBS) and sequences downstream of the PBS. In addition, quantitative real-time PCR analysis of reverse transcription products revealed that the mutant RTs were substantially inefficient in plus-strand DNA transfer relative to the wild-type control. These results indicate that the MLV RNase H primer grip is an important determinant of in vivo fidelity of DNA synthesis and suggest that the mutant RT was unable to copy through the DNA-RNA junction of the minus-strand DNA and the tRNA because of its bent conformation resulting in error-prone plus-strand DNA transfer.
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Affiliation(s)
- Jean L Mbisa
- HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, Maryland 21702-1201, USA
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534
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Gilbert PB. A modified false discovery rate multiple-comparisons procedure for discrete data, applied to human immunodeficiency virus genetics. J R Stat Soc Ser C Appl Stat 2005. [DOI: 10.1111/j.1467-9876.2005.00475.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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535
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van Marle G, Power C. Human immunodeficiency virus type 1 genetic diversity in the nervous system: Evolutionary epiphenomenon or disease determinant? J Neurovirol 2005; 11:107-28. [PMID: 16036790 DOI: 10.1080/13550280590922838] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Over the past decade there has been a revolution in the understanding and care of human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS)-associated disease. Much of this progress stems from a broader recognition of the importance of differences in viral types, including receptor preference(s), replication properties, and reservoirs, as contributing factors to immunosuppresion and disease progression. In contrast, there is limited conceptualizatin of viral diversity and turnover in the brain and circulation in relation to neurocognitive impairments. Herein, the authors review current concepts regarding viral molecular diversity and phenotypes together with features of HIV-1 neuroinvasion, neurotropism, neurovirulence and neurosusceptiblity. Viral genetic and antigenic diversity is reduced within the brain compared to blood or other systemic organs within individuals. Conversely, viral molecular heterogeneity is greater in patients with HIV-associated dementia compared to nondemented patients, depending on the viral gene examined. Individual viral proteins exert multiple neuropathogenic effects, although the neurological consequences of different viral polymorphisms remain uncertain. Nonetheless, host genetic polymorphisms clearly influence neurological disease outcomes and likely dictate both acquired and innate immune responses, which in turn shape viral evolution within the host. Emerging issues include widespread antiretroviral therapy resistance and increasing awareness of viral superinfections together with viral recombination, all of which are likely to impact on both HIV genetic variation and neuropathogenesis. With the persisting prevalence of HIV-induced neurocognitive disabilities, despite marked improvements in managing immunosuppression, it remains imperative to fully define and understand the mechanisms by which viral dynamics and diversity contribute to neurological disease, permitting the development of new therapeutic strategies.
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Affiliation(s)
- Guido van Marle
- Department of Clinical Neurosciences, University of Calgary, Calgary, AB, Canada
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536
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O'Connor DH, McDermott AB, Krebs KC, Dodds EJ, Miller JE, Gonzalez EJ, Jacoby TJ, Yant L, Piontkivska H, Pantophlet R, Burton DR, Rehrauer WM, Wilson N, Hughes AL, Watkins DI. A dominant role for CD8+-T-lymphocyte selection in simian immunodeficiency virus sequence variation. J Virol 2004; 78:14012-22. [PMID: 15564508 PMCID: PMC533930 DOI: 10.1128/jvi.78.24.14012-14022.2004] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CD8(+) T lymphocytes (CD8-TL) select viral escape variants in both human immunodeficiency virus and simian immunodeficiency virus (SIV) infections. The frequency of CD8-TL viral escape as well as the contribution of escape to overall virus diversification has not been assessed. We quantified CD8-TL selection in SIV infections by sequencing viral genomes from 35 SIVmac239-infected animals at the time of euthanasia. Here we show that positive selection for sequences encoding 46 known CD8-TL epitopes is comparable to the positive selection observed for the variable loops of env. We also found that >60% of viral variation outside of the viral envelope occurs within recognized CD8-TL epitopes. Therefore, we conclude that CD8-TL selection is the dominant cause of SIV diversification outside of the envelope.
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Affiliation(s)
- David H O'Connor
- Wisconsin Primate Research Center, Department of Pathology, Laboratoty of Medicine, University of Wisconsin, 1300 University Ave., Madison, WI 53706, USA
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537
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Binley JM, Wrin T, Korber B, Zwick MB, Wang M, Chappey C, Stiegler G, Kunert R, Zolla-Pazner S, Katinger H, Petropoulos CJ, Burton DR. Comprehensive cross-clade neutralization analysis of a panel of anti-human immunodeficiency virus type 1 monoclonal antibodies. J Virol 2004; 78:13232-52. [PMID: 15542675 PMCID: PMC524984 DOI: 10.1128/jvi.78.23.13232-13252.2004] [Citation(s) in RCA: 585] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2004] [Accepted: 07/09/2004] [Indexed: 12/20/2022] Open
Abstract
Broadly neutralizing monoclonal antibodies (MAbs) are potentially important tools in human immunodeficiency virus type 1 (HIV-1) vaccine design. A few rare MAbs have been intensively studied, but we still have a limited appreciation of their neutralization breadth. Using a pseudovirus assay, we evaluated MAbs from clade B-infected donors and a clade B HIV(+) plasma against 93 viruses from diverse backgrounds. Anti-gp120 MAbs exhibited greater activity against clade B than non-B viruses, whereas anti-gp41 MAbs exhibited broad interclade activity. Unexpectedly, MAb 4E10 (directed against the C terminus of the gp41 ectodomain) neutralized all 90 viruses with moderate potency. MAb 2F5 (directed against an epitope adjacent to that of 4E10) neutralized 67% of isolates, but none from clade C. Anti-gp120 MAb b12 (directed against an epitope overlapping the CD4 binding site) neutralized 50% of viruses, including some from almost every clade. 2G12 (directed against a high-mannose epitope on gp120) neutralized 41% of the viruses, but none from clades C or E. MAbs to the gp120 V3 loop, including 447-52D, neutralized a subset of clade B viruses (up to 45%) but infrequently neutralized other clades (=7%). MAbs b6 (directed against the CD4 binding site) and X5 (directed against a CD4-induced epitope of gp120) neutralized only sensitive primary clade B viruses. The HIV(+) plasma neutralized 70% of the viruses, including some from all major clades. Further analysis revealed five neutralizing immunotypes that were somewhat associated with clades. As well as the significance for vaccine design, our data have implications for passive-immunization studies in countries where clade C viruses are common, given that only MAbs b12 and 4E10 were effective against viruses from this clade.
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Affiliation(s)
- James M Binley
- IMM2, Department of Immunology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
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538
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Silvera P, Savary JR, Livingston V, White J, Manson KH, Wyand MH, Salk PL, Moss RB, Lewis MG. Vaccination with gp120-depleted HIV-1 plus immunostimulatory CpG oligodeoxynucleotides in incomplete Freund's adjuvant stimulates cellular and humoral immunity in rhesus macaques. Vaccine 2004; 23:827-39. [PMID: 15542208 DOI: 10.1016/j.vaccine.2004.06.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2004] [Revised: 06/22/2004] [Accepted: 06/28/2004] [Indexed: 11/30/2022]
Abstract
Whole killed human immunodeficiency virus type 1 (HIV-1) immunogens contain the more conserved epitopes of HIV-1 and therefore may provide some utility as potential HIV-1 vaccine candidates. Previous studies have shown that synthetic oligodeoxynucleotides (ODN) containing unmethylated cytosine-guanine (CpG) dinucleotides trigger rapid stimulation of both CD4+ and CD8+ T cells. Here, we investigated whether immunization of rhesus macaques with an inactivated gp120-depleted HIV-1 immunogen, emulsified in incomplete Freund's adjuvant (IFA) together with immunostimulatory CpG-containing ODN (ODN 2006), would elicit HIV-specific cellular and humoral immune responses. High titer anti-p24 antibody levels were induced in all four immunized animals that were sustained 6 weeks after the fifth and final boost at 23 months. These anti-gag antibodies mapped to linear B-cell epitopes within the matrix (MA), capsid (CA), p2, nucleocapsid (NC) and p6 proteins of HIV-1 gag. HIV-specific interferon-gamma-producing CD4+ and CD8+ T-cell responses were measured before and after the fourth and fifth immunizations by both intracellular cytokine (ICC) and ELISPOT techniques; responses were detected in three of the four immunized animals. CD4+ T-cell epitopes appear to map within amino acids 261-290 and 291-320 of p24 CA protein. Immunizations were well tolerated both locally and systemically. Based on these results, further studies of this approach are warranted.
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Affiliation(s)
- Peter Silvera
- Infectious Disease Research Department, Southern Research Institute, 431 Aviation Way, Frederick, MD 21701, USA.
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539
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McKinney DM, Skvoretz R, Livingston BD, Wilson CC, Anders M, Chesnut RW, Sette A, Essex M, Novitsky V, Newman MJ. Recognition of variant HIV-1 epitopes from diverse viral subtypes by vaccine-induced CTL. THE JOURNAL OF IMMUNOLOGY 2004; 173:1941-50. [PMID: 15265928 DOI: 10.4049/jimmunol.173.3.1941] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Recognition by CD8(+) T lymphocytes (CTL) of epitopes that are derived from conserved gene products, such as Gag and Pol, is well documented and conceptually supports the development of epitope-based vaccines for use against diverse HIV-1 subtypes. However, many CTL epitopes from highly conserved regions within the HIV-1 genome are highly variable, when assessed by comparison of amino acid sequences. The TCR is somewhat promiscuous with respect to peptide binding, and, as such, CTL can often recognize related epitopes. In these studies, we evaluated CTL recognition of five sets of variant HIV-1 epitopes restricted to HLA-A*0201 and HLA-A*1101 using HLA transgenic mice. We found that numerous different amino acid substitutions can be introduced into epitopes without abrogating their recognition by CTL. Based on our findings, we constructed an algorithm to predict those CTL epitopes capable of inducing responses in the HLA transgenic mice to the greatest numbers of variant epitopes. Similarity of CTL specificity for variant epitopes was demonstrated for humans using PBMC from HIV-1-infected individuals and CTL lines produced in vitro using PBMC from HIV-1-uninfected donors. We believe the ability to predict CTL epitope immunogenicity and recognition patterns of variant epitopes can be useful for designing vaccines against multiple subtypes and circulating recombinant forms of HIV-1.
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MESH Headings
- AIDS Vaccines/immunology
- Algorithms
- Amino Acid Sequence
- Amino Acid Substitution
- Animals
- Antigenic Variation/genetics
- Antigenic Variation/immunology
- Epitopes/chemistry
- Epitopes/genetics
- Epitopes/immunology
- Gene Products, env/chemistry
- Gene Products, env/immunology
- Gene Products, gag/chemistry
- Gene Products, gag/immunology
- Gene Products, pol/chemistry
- Gene Products, pol/immunology
- Genes, MHC Class I
- HIV Antigens/chemistry
- HIV Antigens/genetics
- HIV Antigens/immunology
- HIV Infections/immunology
- HIV-1/classification
- HIV-1/immunology
- HLA-A2 Antigen/genetics
- HLA-A2 Antigen/immunology
- HLA-A3 Antigen/genetics
- HLA-A3 Antigen/immunology
- Humans
- Mice
- Mice, Transgenic
- Peptide Fragments/chemical synthesis
- Peptide Fragments/chemistry
- Peptide Fragments/immunology
- Receptors, Antigen, T-Cell/immunology
- Sequence Alignment
- T-Cell Antigen Receptor Specificity
- T-Lymphocytes, Cytotoxic/immunology
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540
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Tonon AP, Hoffmann EHE, Silveira LAD, Ribeiro AG, Gonçalves CRDS, Ribolla PEM, Wunderlich G, Ferreira MU. Plasmodium falciparum: sequence diversity and antibody recognition of the Merozoite surface protein-2 (MSP-2) in Brazilian Amazonia. Exp Parasitol 2004; 108:114-25. [PMID: 15582508 DOI: 10.1016/j.exppara.2004.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2004] [Revised: 08/03/2004] [Accepted: 08/03/2004] [Indexed: 11/30/2022]
Abstract
The merozoite surface protein-2 (MSP-2) of Plasmodium falciparum comprises repeats flanked by dimorphic domains defining the allelic families FC27 and IC1. Here, we examined sequence diversity at the msp-2 locus in Brazil and its impact on MSP-2 antibody recognition by local patients. Only 25 unique partial sequences of msp-2 were found in 61 isolates examined. The finding of identical msp-2 sequences in unrelated parasites, collected 6-13 years apart, suggests that no major directional selection is exerted by variant-specific immunity in this malaria-endemic area. To examine antibody cross-reactivity, recombinant polypeptides derived from locally prevalent and foreign MSP-2 variants were used in ELISA. Foreign IC1-type variants, such as 3D7 (currently tested for human vaccination), were less frequently recognized than FC27-type and local IC1-type variants. Antibodies discriminated between local and foreign IC1-type variants, but cross-recognized structurally different local IC1-type variants. The use of evolutionary models of MSP-2 is suggested to design vaccines that minimize differences between local parasites and vaccine antigens.
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Affiliation(s)
- Angela Pedroso Tonon
- Departamento de Parasitologia, Instituto de Ciências Biomédicas da Universidade de São Paulo, Av. Prof. Lineu Prestes 1374, Cidade Universitária, 05508-900 São Paulo, Brazil
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541
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Kalish ML, Robbins KE, Pieniazek D, Schaefer A, Nzilambi N, Quinn TC, St Louis ME, Youngpairoj AS, Phillips J, Jaffe HW, Folks TM. Recombinant viruses and early global HIV-1 epidemic. Emerg Infect Dis 2004; 10:1227-34. [PMID: 15324542 PMCID: PMC3323344 DOI: 10.3201/eid1007.030904] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Central Africa was the epicenter of the HIV type 1 (HIV-1) pandemic. Understanding the early epidemic in the Democratic Republic of the Congo, formerly Zaire, could provide insight into how HIV evolved and assist vaccine design and intervention efforts. Using enzyme immunosorbent assays, we tested 3,988 serum samples collected in Kinshasa in the mid-1980s and confirmed seroreactivity by Western blot. Polymerase chain reaction of gag p17, env C2V3C3, and/or gp41; DNA sequencing; and genetic analyses were performed. Gene regions representing all the HIV-1 group M clades and unclassifiable sequences were found. From two or three short gene regions, 37% of the strains represented recombinant viruses, multiple infections, or both, which suggests that if whole genome sequences were available, most of these strains would have mosaic genomes. We propose that the HIV epidemic was well established in central Africa by the early 1980s and that some recombinant viruses most likely seeded the early global epidemic.
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Affiliation(s)
- Marcia L Kalish
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
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542
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Kuiken C, Yusim K, Boykin L, Richardson R. The Los Alamos hepatitis C sequence database. Bioinformatics 2004; 21:379-84. [PMID: 15377502 DOI: 10.1093/bioinformatics/bth485] [Citation(s) in RCA: 321] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
MOTIVATION The hepatitis C virus (HCV) is a significant threat to public health worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and drug design. At present, some 30 000 HCV sequences have been published. A central website that provides annotated sequences and analysis tools will be helpful to HCV scientists worldwide. RESULTS The HCV sequence database collects and annotates sequence data and provides them to the public via a website that contains a user-friendly search interface and a large number of sequence analysis tools, based on the model of the highly regarded Los Alamos HIV database. The HCV sequence database was officially launched in September 2003. Since then, its usage has steadily increased and is now at an average of approximately 280 visits per day from distinct IP addresses. AVAILABILITY The HCV website can be accessed via http://hcv.lanl.gov and http://hcv-db.org.
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Affiliation(s)
- Carla Kuiken
- HCV database, Los Alamos National Laboratory, Los Alamos, NM, USA
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543
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Chugh P, Seth P. Induction of Broad-Based Immune Response Against HIV-1 Subtype C gag DNA Vaccine in Mice. Viral Immunol 2004; 17:423-35. [PMID: 15357908 DOI: 10.1089/vim.2004.17.423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Prevention of HIV infection through an effective vaccine is need of the hour as per the AIDS pandemic scene, particularly in the developing world. Here we report the work done with gag gene construct pJWgagprotease49587 from HIV-1subtype C Indian strain. The construct pJWgagprotease49587 was tested positive for expression in COS-7 cells by p24 antigen capture ELISA, immunoblotting and by transmission electron microscopy that revealed virus like particle formation. Immunogenicity studies showed induction of good lymphoproliferative and cytotoxic (CTL) responses in Balb/c mice. The cytokine repertoire elicited showed a TH1 type of immune response. In an epitope mapping study, IFNgamma secretion by spleen cells from immunized mice was observed to seven peptides from different regions of gag. Recognition of multiple epitopes demonstrates elicitation of a broad based immune response against gag following immunization with the construct. In view of the high propensity of escape mutant induction during the course of HIV infection, it is encouraging to use immunogens eliciting viable immune responses to a broad spectrum of epitopes. Hence the construct pJWgagprotease49587 is a good candidate for immunogenecity testing in nonhuman primates as a probable vaccine candidate.
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Affiliation(s)
- Priti Chugh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
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544
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Gómez CE, Abaitua F, Rodríguez D, Esteban M. Efficient CD8+ T cell response to the HIV-env V3 loop epitope from multiple virus isolates by a DNA prime/vaccinia virus boost (rWR and rMVA strains) immunization regime and enhancement by the cytokine IFN-γ. Virus Res 2004; 105:11-22. [PMID: 15325077 DOI: 10.1016/j.virusres.2004.04.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2004] [Revised: 03/30/2004] [Accepted: 04/02/2004] [Indexed: 12/16/2022]
Abstract
The cytotoxic T-lymphocyte response (CTL) has been shown to be determinant in the clearance of many viral infections and hence, vaccine candidates against AIDS are designed to enhance this arm of the immune system. In this study, we have analyzed the antigen specific immune responses triggered in mice by different combinations of vaccine vehicles expressing the multiepitope polypeptide TAB13. This chimeric protein contains the V3 region of the gp120 from eight different HIV-1 isolates and was efficiently expressed by a DNA vector (DNA-TAB), and also by vaccinia virus recombinants (rVV) based either on the attenuated modified vaccinia virus Ankara (MVA-TAB) or Western Reserve (VV-TAB) strains. Inoculation of a DNA-TAB vector in priming followed by a booster with VV-TAB or MVA-TAB induces a humoral immune response against TAB13 protein and efficiently enhanced the CD8+ T cell response against V3 epitopes from HIV-1 isolates LR150, MN, and IIIB in comparison with animals immunized with two doses of DNA-TAB. A protocol that incorporates a DNA vector expressing IFN-gamma (DNA-IFN-gamma) with DNA-TAB in the priming, followed by a booster with MVA-TAB, triggered the highest values of specific CD8+ T cell response. By examining the cytokine pattern, the immune response induced by these vaccination approaches was predominantly of Th-1 type. These findings establish safe strategies for the enhanced generation of T cell mediated immunity to HIV-1 that can benefit in the design of an effective vaccine against AIDS.
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MESH Headings
- AIDS Vaccines/administration & dosage
- AIDS Vaccines/genetics
- AIDS Vaccines/immunology
- Amino Acid Sequence
- Animals
- Base Sequence
- CD8-Positive T-Lymphocytes/immunology
- Cells, Cultured
- Cricetinae
- Cytokines/analysis
- Epitopes/genetics
- Epitopes/immunology
- Female
- HIV Envelope Protein gp120/genetics
- HIV Envelope Protein gp120/immunology
- HIV-1/immunology
- Immunization, Secondary
- Injections, Intramuscular
- Injections, Intraperitoneal
- Interferon-gamma/genetics
- Interferon-gamma/metabolism
- Mice
- Mice, Inbred BALB C
- Molecular Sequence Data
- Peptide Fragments/genetics
- Peptide Fragments/immunology
- Vaccination/methods
- Vaccines, DNA/administration & dosage
- Vaccines, DNA/genetics
- Vaccines, DNA/immunology
- Vaccines, Synthetic/administration & dosage
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
- Vaccinia virus/genetics
- Viral Vaccines/administration & dosage
- Viral Vaccines/genetics
- Viral Vaccines/immunology
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Affiliation(s)
- Carmen Elena Gómez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, CSIC, Campus Universidad Autónoma, 28049 Madrid, Spain
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545
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Abstract
Since the beginning of the AIDS epidemic in 1981, HIV-1 has demonstrated an amazing ability to mutate. HIV-1 was introduced into the human population in the early to mid twentieth century in central Africa. During ensuing decades, this extraordinary mutational capacity has resulted in the circulation of HIV-1 strains that are quite different from one another, yet still remarkably pathogenic. The potential impact of this viral diversity on treatment, monitoring,and vaccine development is discussed.
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Affiliation(s)
- Cristian Apetrei
- Tulane National Primate Research Center and Department of Tropical Medicine, Tulane University Health Sciences Center, Covington, LA 70433, USA
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546
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Garber DA, Silvestri G, Feinberg MB. Prospects for an AIDS vaccine: three big questions, no easy answers. THE LANCET. INFECTIOUS DISEASES 2004; 4:397-413. [PMID: 15219551 DOI: 10.1016/s1473-3099(04)01056-4] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The unremitting devastation created by the AIDS pandemic will probably only be controlled when a vaccine is developed that is safe, effective, affordable, and simple enough to permit implementation in developing countries where the impact of AIDS is most severe. Although formidable practical, political, economic, social, and ethical challenges face the AIDS vaccine development effort, the most fundamental challenges now reside at the level of the basic biology of HIV-1 infection and pathogenesis. Of these biological considerations, three questions loom especially large: can we design immunogens that will elicit neutralising antibodies that are reactive against a wide variety of primary HIV isolates; will vaccine-elicited cytotoxic T cells be fundamentally better at controlling HIV-1 replication and ameliorating disease progression than those responses that arise during natural HIV infection; and to what extent will the tremendous global genetic diversity of HIV-1 compromise the breadth of vaccine-elicited protective immunity and the overall effectiveness of an AIDS vaccine? Although these are three exceptionally challenging questions, they are now being approached with clear hypotheses whose testing is being facilitated by an ever-improving array of technologies for vaccine design and immunological characterisation. The extent to which the field of AIDS vaccine research can now come together to answer these questions in the best coordinated, most efficient manner will probably be an important determinant of how and when an effective AIDS vaccine will be developed.
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Affiliation(s)
- David A Garber
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA
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547
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Villamide-Herrera L, Ignatius R, Eller MA, Wilkinson K, Griffin C, Mehlhop E, Jones J, Han SY, Lewis MG, Parrish S, Vancott TC, Lifson JD, Schlesinger S, Mascola JR, Pope M. Macaque dendritic cells infected with SIV-recombinant canarypox ex vivo induce SIV-specific immune responses in vivo. AIDS Res Hum Retroviruses 2004; 20:871-84. [PMID: 15320991 DOI: 10.1089/0889222041725136] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Dendritic cells (DCs) infected with recombinant avipox vectors express the introduced genes and activate antigen-specific T cells. DCs exhibit distinct differentiation-dependent immune functions. Moreover, immature DCs are readily infected by canarypox vectors, but undergo tumor necrosis factor (TNF)-alpha-dependent death, while fewer mature DCs get infected and resist dying. A pilot study was performed using the rhesus macaque system to explore whether immature and mature DCs infected with SIV-recombinant canarypox (vCP180) ex vivo could induce primary virus-specific immune responses in vivo. After subcutaneous (sc) reinjection, functional monocyte-derived DCs migrated to lymph nodes (LNs) within 1-2 days and primed T cells in vivo. This was observed by monitoring dye-labeled DCs in the draining LNs and tetanus toxoid (TT)-specific T cell responses after injection of TT-loaded DCs. DCs from simian immunodeficiency virus (SIV)-naïve rhesus macaques were infected with vCP180 (SIVmac142 gag, pol, and env genes), and sc reinjected into donor animals. Low-level SIV-specific T cell proliferation, but little if any interferon (IFN)-gamma production was detected. DCs pulsed with vCP180 in combination with TT and keyhole limpet hemocyanin (KLH) (to activate additional T cells and provide "helper" cytokines) induced SIV-, TT-, and KLH-specific T cell responses, including IFN-gamma responses not seen when vCP180-carrying DCs were used alone. Interleukin (IL)-10 and low-level antibody responses were also observed. This pilot study provides the proof of principle that sc injected ex vivo SIV-recombinant canarypox-infected DCs safely induce low-level SIV-specific immune responses in vivo.
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Affiliation(s)
- L Villamide-Herrera
- Center for Biomedical Research, Population Council, New York, New York 10021, USA
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548
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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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Papin JF, Vahrson W, Dittmer DP. SYBR green-based real-time quantitative PCR assay for detection of West Nile Virus circumvents false-negative results due to strain variability. J Clin Microbiol 2004; 42:1511-8. [PMID: 15070997 PMCID: PMC387603 DOI: 10.1128/jcm.42.4.1511-1518.2004] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Real-time quantitative PCR is used routinely for the high-throughput diagnosis of viral pathogens, such as West Nile virus (WNV). Rapidly evolving RNA viruses present a challenge for diagnosis because they accumulate mutations that may render them undetectable. To explore the effect of sequence variations on assay performance, we generated every possible single point mutation within the target region of the widely used TaqMan assay for WNV and found that the TaqMan assay failed to detect 47% of possible single nucleotide variations in the probe-binding site and was unable to detect any targets with more than two mutations. In response, we developed and validated a less expensive assay with the intercalating dye SYBR green. The SYBR green-based assay was as sensitive as the TaqMan assay for WNV. Importantly, it detected 100% of possible WNV target region variants. The assay developed here adds an additional layer of protection to guard against false-negative results that result from natural variations or drug-directed selection and provides a rapid means to identify such variants for subsequent detailed analysis.
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Affiliation(s)
- James F Papin
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA
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550
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Kapoor A, Jones M, Shafer RW, Rhee SY, Kazanjian P, Delwart EL. Sequencing-based detection of low-frequency human immunodeficiency virus type 1 drug-resistant mutants by an RNA/DNA heteroduplex generator-tracking assay. J Virol 2004; 78:7112-23. [PMID: 15194787 PMCID: PMC421662 DOI: 10.1128/jvi.78.13.7112-7123.2004] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Drug-resistant viruses may be present as minority variants during early treatment failures or following discontinuation of failed antiretroviral regimens. A limitation of the traditional direct PCR population sequencing method is its inability to detect human immunodeficiency virus type 1 (HIV-1) variants present at frequencies lower than 20%. A drug resistance genotyping assay based on the isolation and DNA sequencing of minority HIV protease variants is presented here. A multiple-codon-specific heteroduplex generator probe was constructed to improve the separation of HIV protease genes varying in sequence at 12 codons associated with resistance to protease inhibitors. Using an RNA molecule as probe allowed the simple sequencing of protease variants isolated as RNA/DNA heteroduplexes with different electrophoretic mobilities. The protease gene RNA heteroduplex generator-tracking assay (RNA-HTA) was tested on plasma quasispecies from 21 HIV-1-infected persons in whom one or more protease resistance mutations emerged during therapy or following initiation of salvage regimens. In 11 of 21 cases, RNA-HTA testing of virus from the first episode of virologic failure identified protease resistance mutations not seen by population-based PCR sequencing. In 8 of these 11 cases, all of the low-frequency drug resistance mutations detected exclusively by RNA-HTA during the first episode became detectable by population-based PCR sequencing at the later time point. Distinct sets of protease mutations could be linked on different genomes in patients with high-frequency protease gene lineages. The enhanced detection of minority drug resistance variants using a sequencing-based assay may improve the efficacy of genotype-assisted salvage therapies.
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Affiliation(s)
- Amit Kapoor
- Department of Medicine, University of California, San Francisco, 94118, USA
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