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Wolf T, Calisan KK, Stitz J, Barbe S. The effects of high shear rates on the average hydrodynamic diameter measured in biomimetic HIV Gag virus-like particle dispersions. Front Bioeng Biotechnol 2024; 12:1367405. [PMID: 38860137 PMCID: PMC11163053 DOI: 10.3389/fbioe.2024.1367405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 05/07/2024] [Indexed: 06/12/2024] Open
Abstract
HIV Gag virus-like particles (HIV Gag VLPs) are promising HIV vaccine candidates. In the literature, they are often described as shear-sensitive particles, and authors usually recommend the operation of tangential flow filtration (TFF) gently at shear rates below 4,000 s-1 to 6,000 s-1. This in turn poses a severe limitation to the performance of TFF-mediated concentration of VLPs, which would be substantially enhanced by working at higher shear rates. To our knowledge, studies examining the shear sensitivity of HIV Gag VLPs and providing detailed information and evidence for the fragility of these particles have not been conducted yet. Thus, we investigated the effect of high shear rates on the colloidal stability of mosaic VLPs (Mos-VLPs) as relevant examples for HIV Gag VLPs. For this purpose, Mos-VLPs were exposed to different shear rates ranging from 3,395 s-1 to 22, 365 s-1 for 2 h. The average hydrodynamic diameter (AHD) and the polydispersity index (PDI) of the associated particle size distribution were used as stability indicators and measured after the treatment and during storage through dynamic light scattering. At high shear rates, we observed an increase in both AHD and PDI during the storage of HIV Mos1.Gag VLPs (bVLP-without envelope proteins) and Mos1.Gag + Mos2S.Env VLPs (eVLP-with envelope proteins). eVLPs exhibited higher colloidal stability than bVLPs, and we discuss the potential stabilizing role of envelope proteins. We finally demonstrated that the dispersion medium also has a considerable impact on the stability of Mos-VLPs.
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Affiliation(s)
- Tobias Wolf
- Research Group Medical Biotechnology and Bioengineering, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Leverkusen, Germany
- Institue of Technical Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Kerim Kadir Calisan
- Research Group Medical Biotechnology and Bioengineering, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Leverkusen, Germany
| | - Jörn Stitz
- Research Group Medical Biotechnology and Bioengineering, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Leverkusen, Germany
| | - Stéphan Barbe
- Research Group Medical Biotechnology and Bioengineering, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Leverkusen, Germany
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2
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Xie Z, Lin YC, Steichen JM, Ozorowski G, Kratochvil S, Ray R, Torres JL, Liguori A, Kalyuzhniy O, Wang X, Warner JE, Weldon SR, Dale GA, Kirsch KH, Nair U, Baboo S, Georgeson E, Adachi Y, Kubitz M, Jackson AM, Richey ST, Volk RM, Lee JH, Diedrich JK, Prum T, Falcone S, Himansu S, Carfi A, Yates JR, Paulson JC, Sok D, Ward AB, Schief WR, Batista FD. mRNA-LNP HIV-1 trimer boosters elicit precursors to broad neutralizing antibodies. Science 2024; 384:eadk0582. [PMID: 38753770 DOI: 10.1126/science.adk0582] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 04/03/2024] [Indexed: 05/18/2024]
Abstract
Germline-targeting (GT) HIV vaccine strategies are predicated on deriving broadly neutralizing antibodies (bnAbs) through multiple boost immunogens. However, as the recruitment of memory B cells (MBCs) to germinal centers (GCs) is inefficient and may be derailed by serum antibody-induced epitope masking, driving further B cell receptor (BCR) modification in GC-experienced B cells after boosting poses a challenge. Using humanized immunoglobulin knockin mice, we found that GT protein trimer immunogen N332-GT5 could prime inferred-germline precursors to the V3-glycan-targeted bnAb BG18 and that B cells primed by N332-GT5 were effectively boosted by either of two novel protein immunogens designed to have minimum cross-reactivity with the off-target V1-binding responses. The delivery of the prime and boost immunogens as messenger RNA lipid nanoparticles (mRNA-LNPs) generated long-lasting GCs, somatic hypermutation, and affinity maturation and may be an effective tool in HIV vaccine development.
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Affiliation(s)
- Zhenfei Xie
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Ying-Cing Lin
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Jon M Steichen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel Ozorowski
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sven Kratochvil
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Rashmi Ray
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alessia Liguori
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xuesong Wang
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - John E Warner
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Stephanie R Weldon
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Gordon A Dale
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Kathrin H Kirsch
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Usha Nair
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Sabyasachi Baboo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Erik Georgeson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yumiko Adachi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Kubitz
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Abigail M Jackson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sara T Richey
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Reid M Volk
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeong Hyun Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Thavaleak Prum
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | | | | | | | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James C Paulson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - William R Schief
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Moderna Inc., Cambridge, MA 02139, USA
| | - Facundo D Batista
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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3
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Khan A, Pillay M, Chimukangara B, Gounder L, Manyana S, Francois KL, Chipango K. Identification of HIV-1 subtype CRF18_cpx in a patient with multidrug resistance in KwaZulu-Natal, South Africa: An epidemiological worry? JOURNAL OF CLINICAL VIROLOGY PLUS 2023. [DOI: 10.1016/j.jcvp.2023.100143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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4
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Wang H, Zhao X, Su M, Meng J, Fan W, Shi P. Identification of a New HIV-1 Circulating Recombinant Form CRF112_01B Strain in Baoding City, Hebei Province, China. Curr HIV Res 2022; 20:485-491. [PMID: 36305139 DOI: 10.2174/1570162x21666221027122528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/15/2022] [Accepted: 09/27/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND A large number of HIV-1 recombinants that originated from CRF01_AE and B strains are constantly emerging in men who have sex with men populations in China and deserve more attention and further monitoring. OBJECTIVE To analyze the near-full-length genome structure and recombination characteristics of a new HIV-1 strain (BD226AJ) detected in Baoding City and determine its subtype. CASE REPRESENTATION Viral RNA was extracted from a blood sample collected from an infected individual and reverse transcribed to cDNA. Two overlapping segments of the HIV-1 genome were amplified using a near-endpoint dilution method and sequenced. Recombinant breakpoints were determined using RIP, jpHMM, and SimPlot 3.5.1 software. MEGA v6.0 was used to construct a neighbor-joining phylogenetic tree to determine the homology relationships of this strain. RESULTS AND DISCUSSION We obtained 8830 nucleotides (nt) of the HIV-1 genome sequence by amplification and sequencing, and four recombinant fragments were identified by recombination analysis, namely CRF01_AE (HXB2, 823-4224 nt), subtype B (HXB2, 4225-5991 nt), CRF01_AE (HXB2, 5992-9295 nt), and subtype B (HXB2, 9296-9406 nt). The BLAST results showed that 96% of the sequence was similar to CRF112_01B. The jpHMM results confirmed that BD226AJ was the CRF112_01B strain. CONCLUSION Our results confirm the first epidemic of CRF112_01B in Hebei Province. This finding suggests that HIV-1 CRF112_01B may have been introduced into Hebei by men who have sex with men and indicates that the epidemic trend of this strain should be closely monitored.
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Affiliation(s)
- Hao Wang
- Clinical laboratory, the People's Hospital of Baoding, Baoding, Hebei 071000, China
| | - Xuanhe Zhao
- Clinical laboratory, the Baoding Blood Center, Baoding, Hebei 071051, China
| | - Miaomiao Su
- Infection division, the People's Hospital of Baoding, Baoding, Hebei 071000, China
| | - Juan Meng
- Infection division, the People's Hospital of Baoding, Baoding, Hebei 071000, China
| | - Weiguang Fan
- Clinical laboratory, the People's Hospital of Baoding, Baoding, Hebei 071000, China
| | - Penghui Shi
- Clinical laboratory, the People's Hospital of Baoding, Baoding, Hebei 071000, China
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5
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Rosengarten JF, Schatz S, Wolf T, Barbe S, Stitz J. Components of a HIV-1 vaccine mediate virus-like particle (VLP)-formation and display of envelope proteins exposing broadly neutralizing epitopes. Virology 2022; 568:41-48. [DOI: 10.1016/j.virol.2022.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 12/16/2022]
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6
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Matthew AN, Leidner F, Lockbaum GJ, Henes M, Zephyr J, Hou S, Desaboini NR, Timm J, Rusere LN, Ragland DA, Paulsen JL, Prachanronarong K, Soumana DI, Nalivaika EA, Yilmaz NK, Ali A, Schiffer CA. Drug Design Strategies to Avoid Resistance in Direct-Acting Antivirals and Beyond. Chem Rev 2021; 121:3238-3270. [PMID: 33410674 PMCID: PMC8126998 DOI: 10.1021/acs.chemrev.0c00648] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Drug resistance is prevalent across many diseases, rendering therapies ineffective with severe financial and health consequences. Rather than accepting resistance after the fact, proactive strategies need to be incorporated into the drug design and development process to minimize the impact of drug resistance. These strategies can be derived from our experience with viral disease targets where multiple generations of drugs had to be developed to combat resistance and avoid antiviral failure. Significant efforts including experimental and computational structural biology, medicinal chemistry, and machine learning have focused on understanding the mechanisms and structural basis of resistance against direct-acting antiviral (DAA) drugs. Integrated methods show promise for being predictive of resistance and potency. In this review, we give an overview of this research for human immunodeficiency virus type 1, hepatitis C virus, and influenza virus and the lessons learned from resistance mechanisms of DAAs. These lessons translate into rational strategies to avoid resistance in drug design, which can be generalized and applied beyond viral targets. While resistance may not be completely avoidable, rational drug design can and should incorporate strategies at the outset of drug development to decrease the prevalence of drug resistance.
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Affiliation(s)
- Ashley N. Matthew
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Virginia Commonwealth University
| | - Florian Leidner
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Gordon J. Lockbaum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Mina Henes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Jacqueto Zephyr
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Shurong Hou
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Nages Rao Desaboini
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Jennifer Timm
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Rutgers University
| | - Linah N. Rusere
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Raybow Pharmaceutical
| | - Debra A. Ragland
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- University of North Carolina, Chapel Hill
| | - Janet L. Paulsen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Schrodinger, Inc
| | - Kristina Prachanronarong
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Icahn School of Medicine at Mount Sinai
| | - Djade I. Soumana
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Cytiva
| | - Ellen A. Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
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7
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Santos-Pereira A, Magalhães C, Araújo PMM, Osório NS. Evolutionary Genetics of Mycobacterium tuberculosis and HIV-1: "The Tortoise and the Hare". Microorganisms 2021; 9:147. [PMID: 33440808 PMCID: PMC7827287 DOI: 10.3390/microorganisms9010147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 12/24/2020] [Accepted: 01/06/2021] [Indexed: 12/16/2022] Open
Abstract
The already enormous burden caused by Mycobacterium tuberculosis and Human Immunodeficiency Virus type 1 (HIV-1) alone is aggravated by co-infection. Despite obvious differences in the rate of evolution comparing these two human pathogens, genetic diversity plays an important role in the success of both. The extreme evolutionary dynamics of HIV-1 is in the basis of a robust capacity to evade immune responses, to generate drug-resistance and to diversify the population-level reservoir of M group viral subtypes. Compared to HIV-1 and other retroviruses, M. tuberculosis generates minute levels of genetic diversity within the host. However, emerging whole-genome sequencing data show that the M. tuberculosis complex contains at least nine human-adapted phylogenetic lineages. This level of genetic diversity results in differences in M. tuberculosis interactions with the host immune system, virulence and drug resistance propensity. In co-infected individuals, HIV-1 and M. tuberculosis are likely to co-colonize host cells. However, the evolutionary impact of the interaction between the host, the slowly evolving M. tuberculosis bacteria and the HIV-1 viral "mutant cloud" is poorly understood. These evolutionary dynamics, at the cellular niche of monocytes/macrophages, are also discussed and proposed as a relevant future research topic in the context of single-cell sequencing.
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Affiliation(s)
- Ana Santos-Pereira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Carlos Magalhães
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Pedro M. M. Araújo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Nuno S. Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
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8
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Georgieva M, Buckee CO, Lipsitch M. Models of immune selection for multi-locus antigenic diversity of pathogens. Nat Rev Immunol 2019; 19:55-62. [PMID: 30479379 DOI: 10.1038/s41577-018-0092-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
It is well accepted that pathogens can evade recognition and elimination by the host immune system by varying their antigenic targets. Thus, it has become a truism that host immunity is a major driver and determinant of the antigenic diversity of pathogens. However, it remains puzzling how host immunity selects for antigenic diversity at the level of the pathogen population, given that hosts have acquired immune responses to multiple antigens of most pathogens - sometimes through multiple effectors of both humoral and cellular immunity. In this Opinion article, we address this puzzle and the related question of why pathogens often have diversity at multiple antigenic loci. Here, we describe five hypotheses to explain the polymorphism of multiple antigens in a single pathogen species and highlight research relevant to our current models of thinking about multi-locus antigenic diversity.
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Affiliation(s)
- Maria Georgieva
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .,Department of Physiology, University of Lausanne, Lausanne, Switzerland.
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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9
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Sánchez-Ramón S, Conejero L, Netea MG, Sancho D, Palomares Ó, Subiza JL. Trained Immunity-Based Vaccines: A New Paradigm for the Development of Broad-Spectrum Anti-infectious Formulations. Front Immunol 2018; 9:2936. [PMID: 30619296 PMCID: PMC6304371 DOI: 10.3389/fimmu.2018.02936] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/29/2018] [Indexed: 12/20/2022] Open
Abstract
Challenge with specific microbial stimuli induces long lasting epigenetic changes in innate immune cells that result in their enhanced response to a second challenge by the same or unrelated microbial insult, a process referred to as trained immunity. This opens a new avenue in vaccinology to develop Trained Immunity-based Vaccines (TIbV), defined as vaccine formulations that induce training in innate immune cells. Unlike conventional vaccines, which are aimed to elicit only specific responses to vaccine-related antigens, TIbV aim to stimulate broader responses. As trained immunity is generally triggered by pattern recognition receptors (PRRs), TIbV should be formulated with microbial structures containing suitable PRR-ligands. The TIbV concept we describe here may be used for the development of vaccines focused to promote host resistance against a wide spectrum of pathogens. Under the umbrella of trained immunity, a broad protection can be achieved by: (i) increasing the nonspecific effector response of innate immune cells (e.g., monocyte/macrophages) to pathogens, (ii) harnessing the activation state of dendritic cells to enhance adaptive T cell responses to both specific and nonrelated (bystander) antigens. This capacity of TIbV to promote responses beyond their nominal antigens may be particularly useful when conventional vaccines are not available or when multiple coinfections and/or recurrent infections arise in susceptible individuals. As the set of PRR-ligands chosen is essential not only for stimulating trained immunity but also to drive adaptive immunity, the precise design of TIbV will improve with the knowledge on the functional relationship among the different PRRs. While the TIbV concept is emerging, a number of the current anti-infectious vaccines, immunostimulants, and even vaccine adjuvants may already fall in the TIbV category. This may apply to increase immunogenicity of novel vaccine design approaches based on small molecules, like those achieved by reverse vaccinology.
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Affiliation(s)
- Silvia Sánchez-Ramón
- Department of Clinical Immunology and IdISSC, Hospital Clínico San Carlos, Madrid, Spain.,Department of Immunology, ENT and Ophthalmology, Complutense University School of Medicine, Madrid, Spain
| | | | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Department for Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - David Sancho
- Immunobiology Laboratory, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Óscar Palomares
- Department of Biochemistry and Molecular Biology, School of Chemistry, Complutense University of Madrid, Madrid, Spain
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10
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Safety and antiviral activity of combination HIV-1 broadly neutralizing antibodies in viremic individuals. Nat Med 2018; 24:1701-1707. [PMID: 30258217 PMCID: PMC6221973 DOI: 10.1038/s41591-018-0186-4] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 08/16/2018] [Indexed: 01/20/2023]
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11
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Bobkova MR. [Genetic diversity of human immunodeficiency viruses and antiretroviral therapy]. TERAPEVT ARKH 2018; 88:103-111. [PMID: 28005040 DOI: 10.17116/terarkh20168811103-111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The lecture is devoted to the analysis of the state-of-the-art of the impact of genetic diversity of human immunodeficiency (HIV) viruses on the pattern of infection and the efficiency of antiretroviral therapy (ART). It provides brief information on the origin and evolution of HIV and on the current classification of their genetic variants. The molecular epidemiological situation of HIV infection in Russia and nearby states and the major molecular HIV variants that are dominant in these countries, as well as their origin and prevalence trends are characterized. How the diversity of HIV can affect the efficiency of diagnosis, the transmission of the virus, and the pattern of HIV pathogenesis are briefly reviewed. The comparative data available in the world's scientific literature on these topics are given. More detailed attention is given to the possible causes of varying therapeutic effects against different HIV subtypes, as well as to the specific features of the formation and phenotyping manifestation of ART drug resistance mutations. There is evidence for the necessity of forming a unified follow-up system for treated HIV-infected patients during ART scaling, including in an effort to evaluate the impact of the specific features of the HIV genome on the efficiency of treatment regimens used in Russia.
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Affiliation(s)
- M R Bobkova
- D.I. Ivanovsky Institute of Virology, Honorary Acad. N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, Russia
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12
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Oyarzún P, Kobe B. Recombinant and epitope-based vaccines on the road to the market and implications for vaccine design and production. Hum Vaccin Immunother 2017; 12:763-7. [PMID: 26430814 DOI: 10.1080/21645515.2015.1094595] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Novel vaccination approaches based on rational design of B- and T-cell epitopes - epitope-based vaccines - are making progress in the clinical trial pipeline. The epitope-focused recombinant protein-based malaria vaccine (termed RTS,S) is a next-generation approach that successfully reached phase-III trials, and will potentially become the first commercial vaccine against a human parasitic disease. Progress made on methods such as recombinant DNA technology, advanced cell-culture techniques, immunoinformatics and rational design of immunogens are driving the development of these novel concepts. Synthetic recombinant proteins comprising both B- and T-cell epitopes can be efficiently produced through modern biotechnology and bioprocessing methods, and can enable the induction of large repertoires of immune specificities. In particular, the inclusion of appropriate CD4+ T-cell epitopes is increasingly considered a key vaccine component to elicit robust immune responses, as suggested by results coming from HIV-1 clinical trials. In silico strategies for vaccine design are under active development to address genetic variation in pathogens and several broadly protective "universal" influenza and HIV-1 vaccines are currently at different stages of clinical trials. Other methods focus on improving population coverage in target populations by rationally considering specificity and prevalence of the HLA proteins, though a proof-of-concept in humans has not been demonstrated yet. Overall, we expect immunoinformatics and bioprocessing methods to become a central part of the next-generation epitope-based vaccine development and production process.
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Affiliation(s)
- Patricio Oyarzún
- a Biotechnology Center, Facultad de Ingeniería y Tecnología, Universidad San Sebastián , Concepción , Chile
| | - Bostjan Kobe
- b School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Center, University of Queensland , Brisbane , Australia
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13
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Abstract
PURPOSE OF REVIEW Since 2009 many broadly neutralizing antibodies against HIV have been identified, yet there is still no vaccine capable of inducing such antibodies in humans. This review considers the early observations of HIV sera neutralization in light of more recent studies and highlights areas for future research. RECENT FINDINGS Large clinical cohort studies using standardized neutralization assays and pseudoviruses derived from primary isolates have shown that 10-30% of HIV infections result in some level of serum neutralization breadth. However, less than 10% of individuals develop a greater breadth of neutralization and are termed elite neutralizers. SUMMARY During HIV infection, many individuals develop strain-specific neutralization against their viral quasispecies, and similar immunogen-matched activity can now be induced in animal models. However, only in a minority of infections do broadly neutralizing antibodies develop. Therefore, understanding how the viral diversity, host immune environment, and antibody repertoires intersect to support the generation of neutralization breadth in elite neutralizers could provide guidelines as to how to improve immunization responses.
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Gounder K, Oyaro M, Padayachi N, Zulu TM, de Oliveira T, Wylie J, Ndung'u T. Complex Subtype Diversity of HIV-1 Among Drug Users in Major Kenyan Cities. AIDS Res Hum Retroviruses 2017; 33:500-510. [PMID: 28068781 DOI: 10.1089/aid.2016.0321] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Drug users are increasingly recognized as a key population driving human immunodeficiency virus (HIV) spread in sub-Saharan Africa. To determine HIV-1 subtypes circulating in this population group and explore possible geographic differences, we analyzed HIV-1 sequences among drug users from Nairobi, Mombasa, and Kisumu in Kenya. We sequenced gag and env from 55 drug users. Subtype analysis from 220 gag clonal sequences from 54 of 55 participants (median = 4/participant) showed that 44.4% were A, 16.7% were C, 3.7% were D, and 35.2% were intersubtype recombinants. Of 156 env clonal sequences from 48 of 55 subjects (median = 3/participant), 45.8% were subtype A, 14.6% were C, 6.3% were D, and 33.3% were recombinants. Comparative analysis of both genes showed that 30 (63.8%) participants had concordant subtypes, while 17 (36.2%) were discordant. We identified one genetically linked transmission pair and two cases of dual infection. These data are indicative of extensive HIV-1 intersubtype recombination in Kenya and suggest decline in subtype D prevalence.
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Affiliation(s)
- Kamini Gounder
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Micah Oyaro
- Immunology Unit, Department of Human Pathology, University of Nairobi, Nairobi, Kenya
| | - Nagavelli Padayachi
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Thando Mbali Zulu
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tulio de Oliveira
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Africa Centre for Population Health, University of KwaZulu-Natal, Durban, South Africa
| | - John Wylie
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, Massachusetts
- Max Planck Institute for Infection Biology, Berlin, Germany
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15
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Tibayrenc M, Ayala FJ. Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses? ADVANCES IN PARASITOLOGY 2016; 97:243-325. [PMID: 28325372 DOI: 10.1016/bs.apar.2016.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge. We hypothesize that the PCE features are not mainly due to natural selection but also chiefly originate from in-built genetic properties of pathogens. We show that the PCE model obtains even in microbes that have been considered as 'highly recombining', such as Neisseria meningitidis, and that some clonality features are observed even in Plasmodium, which has been long described as panmictic. Lastly, we provide evidence that PCE features are also observed in viruses, taking into account their extremely fast genetic turnover. The PCE model provides a convenient population genetic framework for any kind of micropathogen. It makes it possible to describe convenient units of analysis (clones and near-clades) for all applied studies. Due to PCE features, these units of analysis are stable in space and time, and clearly delimited. The PCE model opens up the possibility of revisiting the problem of species definition in these organisms. We hypothesize that PCE constitutes a major evolutionary strategy for protozoa, fungi, bacteria, and viruses to adapt to parasitism.
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Affiliation(s)
- M Tibayrenc
- Institut de Recherche pour le Développement, Montpellier, France
| | - F J Ayala
- University of California at Irvine, United States
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16
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Servín-Blanco R, Zamora-Alvarado R, Gevorkian G, Manoutcharian K. Antigenic variability: Obstacles on the road to vaccines against traditionally difficult targets. Hum Vaccin Immunother 2016; 12:2640-2648. [PMID: 27295540 DOI: 10.1080/21645515.2016.1191718] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Despite the impressive impact of vaccines on public health, the success of vaccines targeting many important pathogens and cancers has to date been limited. The burden of infectious diseases today is mainly caused by antigenically variable pathogens (AVPs), which escape immune responses induced by prior infection or vaccination through changes in molecular structures recognized by antibodies or T cells. Extensive genetic and antigenic variability is the major obstacle for the development of new or improved vaccines against "difficult" targets. Alternative, qualitatively new approaches leading to the generation of disease- and patient-specific vaccine immunogens that incorporate complex permanently changing epitope landscapes of intended targets accompanied by appropriate immunomodulators are urgently needed. In this review, we highlight some of the most critical common issues related to the development of vaccines against many pathogens and cancers that escape protective immune responses owing to antigenic variation, and discuss recent efforts to overcome the obstacles by applying alternative approaches for the rational design of new types of immunogens.
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Affiliation(s)
- R Servín-Blanco
- a Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), AP 70228, Cuidad Universitaria , México DF , México
| | - R Zamora-Alvarado
- a Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), AP 70228, Cuidad Universitaria , México DF , México
| | - G Gevorkian
- a Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), AP 70228, Cuidad Universitaria , México DF , México
| | - K Manoutcharian
- a Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), AP 70228, Cuidad Universitaria , México DF , México
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17
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New concepts in HIV-1 vaccine development. Curr Opin Immunol 2016; 41:39-46. [PMID: 27268856 DOI: 10.1016/j.coi.2016.05.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/15/2016] [Accepted: 05/20/2016] [Indexed: 01/13/2023]
Abstract
With 2 million people newly infected with HIV-1 in 2014, an effective HIV-1 vaccine remains a major public health priority. HIV-1 vaccine efficacy trials in humans, complemented by active and passive immunization studies in non-human primates, have identified several key vaccine-induced immunological responses that may correlate with protection against HIV-1 infection. Potential correlates of protection in these studies include V2-specific, polyfunctional, and broadly neutralizing antibody responses, as well as effector memory T cell responses. Here we review how these correlates of protection are guiding current approaches to HIV-1 vaccine development. These approaches include improvements on the ALVAC-HIV/AIDSVAX B/E vaccine regimen used in the RV144 clinical trial in Thailand, adenovirus serotype 26 vectors with gp140 boosting, intravenous infusions of bNAbs, and replicating viral vectors.
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18
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Borggren M, Jensen SS, Heyndrickx L, Palm AA, Gerstoft J, Kronborg G, Hønge BL, Jespersen S, da Silva ZJ, Karlsson I, Fomsgaard A. Neutralizing Antibody Response and Antibody-Dependent Cellular Cytotoxicity in HIV-1-Infected Individuals from Guinea-Bissau and Denmark. AIDS Res Hum Retroviruses 2016; 32:434-42. [PMID: 26621287 DOI: 10.1089/aid.2015.0118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The development of therapeutic and prophylactic HIV vaccines for African countries is urgently needed, but the question of what immunogens to use needs to be answered. One approach is to include HIV envelope immunogens derived from HIV-positive individuals from a geographically concentrated epidemic with more limited viral genetic diversity for a region-based vaccine. To address if there is a basis for a regional selected antibody vaccine, we have screened two regionally separate cohorts from Guinea-Bissau and Denmark for neutralizing antibody activity and antibody-dependent cellular cytotoxicity (ADCC) against local and nonlocal circulating HIV-1 strains. The neutralizing activity did not demonstrate higher potential against local circulating strains according to geography and subtype determination, but the plasma from Danish individuals demonstrated significantly higher inhibitory activity than that from Guinea-Bissau individuals against both local and nonlocal virus strains. Interestingly, an opposite pattern was observed with ADCC activity, where Guinea-Bissau individual plasma demonstrated higher activity than Danish plasma and was specifically against the local circulating subtype. Thus, on basis of samples from these two cohorts, no local-specific neutralizing activity was detected, but a local ADCC response was identified in the Guinea-Bissau samples, suggesting potential use of regional immunogens for an ADCC-inducing vaccine.
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Affiliation(s)
- Marie Borggren
- Virus Research and Development Laboratory, Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Sanne Skov Jensen
- Virus Research and Development Laboratory, Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Leo Heyndrickx
- Biomedical Department, Virology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Angelica A. Palm
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Jan Gerstoft
- Department of Infectious Diseases and Rheumatology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Gitte Kronborg
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Bo Langhoff Hønge
- Bandim Health Project, Indepth Network, Bissau, Guinea-Bissau
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Sanne Jespersen
- Bandim Health Project, Indepth Network, Bissau, Guinea-Bissau
| | | | - Ingrid Karlsson
- Virus Research and Development Laboratory, Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Fomsgaard
- Virus Research and Development Laboratory, Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- Infectious Disease Research Unit, Clinical Institute, University of Southern Denmark, Odense, Denmark
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19
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Danaviah S, de Oliveira T, Gordon M, Govender S, Chelule P, Pillay S, Naicker T, Cassol S, Ndung'u T. Analysis of Dominant HIV Quasispecies Suggests Independent Viral Evolution Within Spinal Granulomas Coinfected with Mycobacterium tuberculosis and HIV-1 Subtype C. AIDS Res Hum Retroviruses 2016; 32:262-70. [PMID: 26564424 DOI: 10.1089/aid.2015.0189] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Extrapulmonary tuberculosis (TB) is a significant public health challenge in South Africa and worldwide, largely fuelled by the HIV epidemic. In spinal TB, Mycobacteria infect the spinal column without dissemination to the spinal cord. The immune microenvironment, target cell characteristics, and other evolutionary forces within granulomas during HIV/TB coinfection are poorly characterized. We investigated whether spinal TB granulomas represent a sequestered anatomical site where independent HIV evolution occurs, and assessed the role of macrophages as a target cell for both HIV and mycobacteria. RNA was extracted from plasma and granulomatous tissue from six antiretroviral-naive HIV-1/spinal TB-coinfected patients, RT-PCR amplified, and the C2-V5 env segment was cloned and sequenced. Analysis of genetic diversity, phylogeny and coalescence patterns was performed on clonal sequences. To investigate their role in HIV sequestration, macrophages and the HIV-1 p24 protein were immune localized and ultrastructural features were studied. Intercompartment diversity measurements and phylogenetic reconstruction revealed anatomically distinct monophyletic HIV-1 clusters in four of six patients. Genotypic CCR5-tropic variants were predominant (98.9%) with conservation of putative N-linked glycosylation sites in both compartments. CD68(+) reactivity was associated with higher tissue viral load (r = 1.0; p < 0.01) but not greater intrapatient diversity (r = 0.60; p > 0.05). Ultrastructural imaging revealed the presence of bacterial and virus-like particles within membrane-bound intracellular compartments of macrophages. Spinal tuberculosis granulomas may form anatomically discreet sites of divergent viral evolution. Macrophages in these granulomas harbored both pathogens, suggesting that they may facilitate the process of viral sequestration within this compartment.
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Affiliation(s)
- Sivapragashini Danaviah
- Africa Centre for Health and Population Studies, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal (UKZN), Durban, South Africa
| | - Tulio de Oliveira
- Africa Centre for Health and Population Studies, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal (UKZN), Durban, South Africa
| | - Michelle Gordon
- Department of Virology, Nelson R. Mandela School of Medicine, UKZN, Durban, South Africa
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), UKZN, Durban, South Africa
| | - Shunmugam Govender
- Department of Orthopedics, Nelson R. Mandela School of Medicine, UKZN, Durban, South Africa
| | - Paul Chelule
- School of Public Health, Sefako Makgatho Health Sciences University, Medunsa, South Africa
| | - Sureshnee Pillay
- Africa Centre for Health and Population Studies, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal (UKZN), Durban, South Africa
| | - Thajasvarie Naicker
- Optics and Imaging Centre, Nelson R. Mandela School of Medicine, UKZN, Durban, South Africa
| | - Sharon Cassol
- MRC Inflammation and Immunity Unit, Department of Immunology, University of Pretoria, Pretoria, South Africa
| | - Thumbi Ndung'u
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), UKZN, Durban, South Africa
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, UKZN, Durban, South Africa
- Max Planck Institute for Infection Biology, Chariteplatz, Berlin, Germany
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, Massachusetts
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20
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Zhuo X, Feschotte C. Cross-Species Transmission and Differential Fate of an Endogenous Retrovirus in Three Mammal Lineages. PLoS Pathog 2015; 11:e1005279. [PMID: 26562410 PMCID: PMC4643047 DOI: 10.1371/journal.ppat.1005279] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 10/23/2015] [Indexed: 11/18/2022] Open
Abstract
Endogenous retroviruses (ERVs) arise from retroviruses chromosomally integrated in the host germline. ERVs are common in vertebrate genomes and provide a valuable fossil record of past retroviral infections to investigate the biology and evolution of retroviruses over a deep time scale, including cross-species transmission events. Here we took advantage of a catalog of ERVs we recently produced for the bat Myotis lucifugus to seek evidence for infiltration of these retroviruses in other mammalian species (>100) currently represented in the genome sequence database. We provide multiple lines of evidence for the cross-ordinal transmission of a gammaretrovirus endogenized independently in the lineages of vespertilionid bats, felid cats and pangolin ~13-25 million years ago. Following its initial introduction, the ERV amplified extensively in parallel in both bat and cat lineages, generating hundreds of species-specific insertions throughout evolution. However, despite being derived from the same viral species, phylogenetic and selection analyses suggest that the ERV experienced different amplification dynamics in the two mammalian lineages. In the cat lineage, the ERV appears to have expanded primarily by retrotransposition of a single proviral progenitor that lost infectious capacity shortly after endogenization. In the bat lineage, the ERV followed a more complex path of germline invasion characterized by both retrotransposition and multiple infection events. The results also suggest that some of the bat ERVs have maintained infectious capacity for extended period of time and may be still infectious today. This study provides one of the most rigorously documented cases of cross-ordinal transmission of a mammalian retrovirus. It also illustrates how the same retrovirus species has transitioned multiple times from an infectious pathogen to a genomic parasite (i.e. retrotransposon), yet experiencing different invasion dynamics in different mammalian hosts.
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Affiliation(s)
- Xiaoyu Zhuo
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- * E-mail:
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21
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Méndez C, Ahlenstiel CL, Kelleher AD. Post-transcriptional gene silencing, transcriptional gene silencing and human immunodeficiency virus. World J Virol 2015; 4:219-244. [PMID: 26279984 PMCID: PMC4534814 DOI: 10.5501/wjv.v4.i3.219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 01/24/2015] [Accepted: 04/29/2015] [Indexed: 02/05/2023] Open
Abstract
While human immunodeficiency virus 1 (HIV-1) infection is controlled through continuous, life-long use of a combination of drugs targeting different steps of the virus cycle, HIV-1 is never completely eradicated from the body. Despite decades of research there is still no effective vaccine to prevent HIV-1 infection. Therefore, the possibility of an RNA interference (RNAi)-based cure has become an increasingly explored approach. Endogenous gene expression is controlled at both, transcriptional and post-transcriptional levels by non-coding RNAs, which act through diverse molecular mechanisms including RNAi. RNAi has the potential to control the turning on/off of specific genes through transcriptional gene silencing (TGS), as well as fine-tuning their expression through post-transcriptional gene silencing (PTGS). In this review we will describe in detail the canonical RNAi pathways for PTGS and TGS, the relationship of TGS with other silencing mechanisms and will discuss a variety of approaches developed to suppress HIV-1 via manipulation of RNAi. We will briefly compare RNAi strategies against other approaches developed to target the virus, highlighting their potential to overcome the major obstacle to finding a cure, which is the specific targeting of the HIV-1 reservoir within latently infected cells.
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22
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Chin'ombe N, Ruhanya V. HIV/AIDS vaccines for Africa: scientific opportunities, challenges and strategies. Pan Afr Med J 2015; 20:386. [PMID: 26185576 PMCID: PMC4499268 DOI: 10.11604/pamj.2015.20.386.4660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 04/13/2015] [Indexed: 01/01/2023] Open
Abstract
More than decades have already elapsed since human immunodeficiency virus (HIV) was identified as the causative agent of acquired immunodeficiency syndrome (AIDS). The HIV has since spread to all parts of the world with devastating effects. In sub-saharan Africa, the HIV/AIDS epidemic has reached unprecedented proportions. Safe, effective and affordable HIV/AIDS vaccines for Africans are therefore urgently needed to contain this public health problem. Although, there are challenges, there are also scientific opportunities and strategies that can be exploited in the development of HIV/AIDS vaccines for Africa. The recent RV144 Phase III trial in Thailand has demonstrated that it is possible to develop a vaccine that can potentially elicit modest protective immunity against HIV infection. The main objective of this review is to outline the key scientific opportunities, challenges and strategies in HIV/AIDS vaccine development in Africa.
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Affiliation(s)
- Nyasha Chin'ombe
- Department of Medical Microbiology, College of Health Sciences, University of Zimbabwe, P O Box A178, Avondale, Harare, Zimbabwe
| | - Vurayai Ruhanya
- Department of Medical Microbiology, College of Health Sciences, University of Zimbabwe, P O Box A178, Avondale, Harare, Zimbabwe
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23
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Stephenson KE, Neubauer GH, Reimer U, Pawlowski N, Knaute T, Zerweck J, Korber BT, Barouch DH. Quantification of the epitope diversity of HIV-1-specific binding antibodies by peptide microarrays for global HIV-1 vaccine development. J Immunol Methods 2015; 416:105-23. [PMID: 25445329 PMCID: PMC4324361 DOI: 10.1016/j.jim.2014.11.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 11/10/2014] [Accepted: 11/10/2014] [Indexed: 01/08/2023]
Abstract
An effective vaccine against human immunodeficiency virus type 1 (HIV-1) will have to provide protection against a vast array of different HIV-1 strains. Current methods to measure HIV-1-specific binding antibodies following immunization typically focus on determining the magnitude of antibody responses, but the epitope diversity of antibody responses has remained largely unexplored. Here we describe the development of a global HIV-1 peptide microarray that contains 6564 peptides from across the HIV-1 proteome and covers the majority of HIV-1 sequences in the Los Alamos National Laboratory global HIV-1 sequence database. Using this microarray, we quantified the magnitude, breadth, and depth of IgG binding to linear HIV-1 sequences in HIV-1-infected humans and HIV-1-vaccinated humans, rhesus monkeys and guinea pigs. The microarray measured potentially important differences in antibody epitope diversity, particularly regarding the depth of epitope variants recognized at each binding site. Our data suggest that the global HIV-1 peptide microarray may be a useful tool for both preclinical and clinical HIV-1 research.
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Affiliation(s)
- Kathryn E Stephenson
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - George H Neubauer
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Ulf Reimer
- JPT Peptide Technologies, Berlin, Germany
| | | | | | | | - Bette T Korber
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States; Ragon Institute of MGH, MIT, and Harvard, Boston, MA, United States.
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24
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Nunes CC, Matte MCC, Dias CF, Araújo LAL, Guimarães LSP, Almeida S, Brígido LFM. The influence of HIV-1 subtypes C, CRF31_BC and B on disease progression and initial virologic response to HAART in a Southern Brazilian cohort. Rev Inst Med Trop Sao Paulo 2014; 56:205-11. [PMID: 24878998 PMCID: PMC4085862 DOI: 10.1590/s0036-46652014000300005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 10/21/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Although most HIV-1 infections in Brazil are due to subtype B, Southern Brazil has a high prevalence of subtype C and recombinant forms, such as CRF31_BC. This study assessed the impact of viral diversity on clinical progression in a cohort of newly diagnosed HIV-positive patients. METHODS From July/2004 to December/2005, 135 HIV-infected patients were recruited. The partial pol region was subtyped by phylogeny. A generalized estimating equation (GEE) model was used to examine the relationship between viral subtype, CD4+ T cell count and viral load levels before antiretroviral therapy. Hazard ratio (Cox regression) was used to evaluate factors associated with viral suppression (viral load < 50 copies/mL at six months). RESULTS Main HIV-1 subtypes included B (29.4%), C (28.2%), and CRF31_BC (23.5%). Subtypes B and C showed a similar trend in CD4+ T cell decline. Comparison of non-B (C and CRF31_BC) and B subtypes revealed no significant difference in the proportion of patients with viral suppression at six months (week 24). Higher CD4+ T cell count and lower viral load were independently associated with viral suppression. CONCLUSION No significant differences were found between subtypes; however, lower viral load and higher CD4+ T cell count before therapy were associated with better response.
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Affiliation(s)
| | - Maria Cristina Cotta Matte
- State Foundation for Health Research and Production, Center for Scientific and Technological Development, Porto Alegre, RS, Brazil
| | - Claudia Fontoura Dias
- Municipal Health Department, STD/AIDS Specialized Care Center, Porto Alegre, RS, Brazil
| | - Leonardo Augusto Luvison Araújo
- State Foundation for Health Research and Production, Center for Scientific and Technological Development, Porto Alegre, RS, Brazil
| | | | - Sabrina Almeida
- State Foundation for Health Research and Production, Center for Scientific and Technological Development, Porto Alegre, RS, Brazil
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Breadth of HIV-1 Env-specific antibody-dependent cellular cytotoxicity: relevance to global HIV vaccine design. AIDS 2014; 28:1859-70. [PMID: 24937308 DOI: 10.1097/qad.0000000000000310] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The objective of this study is to determine the breadth of HIV-1 Env-specific antibody-dependent cellular cytotoxicity (ADCC) in HIV controllers and HIV progressors with a view to design globally relevant HIV vaccines. DESIGN The breadth of ADCC towards four major HIV-1 Env subtypes was measured in vitro for 11 HIV controllers and 11 HIV progressors. METHODS Plasma from 11 HIV controllers (including long-term slow progressors, viremic controllers, elite controller and posttreatment controller) and 11 HIV progressors, mostly infected with HIV-1 subtype B, was analysed for ADCC responses. ADCC assays were performed against 10 HIV-1 gp120 and 8 gp140 proteins from four major HIV-1 subtypes (A, B, C and E) and 3 glycosylation-mutant gp140 proteins. RESULTS ADCC-mediated natural killer cell activation was significantly broader (P = 0.02) and of higher magnitude (P < 0.001) in HIV controllers than in HIV progressors. HIV controllers also showed significantly higher magnitude of ADCC-mediated killing of Env-coated target cells than HIV progressors to both HIV-1 subtype B and the heterologous subtype E gp140 (P = 0.001). We found good ADCC reactivity to subtype B and E Envs, less cross-reactivity to subtype A and minimal cross-reactivity to subtype C Envs. Glycosylation-dependent ADCC epitopes comprise a significant proportion of the total Env-specific ADCC response, as evident from the reduction in ADCC to nonglycosylated form of HIV-1 gp140 (P = 0.004). CONCLUSION HIV controllers have robust ADCC responses that recognize a broad range of HIV-1 Env. Glycosylation of Env was found to be important for recognition of ADCC epitopes. Identifying conserved ADCC epitopes will assist in designing globally relevant ADCC-based HIV vaccines.
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Di Giacomo A. The EFIS-EJI Ruggero Ceppellini Advanced School of Immunology: Malaria, Tuberculosis and HIV/AIDS: novel vaccination strategies against the three major killers. Eur J Immunol 2014; 44:1573-4. [PMID: 24903050 DOI: 10.1002/eji.201470055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Antonio Di Giacomo
- Member, Board of Directors, EFIS-EJI Ceppellini Advanced School of Immunology
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Mangul S, Wu NC, Mancuso N, Zelikovsky A, Sun R, Eskin E. Accurate viral population assembly from ultra-deep sequencing data. Bioinformatics 2014; 30:i329-37. [PMID: 24932001 PMCID: PMC4058922 DOI: 10.1093/bioinformatics/btu295] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
MOTIVATION Next-generation sequencing technologies sequence viruses with ultra-deep coverage, thus promising to revolutionize our understanding of the underlying diversity of viral populations. While the sequencing coverage is high enough that even rare viral variants are sequenced, the presence of sequencing errors makes it difficult to distinguish between rare variants and sequencing errors. RESULTS In this article, we present a method to overcome the limitations of sequencing technologies and assemble a diverse viral population that allows for the detection of previously undiscovered rare variants. The proposed method consists of a high-fidelity sequencing protocol and an accurate viral population assembly method, referred to as Viral Genome Assembler (VGA). The proposed protocol is able to eliminate sequencing errors by using individual barcodes attached to the sequencing fragments. Highly accurate data in combination with deep coverage allow VGA to assemble rare variants. VGA uses an expectation-maximization algorithm to estimate abundances of the assembled viral variants in the population. RESULTS on both synthetic and real datasets show that our method is able to accurately assemble an HIV viral population and detect rare variants previously undetectable due to sequencing errors. VGA outperforms state-of-the-art methods for genome-wide viral assembly. Furthermore, our method is the first viral assembly method that scales to millions of sequencing reads. AVAILABILITY Our tool VGA is freely available at http://genetics.cs.ucla.edu/vga/
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Affiliation(s)
- Serghei Mangul
- Computer Science Department, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA, Department of Computer Science, Georgia State University, Atlanta, GA, 30303 and Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
| | - Nicholas C Wu
- Computer Science Department, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA, Department of Computer Science, Georgia State University, Atlanta, GA, 30303 and Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
| | - Nicholas Mancuso
- Computer Science Department, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA, Department of Computer Science, Georgia State University, Atlanta, GA, 30303 and Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
| | - Alex Zelikovsky
- Computer Science Department, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA, Department of Computer Science, Georgia State University, Atlanta, GA, 30303 and Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
| | - Ren Sun
- Computer Science Department, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA, Department of Computer Science, Georgia State University, Atlanta, GA, 30303 and Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
| | - Eleazar Eskin
- Computer Science Department, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA, Department of Computer Science, Georgia State University, Atlanta, GA, 30303 and Department of Human Genetics, University of California, Los Angeles, CA 90095, USAComputer Science Department, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA, Department of Computer Science, Georgia State University, Atlanta, GA, 30303 and Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
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Immunogen design for HIV-1 and influenza. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1891-1906. [PMID: 24892211 DOI: 10.1016/j.bbapap.2014.05.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/23/2014] [Accepted: 05/26/2014] [Indexed: 12/12/2022]
Abstract
Vaccines provide the most cost effective defense against pathogens. Although vaccines have been designed for a number of viral diseases, a vaccine against HIV-1 still remains elusive. In contrast, while there are excellent influenza vaccines, these need to be changed every few years because of antigenic drift and shift. The recent discovery of a large number of broadly neutralizing antibodies (bNAbs) and structural characterization of the conserved epitopes targeted by them presents an opportunity for structure based HIV-1 and influenza A vaccine design. We discuss strategies to design immunogens either targeting a particular antigenic region or focusing on native structure stabilization. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody.
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Abstract
Despite the great advances made in controlling human immunodeficiency virus type 1 (HIV-1) infection with antiretroviral drug treatment, a safe and efficacious HIV vaccine has yet to be developed. Here, we discuss why clinical trials and vaccine development for HIV have so far been disappointing, with an emphasis on the lack of protective antibodies. We review approaches for developing appropriate HIV immunogens and the stimulation of long-lasting B-cell responses with antibody maturation. We conclude that candidate reagents in the pipeline for HIV vaccine development are unlikely to be particularly effective. Although the major funders of HIV vaccine research and development are placing increasing emphasis on clinical product development, a genuine breakthrough in preventing HIV infection through vaccines is more likely to come from novel immunogen research.
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Affiliation(s)
- F Chiodi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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Vaccine-induced measles virus-specific T cells do not prevent infection or disease but facilitate subsequent clearance of viral RNA. mBio 2014; 5:e01047. [PMID: 24736226 PMCID: PMC3993862 DOI: 10.1128/mbio.01047-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Infection with wild-type measles virus (MeV) induces lifelong protection from reinfection, and parenteral delivery of the live attenuated measles vaccine (LAV) also provides protection from measles. The level of neutralizing antibody is a good indicator of protection, but the independent roles of MeV-specific antibody and T cells have not been identified. In this study, macaques immunized with LAV through a nebulizer and a mouthpiece developed MeV-specific T-cell responses but not neutralizing antibodies. Upon challenge with wild-type MeV, these animals developed rashes and viremias similar to those in naive animals but cleared viral RNA from blood 25 to 40 days faster. The nebulizer-immunized animals also had more robust MeV-specific CD4+ and CD8+ T-cell responses than the naive animals after challenge, characterized by a higher number and better durability of gamma interferon (IFN-γ)-producing cells. Induction of MeV-specific circulating CD4+ and CD8+ T cells capable of producing multiple cytokines correlated with clearance of viral RNA in the nebulizer-immunized macaques. These studies demonstrated that MeV-specific T-cell immunity alone did not prevent measles, but T-cell priming enhanced the magnitude, durability, and polyfunctionality of MeV-specific T cells after challenge infection and correlated with more rapid clearance of MeV RNA. The components of vaccine-induced immunity necessary for protection from infection and disease have not been clearly identified for most vaccines. Vaccine development usually focuses on induction of antibody, but T-cell-based vaccines are also under development. The live attenuated measles vaccine (LAV) given subcutaneously induces both T cells and neutralizing antibody and provides solid protection from infection. LAV delivered to the upper respiratory tract through a nebulizer and mouthpiece induced a T-cell response but no neutralizing antibody. These T-cell-primed macaques demonstrated no protection from rash or viremia when challenged with wild-type MeV, but viral RNA was cleared more rapidly than in unimmunized animals. Thus, T-cell immunity did not protect from infection or acute disease but facilitated virus clearance during recovery. These studies demonstrate the importance and independent roles of T cells and antibody in protection and recovery from measles.
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Abstract
A global human immunodeficiency virus-1 (HIV-1) vaccine will have to elicit immune responses capable of providing protection against a tremendous diversity of HIV-1 variants. In this review, we first describe the current state of the HIV-1 vaccine field, outlining the immune responses that are desired in a global HIV-1 vaccine. In particular, we emphasize the likely importance of Env-specific neutralizing and non-neutralizing antibodies for protection against HIV-1 acquisition and the likely importance of effector Gag-specific T lymphocytes for virologic control. We then highlight four strategies for developing a global HIV-1 vaccine. The first approach is to design specific vaccines for each geographic region that include antigens tailor-made to match local circulating HIV-1 strains. The second approach is to design a vaccine that will elicit Env-specific antibodies capable of broadly neutralizing all HIV-1 subtypes. The third approach is to design a vaccine that will elicit cellular immune responses that are focused on highly conserved HIV-1 sequences. The fourth approach is to design a vaccine to elicit highly diverse HIV-1-specific responses. Finally, we emphasize the importance of conducting clinical efficacy trials as the only way to determine which strategies will provide optimal protection against HIV-1 in humans.
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Affiliation(s)
- Kathryn E Stephenson
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
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Abstract
Pseudogenes are very common in the genomes of a wide range of organisms and, although they were originally considered as genetic junk, now several functions have been attributed to them. One important function of pseudogenes, as discussed in this chapter, is to provide material for genetic diversity. This is most prominent in the case of immunological recognition molecules such as immunoglobulins and B- and T-cell receptors, as well as in the case of antigenic variation in intracellular pathogens. Other examples discussed are olfactory receptors, ribosomal proteins, cytochrome P450s, and pseudokinases.
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Pradeu T, Jaeger S, Vivier E. The speed of change: towards a discontinuity theory of immunity? Nat Rev Immunol 2013; 13:764-9. [DOI: 10.1038/nri3521] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Thirty years on: HIV receptor gymnastics and the prevention of infection. BMC Biol 2013; 11:57. [PMID: 23692808 PMCID: PMC3660199 DOI: 10.1186/1741-7007-11-57] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 05/10/2013] [Indexed: 11/10/2022] Open
Abstract
During 30 years of research on human immunodeficiency virus (HIV), our knowledge of its cellular receptors - CD4, CCR5 and CXCR4 - has illuminated aspects of the pathogenesis of the acquired immune deficiency syndrome (AIDS). Studying how the HIV envelope glycoproteins interact with the receptors led to anti-retroviral drugs based on blocking the docking or fusion of virus to the host cell. Genetic polymorphisms of CCR5 determine resistance to HIV infection and the rate of progression to AIDS. Eliciting neutralizing antibodies to the sites of receptor interaction on HIV glycoproteins is a promising approach to HIV vaccine development.
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Abstract
Most neutralizing antibodies act at the earliest steps of viral infection and block interaction of the virus with cellular receptors to prevent entry into host cells. The inability to induce neutralizing antibodies to HIV has been a major obstacle to HIV vaccine research since the early days of the epidemic. However, in the past three years, the definition of a neutralizing antibody against HIV has been revolutionized by the isolation of extremely broad and potent neutralizing antibodies from HIV-infected individuals. Considerable hurdles remain for inducing neutralizing antibodies to a protective level after immunization. Meanwhile, novel technologies to bypass the induction of antibodies are being explored to provide prophylactic antibody-based interventions. This review addresses the challenge of inducing HIV neutralizing antibodies upon immunization and considers notable recent advances in the field. A greater understanding of the successes and failures for inducing a neutralizing response upon immunization is required to accelerate the development of an effective HIV vaccine.
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Affiliation(s)
- Laura E McCoy
- Wohl Virion Centre, Division of Infection and Immunity, University College London, London WC1E 6BT, England, UK
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Hawke KG, Waddell RG, Gordon DL, Ratcliff RM, Ward PR, Kaldor JM. HIV non-B subtype distribution: emerging trends and risk factors for imported and local infections newly diagnosed in South Australia. AIDS Res Hum Retroviruses 2013; 29:311-7. [PMID: 23098890 DOI: 10.1089/aid.2012.0082] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Monitoring HIV subtype distribution is important for understanding transmission dynamics. Subtype B has historically been dominant in Australia, but in recent years new clades have appeared. Since 2000, clade data have been collected as part of HIV surveillance in South Australia. The aim of this study was to evaluate the prevalence of and risk factors for HIV-1 non-B subtypes. The study population was composed of newly diagnosed, genotyped HIV subjects in South Australia between 2000 and 2010. We analyzed time trends and subtype patterns in this cohort; notification data were aggregated into three time periods (2000-2003, 2004-2006, and 2007-2010). Main outcome measures were number of new non-B infections by year, exposure route, and other demographic characteristics. There were 513 new HIV diagnoses; 425 had information on subtype. The majority (262/425) were in men who have sex with men (MSM), predominantly subtype B and acquired in Australia. Infections acquired in Australia decreased from 77% (2000-2003) to 64% (2007-2010) (p=0.007) and correspondingly the proportion of subtype B declined from 85% to 68% (p=0.002). Non-B infections were predominantly (83%) heterosexual contacts, mostly acquired overseas (74%). The majority (68%) of non-B patients were born outside of Australia. There was a nonsignificant increase from 1.6% to 4.2% in the proportion of locally transmitted non-B cases (p=0.3). Three non-B subtypes and two circulating recombinant forms (CRFs) were identified: CRF_AE (n=41), C (n=36), CRF_AG (n=13), A (n=9), and D (n=2). There has been a substantial increase over the past decade in diagnosed non-B infections, primarily through cases acquired overseas.
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Affiliation(s)
- Karen G. Hawke
- Discipline of Public Health, Flinders University, Adelaide, Australia
| | | | - David L. Gordon
- Department of Microbiology and Infectious Diseases, SA Pathology at Flinders Medical Centre, and Flinders University, Adelaide, Australia
| | - Rodney M. Ratcliff
- Department of Microbiology and Infectious Diseases, SA Pathology at Institute of Medical and Veterinary Science, and School of Biomedical Science, University of Adelaide, Adelaide, Australia
| | - Paul R. Ward
- Discipline of Public Health, Flinders University, Adelaide, Australia
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Holmes EC. What can we predict about viral evolution and emergence? Curr Opin Virol 2012; 3:180-4. [PMID: 23273851 PMCID: PMC3626763 DOI: 10.1016/j.coviro.2012.12.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 12/02/2012] [Accepted: 12/03/2012] [Indexed: 01/14/2023]
Abstract
Predicting the emergence of infectious diseases has been touted as one of the most important goals of biomedical science, with an array of funding schemes and research projects. However, evolutionary biology generally has a dim view of prediction, and there is a danger that erroneous predictions will mean a misuse of resources and undermine public confidence. Herein, I outline what can be realistically predicted about viral evolution and emergence, argue that any success in predicting what may emerge is likely to be limited, but that forecasting how viruses might evolve and spread following emergence is more tractable. I also emphasize that a properly grounded research program in disease prediction must involve a synthesis of ecological and genetic perspectives.
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Affiliation(s)
- Edward C Holmes
- Sydney Emerging Infections and Biosecurity Institute, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
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