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Luthuli B, Gounder K, Deymier MJ, Dong KL, Balazs AB, Mann JK, Ndung'u T. Generation and characterization of infectious molecular clones of transmitted/founder HIV-1 subtype C viruses. Virology 2023; 583:14-26. [PMID: 37084644 DOI: 10.1016/j.virol.2023.04.001] [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: 07/05/2022] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
The genetic diversity of HIV impedes vaccine development. Identifying the viral properties of transmitted/founder (T/F) variants may provide a common vaccine target. To study the biological nature of T/F viruses, we constructed full-length clones from women detected during Fiebig stage I acute HIV-1 infection (AHI) from heterosexual male-to-female (MTF) transmission; and clones after one year of infection using In-Fusion-based cloning. Eighteen full-length T/F clones were generated from 9 women and six chronic infection clones were from 2 individuals. All clones but one were non-recombinant subtype C. Three of the 5 T/F clones and 3 chronic clones tested replicated efficiently in PBMCs and utilised CCR5 coreceptor for cell entry. Transmitted/founder and chronic infection clones displayed heterogenous in vitro replicative capacity and resistance to type I interferon. T/F viruses had shorter Env glycoproteins and fewer N-linked glycosylation sites in Env. Our findings suggest MTF transmission may select viruses with compact envelopes.
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Affiliation(s)
| | - Kamini Gounder
- Africa Health Research Institute, Durban, South Africa; HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Martin J Deymier
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, USA
| | - Krista L Dong
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, USA
| | - Alejandro B Balazs
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, USA
| | - Jaclyn K Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Thumbi Ndung'u
- Africa Health Research Institute, Durban, South Africa; HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa; The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, USA; Division of Infection and Immunity, University College London, London, UK.
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2
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Contribution of the HIV-1 Envelope Glycoprotein to AIDS Pathogenesis and Clinical Progression. Biomedicines 2022; 10:biomedicines10092172. [PMID: 36140273 PMCID: PMC9495913 DOI: 10.3390/biomedicines10092172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/21/2022] [Accepted: 08/27/2022] [Indexed: 11/29/2022] Open
Abstract
In the absence of antiviral therapy, HIV-1 infection progresses to a wide spectrum of clinical manifestations that are the result of an entangled contribution of host, immune and viral factors. The contribution of these factors is not completely established. Several investigations have described the involvement of the immune system in the viral control. In addition, distinct HLA-B alleles, HLA-B27, -B57-58, were associated with infection control. The combination of these elements and antiviral host restriction factors results in different clinical outcomes. The role of the viral proteins in HIV-1 infection has been, however, less investigated. We will review contributions dedicated to the pathogenesis of HIV-1 infection focusing on studies identifying the function of the viral envelope glycoprotein (Env) in the clinical progression because of its essential role in the initial events of the virus life-cycle. Some analysis showed that inefficient viral Envs were dominant in non-progressor individuals. These poorly-functional viral proteins resulted in lower cellular activation, viral replication and minor viral loads. This limited viral antigenic production allows a better immune response and a lower immune exhaustion. Thus, the properties of HIV-1 Env are significant in the clinical outcome of the HIV-1 infection and AIDS pathogenesis.
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3
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Pérez-Yanes S, Pernas M, Marfil S, Cabrera-Rodríguez R, Ortiz R, Urrea V, Rovirosa C, Estévez-Herrera J, Olivares I, Casado C, Lopez-Galindez C, Blanco J, Valenzuela-Fernández A. The Characteristics of the HIV-1 Env Glycoprotein Are Linked With Viral Pathogenesis. Front Microbiol 2022; 13:763039. [PMID: 35401460 PMCID: PMC8988142 DOI: 10.3389/fmicb.2022.763039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/31/2022] [Indexed: 12/17/2022] Open
Abstract
The understanding of HIV-1 pathogenesis and clinical progression is incomplete due to the variable contribution of host, immune, and viral factors. The involvement of viral factors has been investigated in extreme clinical phenotypes from rapid progressors to long-term non-progressors (LTNPs). Among HIV-1 proteins, the envelope glycoprotein complex (Env) has been concentrated on in many studies for its important role in the immune response and in the first steps of viral replication. In this study, we analyzed the contribution of 41 Envs from 24 patients with different clinical progression rates and viral loads (VLs), LTNP-Elite Controllers (LTNP-ECs); Viremic LTNPs (vLTNPs), and non-controller individuals contemporary to LTNPs or recent, named Old and Modern progressors. We studied the Env expression, the fusion and cell-to-cell transfer capacities, as well as viral infectivity. The sequence and phylogenetic analysis of Envs were also performed. In every functional characteristic, the Envs from subjects with viral control (LTNP-ECs and vLTNPs) showed significant lower performance compared to those from the progressor individuals (Old and Modern). Regarding sequence analysis, the variable loops of the gp120 subunit of the Env (i.e., V2, V4, and mainly V5) of the progressor individuals showed longer and more glycosylated sequences than controller subjects. Therefore, HIV-1 Envs from virus of patients presenting viremic control and the non-progressor clinical phenotype showed poor viral functions and shorter sequences, whereas functional Envs were associated with virus of patients lacking virological control and with progressor clinical phenotypes. These correlations support the role of Env genotypic and phenotypic characteristics in the in vivo HIV-1 infection and pathogenesis.
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Affiliation(s)
- Silvia Pérez-Yanes
- Unidad de Farmacología, Sección de Medicina, Laboratorio de Inmunología Celular y Viral, Facultad de Ciencias de la Salud de la Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain
| | - María Pernas
- Unidad de Virologia Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia Marfil
- Institut de Recerca de la Sida IrsiCaixa, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Romina Cabrera-Rodríguez
- Unidad de Farmacología, Sección de Medicina, Laboratorio de Inmunología Celular y Viral, Facultad de Ciencias de la Salud de la Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain
| | - Raquel Ortiz
- Institut de Recerca de la Sida IrsiCaixa, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Víctor Urrea
- Institut de Recerca de la Sida IrsiCaixa, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Carla Rovirosa
- Institut de Recerca de la Sida IrsiCaixa, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Judith Estévez-Herrera
- Unidad de Farmacología, Sección de Medicina, Laboratorio de Inmunología Celular y Viral, Facultad de Ciencias de la Salud de la Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain
| | - Isabel Olivares
- Unidad de Virologia Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Madrid, Spain
| | - Concepción Casado
- Unidad de Virologia Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Madrid, Spain
- Concepción Casado,
| | - Cecilio Lopez-Galindez
- Unidad de Virologia Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Madrid, Spain
- Cecilio Lopez-Galindez,
| | - Julià Blanco
- Institut de Recerca de la Sida IrsiCaixa, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Barcelona, Spain
- Chair of Infectious Diseases and Immunity, Faculty of Medicine, Universitat de Vic-Universitat Central de Catalunya (UVic-UCC), Barcelona, Spain
- Julià Blanco,
| | - Agustín Valenzuela-Fernández
- Unidad de Farmacología, Sección de Medicina, Laboratorio de Inmunología Celular y Viral, Facultad de Ciencias de la Salud de la Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain
- *Correspondence: Agustín Valenzuela-Fernández,
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Detecting Selection in the HIV-1 Genome during Sexual Transmission Events. Viruses 2022; 14:v14020406. [PMID: 35215999 PMCID: PMC8876189 DOI: 10.3390/v14020406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/04/2022] [Accepted: 02/11/2022] [Indexed: 01/27/2023] Open
Abstract
Little is known about whether and how variation in the HIV-1 genome affects its transmissibility. Assessing which genomic features of HIV-1 are under positive or negative selection during transmission is challenging, because very few virus particles are typically transmitted, and random genetic drift can dilute genetic signals in the recipient virus population. We analyzed 30 transmitter–recipient pairs from the Zurich Primary HIV Infection Study and the Swiss HIV Cohort Study using near full-length HIV-1 genomes. We developed a new statistical test to detect selection during transmission, called Selection Test in Transmission (SeTesT), based on comparing the transmitter and recipient virus population and accounting for the transmission bottleneck. We performed extensive simulations and found that sensitivity of detecting selection during transmission is limited by the strong population bottleneck of few transmitted virions. When pooling individual test results across patients, we found two candidate HIV-1 genomic features for affecting transmission, namely amino acid positions 3 and 18 of Vpu, which were significant before but not after correction for multiple testing. In summary, SeTesT provides a general framework for detecting selection based on genomic sequencing data of transmitted viruses. Our study shows that a higher number of transmitter–recipient pairs is required to improve sensitivity of detecting selection.
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Kariuki SM, Selhorst P, Abrahams MR, Rebe K, Williamson C, Dorfman JR. Neutralization sensitivity of genital tract HIV-1: shift in selective milieu shapes the population available to transmit. AIDS 2021; 35:1365-1373. [PMID: 33831907 DOI: 10.1097/qad.0000000000002912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Previous studies indicate that transmitted/founder HIV-1 isolates are sensitive to neutralization by the transmitting donor's antibodies. This is true in at least a subset of sexual transmissions. We investigated whether this selection for neutralization-sensitive variants begins in the genital tract of the donor, prior to transmission. DESIGN Laboratory study. METHODS HIV-1 viruses from semen and blood of two male donors living with HIV-1 were tested for neutralization sensitivity to contemporaneous autologous antibodies. RESULTS In one donor, semen-derived clones (n = 10, geometric mean ID50 = 176) were 1.75-fold [95% confidence interval (CI) 1.11-2.76, P = 0.018] more sensitive than blood-derived clones (n = 12, geometric mean ID50 = 111) to the individual's own contemporaneous neutralizing antibodies. Enhanced overall neutralization sensitivity of the semen-derived clones could not explain the difference because these semen-derived isolates showed a trend of being less sensitive to neutralization by a pool of heterologous clade-matched sera. This relative sensitivity of semen-derived clones was not observed in a second donor who did not exhibit obvious independent HIV-1 replication in the genital tract. A Bayesian analysis suggested that the set of semen sequences that we analysed originated from a blood sequence. CONCLUSION In some instances, selection for neutralization-sensitive variants during HIV-1 transmission begins in the genital tract of the donor and this may be driven by independent HIV-1 replication in this compartment. Thus, a shift in the selective milieu in the male genital tract allows outgrowth of neutralization-sensitive HIV-1 variants, shaping the population of isolates available for transmission to a new host.
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Affiliation(s)
- Samuel Mundia Kariuki
- Division of Immunology, Department of Pathology, University of Cape Town
- International Centre for Genetic Engineering and Biotechnology, Cape Town, Cape Town, South Africa
- Department of Biological Sciences, School of Science, University of Eldoret, Kenya
| | - Philippe Selhorst
- Division of Medical Virology, Department of Pathology, and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town
| | - Melissa-Rose Abrahams
- Division of Medical Virology, Department of Pathology, and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town
| | - Kevin Rebe
- ANOVA Health Institute, Cape Town
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town
| | - Carolyn Williamson
- Division of Medical Virology, Department of Pathology, and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town
| | - Jeffrey R Dorfman
- Division of Immunology, Department of Pathology, University of Cape Town
- Division of Medical Virology, Department of Pathology, University of Stellenbosch, Cape Town, South Africa
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Karch CP, Burkhard P, Matyas GR, Beck Z. The diversity of HIV-1 fights against vaccine efficacy: how self-assembling protein nanoparticle technology may fight back. Nanomedicine (Lond) 2021; 16:673-680. [PMID: 33715403 DOI: 10.2217/nnm-2020-0450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An efficacious HIV-1 vaccine has remained an elusive target for almost 40 years. The sheer diversity of the virus is one of the major roadblocks for vaccine development. HIV-1 frequently mutates and various strains predominate in different geographic regions, making the development of a globally applicable vaccine extremely difficult. Multiple approaches have been taken to overcome the issue of viral diversity, including sequence optimization, development of consensus and mosaic sequences and the use of different prime-boost approaches. To develop an efficacious vaccine, these approaches may need to be combined. One way to potentially synergize these approaches is to use a rationally designed protein nanoparticle that allows for the native-like presentation of antigens, such as the self-assembling protein nanoparticle.
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Affiliation(s)
- Christopher P Karch
- US Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD 20910, USA.,Henry M Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, MD 20817, USA
| | - Peter Burkhard
- Alpha-O Peptides, Lörracherstrasse 50, 4125 Riehen, Switzerland
| | - Gary R Matyas
- US Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD 20910, USA
| | - Zoltan Beck
- US Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD 20910, USA.,Henry M Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, MD 20817, USA.,Current address: VRD, Pfizer, 401 N Middletown Rd, Pearl River, NY 10965, USA
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7
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HIV-1 Envelope Glycosylation and the Signal Peptide. Vaccines (Basel) 2021; 9:vaccines9020176. [PMID: 33669676 PMCID: PMC7922494 DOI: 10.3390/vaccines9020176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/07/2021] [Accepted: 02/16/2021] [Indexed: 12/25/2022] Open
Abstract
The RV144 trial represents the only vaccine trial to demonstrate any protective effect against HIV-1 infection. While the reason(s) for this protection are still being evaluated, it serves as justification for widespread efforts aimed at developing new, more effective HIV-1 vaccines. Advances in our knowledge of HIV-1 immunogens and host antibody responses to these immunogens are crucial to informing vaccine design. While the envelope (Env) protein is the only viral protein present on the surface of virions, it exists in a complex trimeric conformation and is decorated with an array of variable N-linked glycans, making it an important but difficult target for vaccine design. Thus far, efforts to elicit a protective humoral immune response using structural mimics of native Env trimers have been unsuccessful. Notably, the aforementioned N-linked glycans serve as a component of many of the epitopes crucial for the induction of potentially protective broadly neutralizing antibodies (bnAbs). Thus, a greater understanding of Env structural determinants, most critically Env glycosylation, will no doubt be of importance in generating effective immunogens. Recent studies have identified the HIV-1 Env signal peptide (SP) as an important contributor to Env glycosylation. Further investigation into the mechanisms by which the SP directs glycosylation will be important, both in the context of understanding HIV-1 biology and in order to inform HIV-1 vaccine design.
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8
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Lumngwena EN, Shuping L, Bernitz N, Woodman Z. HIV-1 subtype C Envelope function becomes less sensitive to N-glycosylation deletion during disease progression. BMC Res Notes 2019; 12:340. [PMID: 31208438 PMCID: PMC6580609 DOI: 10.1186/s13104-019-4375-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/04/2019] [Accepted: 06/07/2019] [Indexed: 12/27/2022] Open
Abstract
Objective As part of a larger study to understand how Envelope N-glycosylation influences HIV-1 pathogenesis, we selected a participant infected with a single Subtype C variant and determined whether deletion of specific potential N-glycan sites (PNGs) impacted Envelope function longitudinally. Results We deleted five PNGs previously linked to HIV-1 transmission of two matched Envelope clones representing variants at 5 and 173 weeks post-infection. The transmitted founder (TF) had significantly better pseudovirus entry efficiency than the chronic infection (CI) variant. Deletion of all PNGs significantly reduced TF entry efficiency, binding to dendritic cell-specific intracellular adhesion molecule 3 grabbing non-integrin (DC-SIGN) receptor and trans-infection. However, mutational analysis did not affect the phenotype of the CI Envelope to the same extent. Notably, deletion of the PNGs at N241 and N448 had no effect on CI Envelope function, suggesting that some PNGs might only be important during acute infection. Therefore, vaccines that elicit antibodies against N-glycans important for TF Envelope function could drive the loss of PNGs during immune escape, abrogating viral replication. Conversely, changes in N-glycosylation might have no effect on some variants, reducing vaccine efficacy. This finding highlights the need for further investigation into the role of Envelope N-glycosylation in HIV-1 pathogenesis.
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Affiliation(s)
- Evelyn Ngwa Lumngwena
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Centre for the Study of Emerging and Re-Emerging Infections (CREMER), Institute for Medical Research and Medicinal Plants Studies (IMPM), Ministry of Scientific Research and Innovation (MINRESI), Yaoundé, Cameroon
| | - Liliwe Shuping
- Division of the National Laboratory Service, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Netanya Bernitz
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Zenda Woodman
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
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Comparisons of Human Immunodeficiency Virus Type 1 Envelope Variants in Blood and Genital Fluids near the Time of Male-to-Female Transmission. J Virol 2019; 93:JVI.01769-18. [PMID: 30996101 DOI: 10.1128/jvi.01769-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 03/15/2019] [Indexed: 11/20/2022] Open
Abstract
To better understand the transmission of human immunodeficiency virus type 1 (HIV-1), the genetic characteristics of blood and genital viruses from males were compared to those of the imputed founding virus population in their female partners. Initially serodiscordant heterosexual African couples with sequence-confirmed male-to-female HIV-1 transmission and blood and genital specimens collected near the time of transmission were studied. Single viral templates from blood plasma and genital tract RNA and DNA were sequenced across HIV-1 env gp160. Eight of 29 couples examined yielded viral sequences from both tissues. Analysis of these couples' sequences demonstrated, with one exception, that the women's founding viral populations arose from a single viral variant and were CCR5 tropic, even though CXCR4 variants were detected within four males. The median genetic distance of the imputed most recent common ancestor of the women's founder viruses showed that they were closer to the semen viruses than to the blood viruses of their transmitting male partner, but this finding was biased by detection of a greater number of viral clades in the blood. Using multiple assays, the blood and genital viruses were consistently found to be compartmentalized in only two of eight men. No distinct amino acid signatures in the men's viruses were found to link to the women's founders, nor did the women's env sequences have shorter variable loops or fewer N-linked glycosylation sites. The lack of selective factors, except for coreceptor tropism, is consistent with others' findings in male-to-female and high-risk transmissions. The infrequent compartmentalization between the transmitters' blood and semen viruses suggests that cell-free blood virus likely includes HIV-1 sequences representative of those of viruses in semen.IMPORTANCE Mucosal transmissions account for the majority of HIV-1 infections. Identification of the viral characteristics associated with transmission would facilitate vaccine design. This study of HIV strains from transmitting males and their seroconverting female partners found that the males' genital tract viruses were rarely distinct from the blood variants. The imputed founder viruses in women were genetically similar to both the blood and genital tract variants of their male partners, indicating a lack of evidence for genital tract-specific lineages. These findings suggest that targeting vaccine responses to variants found in blood are likely to also protect from genital tract variants.
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10
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Warren CJ, Meyerson NR, Dirasantha O, Feldman ER, Wilkerson GK, Sawyer SL. Selective use of primate CD4 receptors by HIV-1. PLoS Biol 2019; 17:e3000304. [PMID: 31181085 PMCID: PMC6586362 DOI: 10.1371/journal.pbio.3000304] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/20/2019] [Accepted: 05/15/2019] [Indexed: 12/15/2022] Open
Abstract
Individuals chronically infected with HIV-1 harbor complex viral populations within their bloodstreams. Recently, it has come to light that when these people infect others, the new infection is typically established by only one or a small number of virions from within this complex viral swarm. An important goal is to characterize the biological properties of HIV-1 virions that seed and exist early in new human infections because these are potentially the only viruses against which a prophylactic HIV-1 vaccine would need to elicit protection. This includes understanding how the Envelope (Env) protein of these virions interacts with the T-cell receptor CD4, which supports attachment and entry of HIV-1 into target cells. We examined early HIV-1 isolates for their ability to infect cells via the CD4 receptor of 15 different primate species. Primates were the original source of HIV-1 and now serve as valuable animal models for studying HIV-1. We find that most primary isolates of HIV-1 from the blood, including early isolates, are highly selective and enter cells through some primate CD4 receptor orthologs but not others. This phenotype is remarkably consistent, regardless of route of transmission, viral subtype, or time of isolation post infection. We show that the weak CD4 binding affinity of blood-derived HIV-1 isolates is what makes them sensitive to the small sequence differences in CD4 from one primate species to the next. To substantiate this, we engineered an early HIV-1 Env to have high, medium, or low binding affinity to CD4, and we show that it loses the ability to enter cells via the CD4 receptor of many primate species as the binding affinity gets weaker. Based on the phenotype of selective use of primate CD4, we find that weak CD4 binding appears to be a nearly universal property of HIV-1 circulating in the bloodstream. Therefore, weak binding to CD4 must be a selected and important property in the biology of HIV-1 in the body. We identify six primate species that encode CD4 receptors that fully support the entry of early HIV-1 isolates despite their low binding affinity for CD4. These findings will help inform long-standing efforts to model HIV-1 transmission and early disease in primates. The current animal model for HIV, the macaque, encodes a CD4 receptor that is non-permissive for HIV entry. This paper reveals that six primate species encode CD4 receptors compatible with HIV infection, potentially making them powerful tools for the study of HIV biology. Furthermore, weak CD4 binding is a nearly constant, and apparently selected, property of HIV circulating in the human bloodstream.
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Affiliation(s)
- Cody J. Warren
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Nicholas R. Meyerson
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Obaiah Dirasantha
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Emily R. Feldman
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Gregory K. Wilkerson
- Department of Comparative Medicine, Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, Texas, United States of America
| | - Sara L. Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
- * E-mail:
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11
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Seabright GE, Doores KJ, Burton DR, Crispin M. Protein and Glycan Mimicry in HIV Vaccine Design. J Mol Biol 2019; 431:2223-2247. [PMID: 31028779 PMCID: PMC6556556 DOI: 10.1016/j.jmb.2019.04.016] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/12/2019] [Accepted: 04/13/2019] [Indexed: 01/30/2023]
Abstract
Antigenic mimicry is a fundamental tenet of structure-based vaccinology. Vaccine strategies for the human immunodeficiency virus type 1 (HIV-1) focus on the mimicry of its envelope spike (Env) due to its exposed location on the viral membrane and role in mediating infection. However, the virus has evolved to minimize the immunogenicity of conserved epitopes on the envelope spike. This principle is starkly illustrated by the presence of an extensive array of host-derived glycans, which act to shield the underlying protein from antibody recognition. Despite these hurdles, a subset of HIV-infected individuals eventually develop broadly neutralizing antibodies that recognize these virally presented glycans. Effective HIV-1 immunogens are therefore likely to involve some degree of mimicry of both the protein and glycan components of Env. As such, considerable efforts have been made to characterize the structure of the envelope spike and its glycan shield. This review summarizes the recent progress made in this field, with an emphasis on our growing understanding of the factors shaping the glycan shield of Env derived from both virus and soluble immunogens. We argue that recombinant mimics of the envelope spike are currently capable of capturing many features of the native viral glycan shield. Finally, we explore strategies through which the immunogenicity of Env glycans may be enhanced in the development of future immunogens.
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Affiliation(s)
- Gemma E Seabright
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK; School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Katie J Doores
- Department of Infectious Diseases, King's College London, Guy's Hospital, London, SE1 9RT, UK
| | - Dennis R Burton
- Department of Immunology and Microbiology, the Scripps Centre for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), International AIDS Vaccine Initiative Neutralizing Antibody Centre, Scripps Research, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK; Department of Immunology and Microbiology, the Scripps Centre for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), International AIDS Vaccine Initiative Neutralizing Antibody Centre, Scripps Research, La Jolla, CA 92037, USA.
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12
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Variable infectivity and conserved engagement in cell-to-cell viral transfer by HIV-1 Env from Clade B transmitted founder clones. Virology 2018; 526:189-202. [PMID: 30415130 DOI: 10.1016/j.virol.2018.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 10/16/2018] [Accepted: 10/16/2018] [Indexed: 12/12/2022]
Abstract
HIV-1 transmission is usually initiated by a single viral strain called transmitted/ founder (T/F) virus. In in vitro models, HIV-1 can efficiently spread via cell-free and virological synapse (VS)-mediated cell-to-cell infection. Both modes of infection require the viral glycoprotein Envelope (Env). The efficiency with which T/F Envs initiate VS and mediate cell-to-cell infection has not been well characterized. Here we tested a panel of isogenic HIV-1 molecular clones that carry different Clade B T/F Envs. We found that despite variable infectivity among different Env clones in the two modes of infection, T/F Envs generally mediated efficient VS formation and subsequent cell-to-cell transfer. In contrast, in vitro infectivity of the T/F Env clones was more variable and strongly correlated with intrinsic fusogenicity of various Envs. We speculate that the conservation of cell-to-cell transfer by T/F Env is indicative of a biologically important function of Env.
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13
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Brese RL, Gonzalez-Perez MP, Koch M, O'Connell O, Luzuriaga K, Somasundaran M, Clapham PR, Dollar JJ, Nolan DJ, Rose R, Lamers SL. Ultradeep single-molecule real-time sequencing of HIV envelope reveals complete compartmentalization of highly macrophage-tropic R5 proviral variants in brain and CXCR4-using variants in immune and peripheral tissues. J Neurovirol 2018; 24:439-453. [PMID: 29687407 PMCID: PMC7281851 DOI: 10.1007/s13365-018-0633-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/28/2018] [Accepted: 03/19/2018] [Indexed: 01/07/2023]
Abstract
Despite combined antiretroviral therapy (cART), HIV+ patients still develop neurological disorders, which may be due to persistent HIV infection and selective evolution in brain tissues. Single-molecule real-time (SMRT) sequencing technology offers an improved opportunity to study the relationship among HIV isolates in the brain and lymphoid tissues because it is capable of generating thousands of long sequence reads in a single run. Here, we used SMRT sequencing to generate ~ 50,000 high-quality full-length HIV envelope sequences (> 2200 bp) from seven autopsy tissues from an HIV+/cART+ subject, including three brain and four non-brain sites. Sanger sequencing was used for comparison with SMRT data and to clone functional pseudoviruses for in vitro tropism assays. Phylogenetic analysis demonstrated that brain-derived HIV was compartmentalized from HIV outside the brain and that the variants from each of the three brain tissues grouped independently. Variants from all peripheral tissues were intermixed on the tree but independent of the brain clades. Due to the large number of sequences, a clustering analysis at three similarity thresholds (99, 99.5, and 99.9%) was also performed. All brain sequences clustered exclusive of any non-brain sequences at all thresholds; however, frontal lobe sequences clustered independently of occipital and parietal lobes. Translated sequences revealed potentially functional differences between brain and non-brain sequences in the location of putative N-linked glycosylation sites (N-sites), V1 length, V3 charge, and the number of V4 N-sites. All brain sequences were predicted to use the CCR5 co-receptor, while most non-brain sequences were predicted to use CXCR4 co-receptor. Tropism results were confirmed by in vitro infection assays. The study is the first to use a SMRT sequencing approach to study HIV compartmentalization in tissues and supports other reports of limited trafficking between brain and non-brain sequences during cART. Due to the long sequence length, we could observe changes along the entire envelope gene, likely caused by differential selective pressure in the brain that may contribute to neurological disease.
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Affiliation(s)
- Robin L Brese
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech 2, 373 Plantation Street, Worcester, MA, 01605, USA
| | - Maria Paz Gonzalez-Perez
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech 2, 373 Plantation Street, Worcester, MA, 01605, USA
| | - Matthew Koch
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech 2, 373 Plantation Street, Worcester, MA, 01605, USA
| | - Olivia O'Connell
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech 2, 373 Plantation Street, Worcester, MA, 01605, USA
| | - Katherine Luzuriaga
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech 2, 373 Plantation Street, Worcester, MA, 01605, USA
| | - Mohan Somasundaran
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech 2, 373 Plantation Street, Worcester, MA, 01605, USA
| | - Paul R Clapham
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech 2, 373 Plantation Street, Worcester, MA, 01605, USA
| | | | - David J Nolan
- Bioinfoexperts, LLC, 718 Bayou Ln, Thibodaux, LA, 70301, USA
| | - Rebecca Rose
- Bioinfoexperts, LLC, 718 Bayou Ln, Thibodaux, LA, 70301, USA.
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14
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Dapp MJ, Kober KM, Chen L, Westfall DH, Wong K, Zhao H, Hall BM, Deng W, Sibley T, Ghorai S, Kim K, Chen N, McHugh S, Au L, Cohen M, Anastos K, Mullins JI. Patterns and rates of viral evolution in HIV-1 subtype B infected females and males. PLoS One 2017; 12:e0182443. [PMID: 29045410 PMCID: PMC5646779 DOI: 10.1371/journal.pone.0182443] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/18/2017] [Indexed: 12/18/2022] Open
Abstract
Biological sex differences affect the course of HIV infection, with untreated women having lower viral loads compared to their male counterparts but, for a given viral load, women have a higher rate of progression to AIDS. However, the vast majority of data on viral evolution, a process that is clearly impacted by host immunity and could be impacted by sex differences, has been derived from men. We conducted an intensive analysis of HIV-1 gag and env-gp120 evolution taken over the first 6–11 years of infection from 8 Women’s Interagency HIV Study (WIHS) participants who had not received combination antiretroviral therapy (ART). This was compared to similar data previously collected from men, with both groups infected with HIV-1 subtype B. Early virus populations in men and women were generally homogenous with no differences in diversity between sexes. No differences in ensuing nucleotide substitution rates were found between the female and male cohorts studied herein. As previously reported for men, time to peak diversity in env-gp120 in women was positively associated with time to CD4+ cell count below 200 (P = 0.017), and the number of predicted N-linked glycosylation sites generally increased over time, followed by a plateau or decline, with the majority of changes localized to the V1-V2 region. These findings strongly suggest that the sex differences in HIV-1 disease progression attributed to immune system composition and sensitivities are not revealed by, nor do they impact, global patterns of viral evolution, the latter of which proceeds similarly in women and men.
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Affiliation(s)
- Michael J. Dapp
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Kord M. Kober
- Department of Physiological Nursing, University of California at San Francisco, California, United States of America
| | - Lennie Chen
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Dylan H. Westfall
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Kim Wong
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Hong Zhao
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Breana M. Hall
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Wenjie Deng
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Thomas Sibley
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Suvankar Ghorai
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Katie Kim
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Natalie Chen
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Sarah McHugh
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Lily Au
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Mardge Cohen
- The Core Center, Bureau of Health Services of Cook County, Chicago, Illinois, United States of America
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - James I. Mullins
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Global Health, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- * E-mail:
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15
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Choi JY, Pond SLK, Anderson CM, Richman DD, Smith DM. Molecular Features of the V1-V4 Coding Region of Sexually Transmitted Human Immunodeficiency Virus Type 1. J Infect Dis 2017; 215:1506-1513. [PMID: 28419276 DOI: 10.1093/infdis/jix184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/10/2017] [Indexed: 12/22/2022] Open
Abstract
Background Investigations into which human immunodeficiency virus type 1 (HIV-1) sequence features may be selected for transmission during sexual exposure have been hampered by the small number of characterized transmission pairs in individual studies. Methods To boost statistical power to detect differences in glycosylation, length, and electrical charge in the HIV-1 V1-V4 coding region, we reanalyzed all available 2485 env sequences derived from 114 subjects representing 58 transmission pairs from previous studies using mixed-effects linear regression and an approach to approximate the unobserved transmitted virus. Results The recipient partner had a shorter V1-V4 region and fewer potential N-linked glycosylation sites (PNGS) than sequences from the source partner. We also detected a trend toward more PNGS and lower isoelectric points in transmitted sequences with source partner and the evolutionary tendency to shorten V1-V4 sequences, reduce the number of PNGS, and lower isoelectric points in the recipient following transmission. Conclusions By using all available well-characterized env sequences from transmission pairs via sexual exposure, we were able to identify several important virologic factors that may be important in the development of biomedical preventive interventions.
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Affiliation(s)
- Jun Yong Choi
- Department of Internal Medicine and AIDS Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | | | | | - Douglas D Richman
- Departments of 2Medicine and.,Pathology, University of California, San Diego, La Jolla, and.,Veterans Affairs San Diego Healthcare System, California
| | - Davey M Smith
- Departments of 2Medicine and.,Veterans Affairs San Diego Healthcare System, California
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16
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Kariuki SM, Selhorst P, Ariën KK, Dorfman JR. The HIV-1 transmission bottleneck. Retrovirology 2017; 14:22. [PMID: 28335782 PMCID: PMC5364581 DOI: 10.1186/s12977-017-0343-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/05/2017] [Indexed: 02/07/2023] Open
Abstract
It is well established that most new systemic infections of HIV-1 can be traced back to one or a limited number of founder viruses. Usually, these founders are more closely related to minor HIV-1 populations in the blood of the presumed donor than to more abundant lineages. This has led to the widely accepted idea that transmission selects for viral characteristics that facilitate crossing the mucosal barrier of the recipient’s genital tract, although the specific selective forces or advantages are not completely defined. However, there are other steps along the way to becoming a founder virus at which selection may occur. These steps include the transition from the donor’s general circulation to the genital tract compartment, survival within the transmission fluid, and establishment of a nascent stable local infection in the recipient’s genital tract. Finally, there is the possibility that important narrowing events may also occur during establishment of systemic infection. This is suggested by the surprising observation that the number of founder viruses detected after transmission in intravenous drug users is also limited. Although some of these steps may be heavily selective, others may result mostly in a stochastic narrowing of the available founder pool. Collectively, they shape the initial infection in each recipient.
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Affiliation(s)
- Samuel Mundia Kariuki
- Division of Immunology, Department of Pathology, Falmouth 3.25, University of Cape Town, Anzio Rd, Observatory, Cape Town, 7925, South Africa.,International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa.,Department of Biological Sciences, University of Eldoret, Eldoret, Kenya
| | - Philippe Selhorst
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Kevin K Ariën
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Jeffrey R Dorfman
- Division of Immunology, Department of Pathology, Falmouth 3.25, University of Cape Town, Anzio Rd, Observatory, Cape Town, 7925, South Africa.
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17
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Nakamura KJ, Heath L, Sobrera ER, Wilkinson TA, Semrau K, Kankasa C, Tobin NH, Webb NE, Lee B, Thea DM, Kuhn L, Mullins JI, Aldrovandi GM. Breast milk and in utero transmission of HIV-1 select for envelope variants with unique molecular signatures. Retrovirology 2017; 14:6. [PMID: 28122636 PMCID: PMC5267468 DOI: 10.1186/s12977-017-0331-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 01/12/2017] [Indexed: 01/06/2023] Open
Abstract
Background Mother-to-child transmission of human immunodeficiency virus-type 1 (HIV-1) poses a serious health threat in developing countries, and adequate interventions are as yet unrealized. HIV-1 infection is frequently initiated by a single founder viral variant, but the factors that influence particular variant selection are poorly understood. Results Our analysis of 647 full-length HIV-1 subtype C and G viral envelope sequences from 22 mother–infant pairs reveals unique genotypic and phenotypic signatures that depend upon transmission route. Relative to maternal strains, intrauterine HIV transmission selects infant variants that have shorter, less-glycosylated V1 loops that are more resistant to soluble CD4 (sCD4) neutralization. Transmission through breastfeeding selects for variants with fewer potential glycosylation sites in gp41, are more sensitive to the broadly neutralizing antibodies PG9 and PG16, and that bind sCD4 with reduced cooperativity. Furthermore, experiments with Affinofile cells indicate that infant viruses, regardless of transmission route, require increased levels of surface CD4 receptor for productive infection. Conclusions These data provide the first evidence for transmission route-specific selection of HIV-1 variants, potentially informing therapeutic strategies and vaccine designs that can be tailored to specific modes of vertical HIV transmission. Electronic supplementary material The online version of this article (doi:10.1186/s12977-017-0331-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kyle J Nakamura
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, USA.,Systems Biology and Disease Program, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Laura Heath
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Edwin R Sobrera
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Thomas A Wilkinson
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Katherine Semrau
- Division of Global Health Equity, Brigham and Women's Hospital, Harvard Medical School, and Ariadne Labs, Boston, MA, USA
| | - Chipepo Kankasa
- University Teaching Hospital, University of Zambia, Lusaka, Zambia
| | - Nicole H Tobin
- Division of Pediatric Infectious Diseases, Department of Pediatrics, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, CA, USA
| | - Nicholas E Webb
- Division of Pediatric Infectious Diseases, Department of Pediatrics, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, CA, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Donald M Thea
- Division of Global Health Equity, Brigham and Women's Hospital, Harvard Medical School, and Ariadne Labs, Boston, MA, USA
| | - Louise Kuhn
- Department of Epidemiology, Columbia University, New York, NY, USA
| | - James I Mullins
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Grace M Aldrovandi
- Division of Pediatric Infectious Diseases, Department of Pediatrics, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, CA, USA.
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18
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Infection of rhesus macaques with a pool of simian immunodeficiency virus with the envelope genes from acute HIV-1 infections. AIDS Res Ther 2016; 13:41. [PMID: 27906032 PMCID: PMC5124249 DOI: 10.1186/s12981-016-0125-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/16/2016] [Indexed: 01/29/2023] Open
Abstract
Background New simian–human immunodeficiency chimeric viruses with an HIV-1 env (SHIVenv) are critical for studies on HIV pathogenesis, vaccine development, and microbicide testing. Macaques are typically exposed to single CCR5-using SHIVenv which in most instances does not reflect the conditions during acute/early HIV infection (AHI) in humans. Instead of individual and serial testing new SHIV constructs, a pool of SHIVenv_B derived from 16 acute HIV-1 infections were constructed using a novel yeast-based SHIV cloning approach and then used to infect macaques. Results Even though none of the 16 SHIVenvs contained the recently reported mutations in env genes that could significantly enhance their binding affinity to RhCD4, one SHIVenv (i.e. SHIVenv_B3-PRB926) established infection in macaques exposed to this pool. AHI SHIVenv_B viruses as well as their HIVenv_B counterparts were analyzed for viral protein content, function, and fitness to identify possible difference between SHIVenv_B3-PRB926 and the other 15 SHIVenvs in the pool. All of the constructs produced SHIV or HIV chimeric with wild type levels of capsid (p27 and p24) content, reverse transcriptase (RT) activity, and expressed envelope glycoproteins that could bind to cell receptors CD4/CCR5 and mediate virus entry. HIV-1env_B chimeric viruses were propagated in susceptible cell lines but the 16 SHIVenv_B variants showed only limited replication in macaque peripheral blood mononuclear cells (PBMCs) and 174×CEM.CCR5 cell line. AHI chimeric viruses including HIVenv_B3 showed only minor variations in cell entry efficiency and kinetics as well as replicative fitness in human PBMCs. Reduced number of N-link glycosylation sites and slightly greater CCR5 affinity/avidity was the only distinguishing feature of env_B3 versus other AHI env’s in the pool, a feature also observed in the HIV establishing new infections in humans. Conclusion Despite the inability to propagate in primary cells and cell lines, a pool of 16 SHIVenv viruses could establish infection but only one virus, SHIVenv_B3 was isolated in the macaque and then shown to repeatedly infected macaques. This SHIVenv_B3 virus did not show any distinct phenotypic property from the other 15 SHIVenv viruses but did have the fewest N-linked glycosylation sites. Electronic supplementary material The online version of this article (doi:10.1186/s12981-016-0125-8) contains supplementary material, which is available to authorized users.
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19
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Diversification in the HIV-1 Envelope Hyper-variable Domains V2, V4, and V5 and Higher Probability of Transmitted/Founder Envelope Glycosylation Favor the Development of Heterologous Neutralization Breadth. PLoS Pathog 2016; 12:e1005989. [PMID: 27851829 PMCID: PMC5112890 DOI: 10.1371/journal.ppat.1005989] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/11/2016] [Indexed: 11/19/2022] Open
Abstract
A recent study of plasma neutralization breadth in HIV-1 infected individuals at nine International AIDS Vaccine Initiative (IAVI) sites reported that viral load, HLA-A*03 genotype, and subtype C infection were strongly associated with the development of neutralization breadth. Here, we refine the findings of that study by analyzing the impact of the transmitted/founder (T/F) envelope (Env), early Env diversification, and autologous neutralization on the development of plasma neutralization breadth in 21 participants identified during recent infection at two of those sites: Kigali, Rwanda (n = 9) and Lusaka, Zambia (n = 12). Single-genome analysis of full-length T/F Env sequences revealed that all 21 individuals were infected with a highly homogeneous population of viral variants, which were categorized as subtype C (n = 12), A1 (n = 7), or recombinant AC (n = 2). An extensive amino acid sequence-based analysis of variable loop lengths and glycosylation patterns in the T/F Envs revealed that a lower ratio of NXS to NXT-encoded glycan motifs correlated with neutralization breadth. Further analysis comparing amino acid sequence changes, insertions/deletions, and glycan motif alterations between the T/F Env and autologous early Env variants revealed that extensive diversification focused in the V2, V4, and V5 regions of gp120, accompanied by contemporaneous viral escape, significantly favored the development of breadth. These results suggest that more efficient glycosylation of subtype A and C T/F Envs through fewer NXS-encoded glycan sites is more likely to elicit antibodies that can transition from autologous to heterologous neutralizing activity following exposure to gp120 diversification. This initiates an Env-antibody co-evolution cycle that increases neutralization breadth, and is further augmented over time by additional viral and host factors. These findings suggest that understanding how variation in the efficiency of site-specific glycosylation influences neutralizing antibody elicitation and targeting could advance the design of immunogens aimed at inducing antibodies that can transition from autologous to heterologous neutralizing activity.
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20
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Becerra JC, Bildstein LS, Gach JS. Recent Insights into the HIV/AIDS Pandemic. MICROBIAL CELL (GRAZ, AUSTRIA) 2016; 3:451-475. [PMID: 28357381 PMCID: PMC5354571 DOI: 10.15698/mic2016.09.529] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 04/27/2016] [Indexed: 12/21/2022]
Abstract
Etiology, transmission and protection: Transmission of HIV, the causative agent of AIDS, occurs predominantly through bodily fluids. Factors that significantly alter the risk of HIV transmission include male circumcision, condom use, high viral load, and the presence of other sexually transmitted diseases. Pathology/Symptomatology: HIV infects preferentially CD4+ T lymphocytes, and Monocytes. Because of their central role in regulating the immune response, depletion of CD4+ T cells renders the infected individual incapable of adequately responding to microorganisms otherwise inconsequential. Epidemiology, incidence and prevalence: New HIV infections affect predominantly young heterosexual women and homosexual men. While the mortality rates of AIDS related causes have decreased globally in recent years due to the use of highly active antiretroviral therapy (HAART) treatment, a vaccine remains an elusive goal. Treatment and curability: For those afflicted HIV infection remains a serious illness. Nonetheless, the use of advanced therapeutics have transformed a dire scenario into a chronic condition with near average life spans. When to apply those remedies appears to be as important as the remedies themselves. The high rate of HIV replication and the ability to generate variants are central to the viral survival strategy and major barriers to be overcome. Molecular mechanisms of infection: In this review, we assemble new details on the molecular events from the attachment of the virus, to the assembly and release of the viral progeny. Yet, much remains to be learned as understanding of the molecular mechanisms used in viral replication and the measures engaged in the evasion of immune surveillance will be important to develop effective interventions to address the global HIV pandemic.
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Affiliation(s)
- Juan C. Becerra
- Department of Medicine, Division of Infectious Diseases, University
of California, Irvine, Irvine, CA 92697, USA
| | | | - Johannes S. Gach
- Department of Medicine, Division of Infectious Diseases, University
of California, Irvine, Irvine, CA 92697, USA
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21
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Oberle CS, Joos B, Rusert P, Campbell NK, Beauparlant D, Kuster H, Weber J, Schenkel CD, Scherrer AU, Magnus C, Kouyos R, Rieder P, Niederöst B, Braun DL, Pavlovic J, Böni J, Yerly S, Klimkait T, Aubert V, Trkola A, Metzner KJ, Günthard HF. Tracing HIV-1 transmission: envelope traits of HIV-1 transmitter and recipient pairs. Retrovirology 2016; 13:62. [PMID: 27595568 PMCID: PMC5011806 DOI: 10.1186/s12977-016-0299-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 08/22/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Mucosal HIV-1 transmission predominantly results in a single transmitted/founder (T/F) virus establishing infection in the new host despite the generally high genetic diversity of the transmitter virus population. To what extent HIV-1 transmission is a stochastic process or driven by selective forces that allow T/F viruses best to overcome bottlenecks in transmission has not been conclusively resolved. Building on prior investigations that suggest HIV-1 envelope (Env) features to contribute in the selection process during transmission, we compared phenotypic virus characteristics of nine HIV-1 subtype B transmission pairs, six men who have sex with men and three male-to-female transmission pairs. RESULTS All recipients were identified early in acute infection and harbored based on extensive sequencing analysis a single T/F virus allowing a controlled analysis of virus properties in matched transmission pairs. Recipient and transmitter viruses from the closest time point to transmission showed no signs of selection for specific Env modifications such as variable loop length and glycosylation. Recipient viruses were resistant to circulating plasma antibodies of the transmitter and also showed no altered sensitivity to a large panel of entry inhibitors and neutralizing antibodies. The recipient virus did not consistently differ from the transmitter virus in terms of entry kinetics, cell-cell transmission and replicative capacity in primary cells. Our paired analysis revealed a higher sensitivity of several recipient virus isolates to interferon-α (IFNα) which suggests that resistance to IFNα cannot be a general driving force in T/F establishment. CONCLUSIONS With the exception of increased IFNα sensitivity, none of the phenotypic virus properties we investigated clearly distinguished T/F viruses from their matched transmitter viruses supporting the notion that at least in subtype B infection HIV-1 transmission is to a considerable extent stochastic.
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Affiliation(s)
- Corinna S Oberle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Beda Joos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Peter Rusert
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Nottania K Campbell
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - David Beauparlant
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Herbert Kuster
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jacqueline Weber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Corinne D Schenkel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra U Scherrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Carsten Magnus
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Philip Rieder
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Barbara Niederöst
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Dominique L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Jovan Pavlovic
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sabine Yerly
- Laboratory of Virology, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Thomas Klimkait
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Vincent Aubert
- Division of Immunology and Allergy, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland. .,Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
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Immunoinformatics Study of gp120 of Human Immunodeficiency Virus Type 1 Subtype CRF35_AD Isolated from Iranian Patients. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2016. [DOI: 10.5812/archcid.36270] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Ashokkumar M, Tripathy SP, Hanna LE. Variability in V1V2 and PNGs in Pediatric HIV-1 Viral Variants Transmitted Through Vertical Route. AIDS Res Hum Retroviruses 2016; 32:942-943. [PMID: 27309849 DOI: 10.1089/aid.2016.0093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Manickam Ashokkumar
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (ICMR), Chennai, India
| | - Srikanth P. Tripathy
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (ICMR), Chennai, India
| | - Luke Elizabeth Hanna
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (ICMR), Chennai, India
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Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus. PLoS Pathog 2016; 12:e1005619. [PMID: 27163788 PMCID: PMC4862634 DOI: 10.1371/journal.ppat.1005619] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 04/18/2016] [Indexed: 01/18/2023] Open
Abstract
Due to the stringent population bottleneck that occurs during sexual HIV-1 transmission, systemic infection is typically established by a limited number of founder viruses. Elucidation of the precise forces influencing the selection of founder viruses may reveal key vulnerabilities that could aid in the development of a vaccine or other clinical interventions. Here, we utilize deep sequencing data and apply a genetic distance-based method to investigate whether the mode of sexual transmission shapes the nascent founder viral genome. Analysis of 74 acute and early HIV-1 infected subjects revealed that 83% of men who have sex with men (MSM) exhibit a single founder virus, levels similar to those previously observed in heterosexual (HSX) transmission. In a metadata analysis of a total of 354 subjects, including HSX, MSM and injecting drug users (IDU), we also observed no significant differences in the frequency of single founder virus infections between HSX and MSM transmissions. However, comparison of HIV-1 envelope sequences revealed that HSX founder viruses exhibited a greater number of codon sites under positive selection, as well as stronger transmission indices possibly reflective of higher fitness variants. Moreover, specific genetic “signatures” within MSM and HSX founder viruses were identified, with single polymorphisms within gp41 enriched among HSX viruses while more complex patterns, including clustered polymorphisms surrounding the CD4 binding site, were enriched in MSM viruses. While our findings do not support an influence of the mode of sexual transmission on the number of founder viruses, they do demonstrate that there are marked differences in the selection bottleneck that can significantly shape their genetic composition. This study illustrates the complex dynamics of the transmission bottleneck and reveals that distinct genetic bottleneck processes exist dependent upon the mode of HIV-1 transmission. While the global spread of HIV-1 has been fueled by sexual transmission the genetic determinants underlying the transmission bottleneck remains poorly understood. Here we characterized founder virus population diversity from next generation sequencing data in a cohort of 74 acute and early HIV-1 infected individuals. We observe that the risk of multi-variant infection in men-who-have-sex-with-men (MSM) is not greater than that observed for heterosexuals (HSX), contrary to reports of higher rates of multiple founder virus infections in higher-risk MSM transmissions. These findings were further supported through a metadata analysis of 354 acute and early HIV-1 subjects. We did, however, observe differences between HSM and MSM founder viruses, including a higher selection barrier in HSX transmission with founder viruses being more cohort consensus-like that may be reflective of increased replicative fitness. We also identified a number of residues within Envelope that behave in a risk-dependent manner and could be key for HIV-1 transmission. These novel insights improve our understanding of the HIV-1 transmission bottleneck and underscore the differential selective pressures that founder viruses within the two major transmission risk groups are subjected to.
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Abstract
Although the use of phylogenetic trees in epidemiological investigations has become commonplace, their epidemiological interpretation has not been systematically evaluated. Here, we use an HIV-1 within-host coalescent model to probabilistically evaluate transmission histories of two epidemiologically linked hosts. Previous critique of phylogenetic reconstruction has claimed that direction of transmission is difficult to infer, and that the existence of unsampled intermediary links or common sources can never be excluded. The phylogenetic relationship between the HIV populations of epidemiologically linked hosts can be classified into six types of trees, based on cladistic relationships and whether the reconstruction is consistent with the true transmission history or not. We show that the direction of transmission and whether unsampled intermediary links or common sources existed make very different predictions about expected phylogenetic relationships: (i) Direction of transmission can often be established when paraphyly exists, (ii) intermediary links can be excluded when multiple lineages were transmitted, and (iii) when the sampled individuals' HIV populations both are monophyletic a common source was likely the origin. Inconsistent results, suggesting the wrong transmission direction, were generally rare. In addition, the expected tree topology also depends on the number of transmitted lineages, the sample size, the time of the sample relative to transmission, and how fast the diversity increases after infection. Typically, 20 or more sequences per subject give robust results. We confirm our theoretical evaluations with analyses of real transmission histories and discuss how our findings should aid in interpreting phylogenetic results.
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Abstract
Rigorous testing of new HIV-prevention strategies is a time-consuming and expensive undertaking. Thus, making well informed decisions on which candidate-prevention approaches are most likely to provide the most benefit is critical to appropriately prioritizing clinical testing. In the case of biological interventions, the decision to test a given prevention approach in human trials rests largely on evidence of protection in preclinical studies. The ability of preclinical studies to predict efficacy in humans may depend on how well the model recapitulates key biological features of HIV transmission relevant to the question at hand. Here, we review our current understanding of the biology of HIV transmission based on data from animal models, cell culture, and viral sequence analysis from human infection. We summarize studies of the bottleneck in viral transmission; the characteristics of transmitted viruses; the establishment of infection; and the contribution of cell-free and cell-associated virus. We seek to highlight the implications of HIV-transmission biology for development of prevention interventions, and to discuss the limitations of existing preclinical models.
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Deymier MJ, Ende Z, Fenton-May AE, Dilernia DA, Kilembe W, Allen SA, Borrow P, Hunter E. Heterosexual Transmission of Subtype C HIV-1 Selects Consensus-Like Variants without Increased Replicative Capacity or Interferon-α Resistance. PLoS Pathog 2015; 11:e1005154. [PMID: 26378795 PMCID: PMC4574710 DOI: 10.1371/journal.ppat.1005154] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 08/17/2015] [Indexed: 12/21/2022] Open
Abstract
Heterosexual transmission of HIV-1 is characterized by a genetic bottleneck that selects a single viral variant, the transmitted/founder (TF), during most transmission events. To assess viral characteristics influencing HIV-1 transmission, we sequenced 167 near full-length viral genomes and generated 40 infectious molecular clones (IMC) including TF variants and multiple non-transmitted (NT) HIV-1 subtype C variants from six linked heterosexual transmission pairs near the time of transmission. Consensus-like genomes sensitive to donor antibodies were selected for during transmission in these six transmission pairs. However, TF variants did not demonstrate increased viral fitness in terms of particle infectivity or viral replicative capacity in activated peripheral blood mononuclear cells (PBMC) and monocyte-derived dendritic cells (MDDC). In addition, resistance of the TF variant to the antiviral effects of interferon-α (IFN-α) was not significantly different from that of non-transmitted variants from the same transmission pair. Thus neither in vitro viral replicative capacity nor IFN-α resistance discriminated the transmission potential of viruses in the quasispecies of these chronically infected individuals. However, our findings support the hypothesis that within-host evolution of HIV-1 in response to adaptive immune responses reduces viral transmission potential. Despite the available HIV-1 diversity present in a chronically infected individual, single viral variants are transmitted in 80–90% of heterosexual transmission events. These breakthrough viruses may have unique properties that confer a higher capacity to transmit. Determining these properties could help inform the rational design of vaccines and enhance our understanding of viral transmission. We isolated the transmitted variant and a set of related non-transmitted variants from the transmitting partner near the estimated date of transmission from six epidemiologically linked transmission pairs to investigate viral correlates of transmission. The simplest explanation that transmitted variants are inherently more infectious or faster replicators in vitro did not hold true. In addition, transmitted variants did not replicate more efficiently than their non-transmitted counterparts in dendritic cells or in the presence of interferon-alpha in vitro, suggesting that they are not uniquely adapted to these components of the innate immune system. More ancestral genomes that were relatively sensitive to antibody neutralization tended to transmit, supporting previous reports that mutational escape away from the adaptive immune response likely reduces the ability to transmit. Our investigation into the traits of transmitted HIV-1 variants adds to the understanding of viral determinants of transmission.
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Affiliation(s)
- Martin J. Deymier
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Zachary Ende
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | | | - Dario A. Dilernia
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | | | - Susan A. Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Persephone Borrow
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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Abstract
HIV-1 infection typically results from the transmission of a single viral variant, the transmitted/founder (T/F) virus. Studies of these HIV-1 variants provide critical information about the transmission bottlenecks and the selective pressures acting on the virus in the transmission fluid and in the recipient tissues. These studies reveal that T/F virus phenotypes are shaped by stochastic and selective forces that restrict transmission and may be targets for prevention strategies. In this Review, we highlight how studies of T/F viruses contribute to a better understanding of the biology of HIV-1 transmission and discuss how these findings affect HIV-1 prevention strategies.
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Han J, Liu S, Guo W, Bao Z, Wang X, Li L, Liu Y, Zhuang D, Li H, Jia L, Gui T, Sui H, Li T, Li J. Development of an HIV-1 Subtype Panel in China: Isolation and Characterization of 30 HIV-1 Primary Strains Circulating in China. PLoS One 2015; 10:e0127696. [PMID: 26018591 PMCID: PMC4446268 DOI: 10.1371/journal.pone.0127696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/17/2015] [Indexed: 11/18/2022] Open
Abstract
Background The complex epidemic and significant diversity of HIV-1 strains in China pose serious challenges for surveillance and diagnostic assays, vaccine development and clinical management. There is a lack of HIV-1 isolates in current canonical HIV-1 subtype panels that can represent HIV-1 diversity in China; an HIV-1 subtype panel for China is urgently needed. Methods Blood samples were collected from HIV-1 infected patients participating in the drug-resistance surveillance program in China. The samples were isolated, cultured and stored as neat culture supernatant. The HIV-1 isolates were fully characterized. The panel was used to compare 2 viral load assays and 2 p24 assays as the examples of how this panel could be used. Results An HIV-1 subtype panel for China composed of 30 HIV-1 primary strains of four subtypes (B [including Thai-B], CRF01_AE, CRF07_BC and G) was established. The samples were isolated and cultured to a high-titer (106-109 copies/ml)/high-volume (40ml). The HIV-1 isolates were fully characterized by the final viral load, p24 concentration, gag-pol and envC2V3 sequencing, co-receptor prediction, determination of the four amino acids at the tip of the env V3-loop, glycosylation sites in the V3 loop and the drug-resistance mutations. The comparison of two p24 assays and two viral load assays on the isolates illustrated how this panel may be used for the evaluation of diagnostic assay performance. The Pearson value between p24 assays were 0.938. The viral load results showed excellent concordance and agreement for samples of Thai-B, but lower correlations for samples of CRF01_AE. Conclusion The current panel of 30 HIV-1 isolates served as a basis for the development of a comprehensive panel of fully characterized viral isolates, which could reflect the current dynamic and complex HIV-1 epidemic in China. This panel will be available to support HIV-1 research, assay evaluation, vaccine and drug development.
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Affiliation(s)
- Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Siyang Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Wei Guo
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Daomin Zhuang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Tao Gui
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Hongshuai Sui
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
- * E-mail:
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Musich T, O'Connell O, Gonzalez-Perez MP, Derdeyn CA, Peters PJ, Clapham PR. HIV-1 non-macrophage-tropic R5 envelope glycoproteins are not more tropic for entry into primary CD4+ T-cells than envelopes highly adapted for macrophages. Retrovirology 2015; 12:25. [PMID: 25809903 PMCID: PMC4373511 DOI: 10.1186/s12977-015-0141-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/15/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Non-mac-tropic HIV-1 R5 viruses are predominantly transmitted and persist in immune tissue even in AIDS patients who carry highly mac-tropic variants in the brain. Non-mac-tropic R5 envelopes (Envs) require high CD4 levels for infection contrasting with highly mac-tropic Envs, which interact more efficiently with CD4 and mediate infection of macrophages that express low CD4. Non-mac-tropic R5 Envs predominantly target T-cells during transmission and in immune tissue where they must outcompete mac-tropic variants. Here, we investigated whether Env+ pseudoviruses bearing transmitted/founder (T/F), early and late disease non-mac-tropic R5 envelopes mediated more efficient infection of CD4+ T-cells compared to those with highly mac-tropic Envs. RESULTS Highly mac-tropic Envs mediated highest infectivity for primary T-cells, Jurkat/CCR5 cells, myeloid dendritic cells, macrophages, and HeLa TZM-bl cells, although this was most dramatic on macrophages. Infection of primary T-cells mediated by all Envs was low. However, infection of T-cells was greatly enhanced by increasing virus attachment with DEAE dextran and spinoculation, which enhanced the three Env+ virus groups to similar extents. Dendritic cell capture of viruses and trans-infection also greatly enhanced infection of primary T-cells. In trans-infection assays, non-mac-tropic R5 Envs were preferentially enhanced and those from late disease mediated levels of T-cell infection that were equivalent to those mediated by mac-tropic Envs. CONCLUSIONS Our results demonstrate that T/F, early or late disease non-mac-tropic R5 Envs do not preferentially mediate infection of primary CD4+ T-cells compared to highly mac-tropic Envs from brain tissue. We conclude that non-macrophage-tropism of HIV-1 R5 Envs in vitro is determined predominantly by a reduced capacity to target myeloid cells via low CD4 rather than a specific adaptation for T-cells entry that precludes macrophage infection.
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Junqueira DM, Medeiros RMD, Leite TCNF, Guimarães ML, Gräf T, Pinto AR, Almeida SEDM. Detection of the B"-GWGR variant in the southernmost region of Brazil: unveiling the complexity of the human immunodeficiency virus-1 subtype B epidemic. Mem Inst Oswaldo Cruz 2014; 108:735-40. [PMID: 24037196 PMCID: PMC3970682 DOI: 10.1590/0074-0276108062013010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 06/26/2013] [Indexed: 12/17/2022] Open
Abstract
Typical human immunodeficiency virus-1 subtype B (HIV-1B) sequences present a GPGR signature at the tip of the variable region 3 (V3) loop; however, unusual motifs harbouring a GWGR signature have also been isolated. Although epidemiological studies have detected this variant in approximately 17-50% of the total infections in Brazil, the prevalence of B"-GWGR in the southernmost region of Brazil is not yet clear. This study aimed to investigate the C2-V3 molecular diversity of the HIV-1B epidemic in southernmost Brazil. HIV-1 seropositive patients were ana-lysed at two distinct time points in the state of Rio Grande do Sul (RS98 and RS08) and at one time point in the state of Santa Catarina (SC08). Phylogenetic analysis classified 46 individuals in the RS98 group as HIV-1B and their molecular signatures were as follows: 26% B"-GWGR, 54% B-GPGR and 20% other motifs. In the RS08 group, HIV-1B was present in 32 samples: 22% B"-GWGR, 59% B-GPGR and 19% other motifs. In the SC08 group, 32 HIV-1B samples were found: 28% B"-GWGR, 59% B-GPGR and 13% other motifs. No association could be established between the HIV-1B V3 signatures and exposure categories in the HIV-1B epidemic in RS. However, B-GPGR seemed to be related to heterosexual individuals in the SC08 group. Our results suggest that the established B"-GWGR epidemics in both cities have similar patterns, which is likely due to their geographical proximity and cultural relationship.
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Affiliation(s)
- Dennis Maletich Junqueira
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde,, Porto AlegreRS, Brasil
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Defining differential genetic signatures in CXCR4- and the CCR5-utilizing HIV-1 co-linear sequences. PLoS One 2014; 9:e107389. [PMID: 25265194 PMCID: PMC4180074 DOI: 10.1371/journal.pone.0107389] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/07/2014] [Indexed: 11/29/2022] Open
Abstract
The adaptation of human immunodeficiency virus type-1 (HIV-1) to an array of physiologic niches is advantaged by the plasticity of the viral genome, encoded proteins, and promoter. CXCR4-utilizing (X4) viruses preferentially, but not universally, infect CD4+ T cells, generating high levels of virus within activated HIV-1-infected T cells that can be detected in regional lymph nodes and peripheral blood. By comparison, the CCR5-utilizing (R5) viruses have a greater preference for cells of the monocyte-macrophage lineage; however, while R5 viruses also display a propensity to enter and replicate in T cells, they infect a smaller percentage of CD4+ T cells in comparison to X4 viruses. Additionally, R5 viruses have been associated with viral transmission and CNS disease and are also more prevalent during HIV-1 disease. Specific adaptive changes associated with X4 and R5 viruses were identified in co-linear viral sequences beyond the Env-V3. The in silico position-specific scoring matrix (PSSM) algorithm was used to define distinct groups of X4 and R5 sequences based solely on sequences in Env-V3. Bioinformatic tools were used to identify genetic signatures involving specific protein domains or long terminal repeat (LTR) transcription factor sites within co-linear viral protein R (Vpr), trans-activator of transcription (Tat), or LTR sequences that were preferentially associated with X4 or R5 Env-V3 sequences. A number of differential amino acid and nucleotide changes were identified across the co-linear Vpr, Tat, and LTR sequences, suggesting the presence of specific genetic signatures that preferentially associate with X4 or R5 viruses. Investigation of the genetic relatedness between X4 and R5 viruses utilizing phylogenetic analyses of complete sequences could not be used to definitively and uniquely identify groups of R5 or X4 sequences; in contrast, differences in the genetic diversities between X4 and R5 were readily identified within these co-linear sequences in HIV-1-infected patients.
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Impact of clade, geography, and age of the epidemic on HIV-1 neutralization by antibodies. J Virol 2014; 88:12623-43. [PMID: 25142591 DOI: 10.1128/jvi.01705-14] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
UNLABELLED Neutralizing antibodies (nAbs) are a high priority for vaccines that aim to prevent the acquisition of HIV-1 infection. Vaccine effectiveness will depend on the extent to which induced antibodies neutralize the global diversity of circulating HIV-1 variants. Using large panels of genetically and geographically diverse HIV-1 Env-pseudotyped viruses and chronic infection plasma samples, we unambiguously show that cross-clade nAb responses are commonly induced in response to infection by any virus clade. Nonetheless, neutralization was significantly greater when the plasma clade matched the clade of the virus being tested. This within-clade advantage was diminished in older, more-diverse epidemics in southern Africa, the United States, and Europe compared to more recent epidemics in Asia. It was most pronounced for circulating recombinant form (CRF) 07_BC, which is common in China and is the least-divergent lineage studied; this was followed by the slightly more diverse Asian CRF01_AE. We found no evidence that transmitted/founder viruses are generally more susceptible to neutralization and are therefore easier targets for vaccination than chronic viruses. Features of the gp120 V1V2 loop, in particular, length, net charge, and number of N-linked glycans, were associated with Env susceptibility and plasma neutralization potency in a manner consistent with neutralization escape being a force that drives viral diversification and plasma neutralization breadth. The overall susceptibility of Envs and potencies of plasma samples were highly predictive of the neutralization outcome of any single virus-plasma combination. These findings highlight important considerations for the design and testing of candidate HIV-1 vaccines that aim to elicit effective nAbs. IMPORTANCE An effective HIV-1 vaccine will need to overcome the extraordinary variability of the virus, which is most pronounced in the envelope glycoproteins (Env), which are the sole targets for neutralizing antibodies (nAbs). Distinct genetic lineages, or clades, of HIV-1 occur in different locales that may require special consideration when designing and testing vaccines candidates. We show that nAb responses to HIV-1 infection are generally active across clades but are most potent within clades. Because effective vaccine-induced nAbs are likely to share these properties, optimal coverage of a particular clade or combination of clades may require clade-matched immunogens. Optimal within-clade coverage might be easier to achieve in regions such as China and Thailand, where the epidemic is more recent and the virus less diverse than in southern Africa, the United States, and Europe. Finally, features of the first and second hypervariable regions of gp120 (V1V2) may be critical for optimal vaccine design.
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Abstract
UNLABELLED Recall T cell responses to HIV-1 antigens are used as a surrogate for endogenous cellular immune responses generated during infection. Current methods of identifying antigen-specific T cell reactivity in HIV-1 infection use bulk peripheral blood mononuclear cells (PBMC) yet ignore professional antigen-presenting cells (APC) that could reveal otherwise hidden responses. In the present study, peptides representing autologous variants of major histocompatibility complex (MHC) class I-restricted epitopes from HIV-1 Gag and Env were used as antigens in gamma interferon (IFN-γ) enzyme-linked immunosorbent spot (ELISpot) and polyfunctional cytokine assays. Here we show that dendritic cells (DC) enhanced T cell reactivity at all stages of disease progression but specifically restored T cell reactivity after combination antiretroviral therapy (cART) to early infection levels. Type 1 cytokine secretion was also enhanced by DC and was most apparent late post-cART. We additionally show that DC reveal polyfunctional T cell responses after many years of treatment, when potential immunotherapies would be implemented. These data underscore the potential efficacy of DC immunotherapy that aims to awaken a dormant, autologous, HIV-1-specific CD8+ T cell response. IMPORTANCE Assessment of endogenous HIV-1-specific T cell responses is critical for generating immunotherapies for subjects on cART. Current assays ignore the ability of dendritic cells to reveal these responses and may therefore underestimate the breadth and magnitude of T cell reactivity. As DC do not prime new responses in these assays, it can be assumed that the observed responses are not detected without appropriate stimulation. This is important because dogma states that HIV-1 mutates to evade host recognition and that CD8+ cytotoxic T lymphocyte (CTL) failure is due to the inability of T cells to recognize the autologous virus. The results presented here indicate that responses to autologous virus are generated during infection but may need additional stimulation to be effective. Detecting the breadth and magnitude of HIV-1-specific T cell reactivity generated in vivo is of the utmost importance for generating effective DC immunotherapies.
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Cenci A, D'Avenio G, Tavoschi L, Chiappi M, Becattini S, Narino MDP, Picconi O, Bernasconi D, Fanales-Belasio E, Vardas E, Sukati H, Lo Presti A, Ciccozzi M, Monini P, Ensoli B, Grigioni M, Buttò S. Molecular characterization of HIV-1 subtype C gp-120 regions potentially involved in virus adaptive mechanisms. PLoS One 2014; 9:e95183. [PMID: 24788065 PMCID: PMC4005737 DOI: 10.1371/journal.pone.0095183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/24/2014] [Indexed: 11/17/2022] Open
Abstract
The role of variable regions of HIV-1 gp120 in immune escape of HIV has been investigated. However, there is scant information on how conserved gp120 regions contribute to virus escaping. Here we have studied how molecular sequence characteristics of conserved C3, C4 and V3 regions of clade C HIV-1 gp120 that are involved in HIV entry and are target of the immune response, are modulated during the disease course. We found an increase of “shifting” putative N-glycosylation sites (PNGSs) in the α2 helix (in C3) and in C4 and an increase of sites under positive selection pressure in the α2 helix during the chronic stage of disease. These sites are close to CD4 and to co-receptor binding sites. We also found a negative correlation between electric charges of C3 and V4 during the late stage of disease counteracted by a positive correlation of electric charges of α2 helix and V5 during the same stage. These data allow us to hypothesize possible mechanisms of virus escape involving constant and variable regions of gp120. In particular, new mutations, including new PNGSs occurring near the CD4 and CCR5 binding sites could potentially affect receptor binding affinity and shield the virus from the immune response.
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Affiliation(s)
| | - Giuseppe D'Avenio
- Istituto Superiore di Sanità, Department of Technology and Health, Rome, Italy
| | - Lara Tavoschi
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | - Michele Chiappi
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | | | | | - Orietta Picconi
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | | | | | - Eftyhia Vardas
- Stellenbosch University, Division of Medical Virology, Stellenbosch, South Africa; Lancet Laboratories, Johannesburg, South Africa
| | - Hosea Sukati
- National Center Public Health Laboratory, Manzini, Swaziland
| | - Alessandra Lo Presti
- Istituto Superiore di Sanità, Department of Infectious, Parasitic and Immunomediated Diseases, Rome, Italy
| | - Massimo Ciccozzi
- Istituto Superiore di Sanità, Department of Infectious, Parasitic and Immunomediated Diseases, Rome, Italy; University of Biomedical Campus, Rome, Italy
| | - Paolo Monini
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | - Barbara Ensoli
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | - Mauro Grigioni
- Istituto Superiore di Sanità, Department of Technology and Health, Rome, Italy
| | - Stefano Buttò
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
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Ho YS, Saksena NK. Glycosylation in HIV-1 envelope glycoprotein and its biological implications. Future Virol 2013. [DOI: 10.2217/fvl.13.64] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Glycosylation of HIV-1 envelope proteins (Env gp120/gp41) plays a vital role in viral evasion from the host immune response, which occurs through the masking of key neutralization epitopes and the presentation of the Env glycosylation as ‘self’ to the host immune system. Env glycosylation is generally conserved, yet its continual evolution plays an important role in modulating viral infectivity and Env immunogenicity. Thus, it is believed that Env glycosylation, which is a vital part of the HIV-1 architecture, also controls intra- and inter-clade genetic variations. Discerning intra- and inter-clade glycosylation variations could therefore yield important information for understanding the molecular and biological differences between HIV clades and may assist in effectively designing Env-based immunogens and in clearly understanding HIV vaccines. This review provides an in-depth perspective of various aspects of Env glycosylation in the context of HIV-1 pathogenesis.
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Affiliation(s)
- Yung Shwen Ho
- Computational Bioscience Research Center, Biological & Environmental Sciences & Engineering Division, King Abdullah University of Science & Technology, Thuwal 23955, Kingdom of Saudi Arabia
| | - Nitin K Saksena
- Retroviral Genetics Division, Center for Virus Research, Westmead Millennium Instiute & Westmead Hospital, University of Sydney, Westmead, Sydney, NSW 2145, Australia
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Ping LH, Joseph SB, Anderson JA, Abrahams MR, Salazar-Gonzalez JF, Kincer LP, Treurnicht FK, Arney L, Ojeda S, Zhang M, Keys J, Potter EL, Chu H, Moore P, Salazar MG, Iyer S, Jabara C, Kirchherr J, Mapanje C, Ngandu N, Seoighe C, Hoffman I, Gao F, Tang Y, Labranche C, Lee B, Saville A, Vermeulen M, Fiscus S, Morris L, Karim SA, Haynes BF, Shaw GM, Korber BT, Hahn BH, Cohen MS, Montefiori D, Williamson C, Swanstrom R. Comparison of viral Env proteins from acute and chronic infections with subtype C human immunodeficiency virus type 1 identifies differences in glycosylation and CCR5 utilization and suggests a new strategy for immunogen design. J Virol 2013; 87:7218-33. [PMID: 23616655 PMCID: PMC3700278 DOI: 10.1128/jvi.03577-12] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 04/15/2013] [Indexed: 12/18/2022] Open
Abstract
Understanding human immunodeficiency virus type 1 (HIV-1) transmission is central to developing effective prevention strategies, including a vaccine. We compared phenotypic and genetic variation in HIV-1 env genes from subjects in acute/early infection and subjects with chronic infections in the context of subtype C heterosexual transmission. We found that the transmitted viruses all used CCR5 and required high levels of CD4 to infect target cells, suggesting selection for replication in T cells and not macrophages after transmission. In addition, the transmitted viruses were more likely to use a maraviroc-sensitive conformation of CCR5, perhaps identifying a feature of the target T cell. We confirmed an earlier observation that the transmitted viruses were, on average, modestly underglycosylated relative to the viruses from chronically infected subjects. This difference was most pronounced in comparing the viruses in acutely infected men to those in chronically infected women. These features of the transmitted virus point to selective pressures during the transmission event. We did not observe a consistent difference either in heterologous neutralization sensitivity or in sensitivity to soluble CD4 between the two groups, suggesting similar conformations between viruses from acute and chronic infection. However, the presence or absence of glycosylation sites had differential effects on neutralization sensitivity for different antibodies. We suggest that the occasional absence of glycosylation sites encoded in the conserved regions of env, further reduced in transmitted viruses, could expose specific surface structures on the protein as antibody targets.
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Affiliation(s)
- Li-Hua Ping
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah B. Joseph
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeffrey A. Anderson
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Melissa-Rose Abrahams
- Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town and National Health Laboratory Services, Cape Town, South Africa
| | | | - Laura P. Kincer
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Florette K. Treurnicht
- Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town and National Health Laboratory Services, Cape Town, South Africa
| | - Leslie Arney
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Suany Ojeda
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ming Zhang
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, Georgia, USA
| | - Jessica Keys
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - E. Lake Potter
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Haitao Chu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Penny Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Maria G. Salazar
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Shilpa Iyer
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Cassandra Jabara
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jennifer Kirchherr
- Duke Human Vaccine Institute, Department of Medicine, Duke University, Durham, North Carolina, USA
| | | | - Nobubelo Ngandu
- Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town and National Health Laboratory Services, Cape Town, South Africa
| | | | - Irving Hoffman
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Feng Gao
- Duke Human Vaccine Institute, Department of Medicine, Duke University, Durham, North Carolina, USA
| | - Yuyang Tang
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Celia Labranche
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Benhur Lee
- Department of Microbiology, Immunology and Molecular Genetics, University of California at Los Angeles, Los Angeles, California, USA
| | - Andrew Saville
- South African National Blood Service, Weltevreden Park, South Africa
| | - Marion Vermeulen
- South African National Blood Service, Weltevreden Park, South Africa
| | - Susan Fiscus
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Salim Abdool Karim
- Center for AIDS Program Research in South Africa, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Department of Medicine, Duke University, Durham, North Carolina, USA
| | - George M. Shaw
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Bette T. Korber
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
- Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Myron S. Cohen
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David Montefiori
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Carolyn Williamson
- Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town and National Health Laboratory Services, Cape Town, South Africa
| | - Ronald Swanstrom
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Abstract
Defining the virus-host interactions responsible for HIV-1 transmission, including the phenotypic requirements of viruses capable of establishing de novo infections, could be important for AIDS vaccine development. Previous analyses have failed to identify phenotypic properties other than chemokine receptor 5 (CCR5) and CD4+ T-cell tropism that are preferentially associated with viral transmission. However, most of these studies were limited to examining envelope (Env) function in the context of pseudoviruses. Here, we generated infectious molecular clones of transmitted founder (TF; n = 27) and chronic control (CC; n = 14) viruses of subtypes B (n = 18) and C (n = 23) and compared their phenotypic properties in assays specifically designed to probe the earliest stages of HIV-1 infection. We found that TF virions were 1.7-fold more infectious (P = 0.049) and contained 1.9-fold more Env per particle (P = 0.048) compared with CC viruses. TF viruses were also captured by monocyte-derived dendritic cells 1.7-fold more efficiently (P = 0.035) and more readily transferred to CD4+ T cells (P = 0.025). In primary CD4+ T cells, TF and CC viruses replicated with comparable kinetics; however, when propagated in the presence of IFN-α, TF viruses replicated to higher titers than CC viruses. This difference was significant for subtype B (P = 0.000013) but not subtype C (P = 0.53) viruses, possibly reflecting demographic differences of the respective patient cohorts. Together, these data indicate that TF viruses are enriched for higher Env content, enhanced cell-free infectivity, improved dendritic cell interaction, and relative IFN-α resistance. These viral properties, which likely act in concert, should be considered in the development and testing of AIDS vaccines.
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Antigenicity and immunogenicity of transmitted/founder, consensus, and chronic envelope glycoproteins of human immunodeficiency virus type 1. J Virol 2013; 87:4185-201. [PMID: 23365441 DOI: 10.1128/jvi.02297-12] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) vaccine development requires selection of appropriate envelope (Env) immunogens. Twenty HIV-1 Env glycoproteins were examined for their ability to bind human anti-HIV-1 monoclonal antibodies (MAbs) and then used as immunogens in guinea pigs to identify promising immunogens. These included five Envs derived from chronically infected individuals, each representing one of five common clades and eight consensus Envs based on these five clades, as well as the consensus of the entire HIV-1 M group, and seven transmitted/founder (T/F) Envs from clades B and C. Sera from immunized guinea pigs were tested for neutralizing activity using 36 HIV-1 Env-pseudotyped viruses. All Envs bound to CD4 binding site, membrane-proximal, and V1/V2 MAbs with similar apparent affinities, although the T/F Envs bound with higher affinity to the MAb 17b, a CCR5 coreceptor binding site antibody. However, the various Envs differed in their ability to induce neutralizing antibodies. Consensus Envs elicited the most potent responses, but neutralized only a subset of viruses, including mostly easy-to-neutralize tier 1 and some more-difficult-to-neutralize tier 2 viruses. T/F Envs elicited fewer potent neutralizing antibodies but exhibited greater breadth than chronic or consensus Envs. Finally, chronic Envs elicited the lowest level and most limited breadth of neutralizing antibodies overall. Thus, each group of Env immunogens elicited a different antibody response profile. The complementary benefits of consensus and T/F Env immunogens raise the possibility that vaccines utilizing a combination of consensus and T/F Envs may be able to induce neutralizing responses with greater breadth and potency than single Env immunogens.
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Gutiérrez S, Michalakis Y, Blanc S. Virus population bottlenecks during within-host progression and host-to-host transmission. Curr Opin Virol 2012; 2:546-55. [DOI: 10.1016/j.coviro.2012.08.001] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 08/01/2012] [Indexed: 12/11/2022]
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Mota TM, Murray JM, Center RJ, Purcell DFJ, McCaw JM. Application of a case-control study design to investigate genotypic signatures of HIV-1 transmission. Retrovirology 2012; 9:54. [PMID: 22731404 PMCID: PMC3419081 DOI: 10.1186/1742-4690-9-54] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 06/25/2012] [Indexed: 12/03/2022] Open
Abstract
Background The characterization of HIV-1 transmission strains may inform the design of an effective vaccine. Shorter variable loops with fewer predicted glycosites have been suggested as signatures enriched in envelope sequences derived during acute HIV-1 infection. Specifically, a transmission-linked lack of glycosites within the V1 and V2 loops of gp120 provides greater access to an α4β7 binding motif, which promotes the establishment of infection. Also, a histidine at position 12 in the leader sequence of Env has been described as a transmission signature that is selected against during chronic infection. The purpose of this study is to measure the association of the presence of an α4β7 binding motif, the number of N-linked glycosites, the length of the variable loops, and the prevalence of histidine at position 12 with HIV-1 transmission. A case–control study design was used to measure the prevalence of these variables between subtype B and C transmission sequences and frequency-matched randomly-selected sequences derived from chronically infected controls. Results Subtype B transmission strains had shorter V3 regions than chronic strains (p = 0.031); subtype C transmission strains had shorter V1 loops than chronic strains (p = 0.047); subtype B transmission strains had more V3 loop glycosites (p = 0.024) than chronic strains. Further investigation showed that these statistically significant results were unlikely to be biologically meaningful. Also, there was no difference observed in the prevalence of a histidine at position 12 among transmission strains and controls of either subtype. Conclusions Although a genetic bottleneck is observed after HIV-1 transmission, our results indicate that summary characteristics of Env hypothesised to be important in transmission are not divergent between transmission and chronic strains of either subtype. The success of a transmission strain to initiate infection may be a random event from the divergent pool of donor viral sequences. The characteristics explored through this study are important, but may not function as genotypic signatures of transmission as previously described.
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Affiliation(s)
- Talia M Mota
- Department of Microbiology and Immunology, University of Melbourne, Parkville, VIC 3010, Australia
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42
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Kanwal S, Mahmood T. Evolutionary pattern of Asian HIV-1 subtype B from 1990 to 2007: in silico analysis based on envelop protein. ScientificWorldJournal 2012; 2012:978917. [PMID: 22645495 PMCID: PMC3354753 DOI: 10.1100/2012/978917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 12/07/2011] [Indexed: 11/26/2022] Open
Abstract
HIV-1 envelop gene is a major target for vaccine development. Envelop protein and its V3 loop is shown to be important determinant of HIV-1 pathogenecity. Herein, the evolutionary pattern of most prevalent HIV-1 subtype B in Asia is determined by analyzing envelop protein and V3 domain based on the 40 randomly selected sequences of HIV-1 from database (Los Alamos), divided into four groups since 1990–2007. Construction of envelop protein phylogeny by using MEGA 5 exhibit the active mutation pattern, increase in potential N-glycosylation sites which were predicted by using online software SignalP-NN. An online available tool Drawgram was used for multiple sequence alignment (MSA) of HIV-1 subtype B envelop region and V3 loop while the alignment was rechecked by using CLUSTAL W and further was analyzed for GPGX motif and conserved region in V3 loop. Variation at fourth position of the GPGX motif and 60% conservation was found in V3 loop. Hence, this diversifying pattern of envelop protein in the Asia formulates the HIV-1 strains more pathogenic during the period of 17 years. These findings might help in understanding significant structural and functional constrains of the mutant viral strains and ultimately in vaccine development.
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Affiliation(s)
- Sobia Kanwal
- Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
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43
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Sato S, Ouellet M, St-Pierre C, Tremblay MJ. Glycans, galectins, and HIV-1 infection. Ann N Y Acad Sci 2012; 1253:133-48. [DOI: 10.1111/j.1749-6632.2012.06475.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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44
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Gijsbers EF, Schuitemaker H, Kootstra NA. HIV-1 transmission and viral adaptation to the host. Future Virol 2012. [DOI: 10.2217/fvl.11.134] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
HIV-1 transmission predominantly occurs via mucosal transmission and blood–blood contact. In most newly infected individuals, outgrowth of a single virus variant has been described. This indicates that HIV-1 transmission is a very inefficient process and is restricted by an extensive transmission bottleneck. The transmission rate is directly correlated to the viral load in the donor and the susceptibility of the recipient, which is influenced by factors such as the integrity of mucosal barriers, target cell availability and genetic host factors. After establishment of infection in the new host, the viral population remains very homogenous until the host immune response drives evolution of the viral quasispecies. This review describes our current knowledge on HIV-1 transmission and recent insights in viral adaption to its host.
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Affiliation(s)
- Esther F Gijsbers
- Department of Experimental Immunology, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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45
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Role of donor genital tract HIV-1 diversity in the transmission bottleneck. Proc Natl Acad Sci U S A 2011; 108:E1156-63. [PMID: 22065783 DOI: 10.1073/pnas.1103764108] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The predominant mode of HIV-1 infection is heterosexual transmission, where a genetic bottleneck is imposed on the virus quasispecies. To probe whether limited genetic diversity in the genital tract (GT) of the transmitting partner drives this bottleneck, viral envelope sequences from the blood and genital fluids of eight transmission pairs from Rwanda and Zambia were analyzed. The chronically infected transmitting partner's virus population was heterogeneous with distinct genital subpopulations, and the virus populations within the GT of two of four women sampled longitudinally exhibited evidence of stability over time intervals on the order of weeks to months. Surprisingly, the transmitted founder variant was not derived from the predominant GT subpopulations. Rather, in each case, the transmitting variant was phylogenetically distinct from the sampled locally replicating population. Although the exact distribution of the virus population present in the GT at the time of transmission cannot be unambiguously defined in these human studies, it is unlikely, based on these data, that the transmission bottleneck is driven in every case by limited viral diversity in the donor GT or that HIV transmission is solely a stochastic event.
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46
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Gnanakaran S, Bhattacharya T, Daniels M, Keele BF, Hraber PT, Lapedes AS, Shen T, Gaschen B, Krishnamoorthy M, Li H, Decker JM, Salazar-Gonzalez JF, Wang S, Jiang C, Gao F, Swanstrom R, Anderson JA, Ping LH, Cohen MS, Markowitz M, Goepfert PA, Saag MS, Eron JJ, Hicks CB, Blattner WA, Tomaras GD, Asmal M, Letvin NL, Gilbert PB, DeCamp AC, Magaret CA, Schief WR, Ban YEA, Zhang M, Soderberg KA, Sodroski JG, Haynes BF, Shaw GM, Hahn BH, Korber B. Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. PLoS Pathog 2011; 7:e1002209. [PMID: 21980282 PMCID: PMC3182927 DOI: 10.1371/journal.ppat.1002209] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2010] [Accepted: 06/26/2011] [Indexed: 12/15/2022] Open
Abstract
Here we have identified HIV-1 B clade Envelope (Env) amino acid signatures from early in infection that may be favored at transmission, as well as patterns of recurrent mutation in chronic infection that may reflect common pathways of immune evasion. To accomplish this, we compared thousands of sequences derived by single genome amplification from several hundred individuals that were sampled either early in infection or were chronically infected. Samples were divided at the outset into hypothesis-forming and validation sets, and we used phylogenetically corrected statistical strategies to identify signatures, systematically scanning all of Env. Signatures included single amino acids, glycosylation motifs, and multi-site patterns based on functional or structural groupings of amino acids. We identified signatures near the CCR5 co-receptor-binding region, near the CD4 binding site, and in the signal peptide and cytoplasmic domain, which may influence Env expression and processing. Two signatures patterns associated with transmission were particularly interesting. The first was the most statistically robust signature, located in position 12 in the signal peptide. The second was the loss of an N-linked glycosylation site at positions 413-415; the presence of this site has been recently found to be associated with escape from potent and broad neutralizing antibodies, consistent with enabling a common pathway for immune escape during chronic infection. Its recurrent loss in early infection suggests it may impact fitness at the time of transmission or during early viral expansion. The signature patterns we identified implicate Env expression levels in selection at viral transmission or in early expansion, and suggest that immune evasion patterns that recur in many individuals during chronic infection when antibodies are present can be selected against when the infection is being established prior to the adaptive immune response.
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Affiliation(s)
- S. Gnanakaran
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tanmoy Bhattacharya
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Marcus Daniels
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Brandon F. Keele
- SAIC-Frederick, National Cancer Institute, Frederick, Maryland, United States of America
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Peter T. Hraber
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Alan S. Lapedes
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tongye Shen
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Molecular Biophysics and Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Brian Gaschen
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Mohan Krishnamoorthy
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Hui Li
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Julie M. Decker
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jesus F. Salazar-Gonzalez
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Shuyi Wang
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Chunlai Jiang
- National Engineering Laboratory of AIDS Vaccine School of Life Science, Jilin University, Changchun, China
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Feng Gao
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Ronald Swanstrom
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffrey A. Anderson
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Li-Hua Ping
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Myron S. Cohen
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Martin Markowitz
- Aaron Diamond AIDS Research Center, an affiliate of the Rockefeller University, New York, New York, United States of America
| | - Paul A. Goepfert
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Michael S. Saag
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Joseph J. Eron
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Charles B. Hicks
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - William A. Blattner
- Institute of Human Virology, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
| | - Georgia D. Tomaras
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Mohammed Asmal
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Norman L. Letvin
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Division of Viral Pathogenesis, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter B. Gilbert
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United State of America
| | - Allan C. DeCamp
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United State of America
| | - Craig A. Magaret
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United State of America
| | - William R. Schief
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Yih-En Andrew Ban
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Arzeda Corporation, Seattle, Washington, United States of America
| | - Ming Zhang
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, Georgia, United States of America
| | - Kelly A. Soderberg
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Joseph G. Sodroski
- Dana-Farber Cancer Institute, Department of Cancer Immunology and AIDS, Boston, Massachusetts, United States of America
| | - Barton F. Haynes
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - George M. Shaw
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Bette Korber
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- * E-mail:
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English S, Katzourakis A, Bonsall D, Flanagan P, Duda A, Fidler S, Weber J, McClure M, Phillips R, Frater J. Phylogenetic analysis consistent with a clinical history of sexual transmission of HIV-1 from a single donor reveals transmission of highly distinct variants. Retrovirology 2011; 8:54. [PMID: 21736738 PMCID: PMC3161944 DOI: 10.1186/1742-4690-8-54] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Accepted: 07/07/2011] [Indexed: 01/27/2023] Open
Abstract
Background To combat the pandemic of human immunodeficiency virus 1 (HIV-1), a successful vaccine will need to cope with the variability of transmissible viruses. Human hosts infected with HIV-1 potentially harbour many viral variants but very little is known about viruses that are likely to be transmitted, or even if there are viral characteristics that predict enhanced transmission in vivo. We show for the first time that genetic divergence consistent with a single transmission event in vivo can represent several years of pre-transmission evolution. Results We describe a highly unusual case consistent with a single donor transmitting highly related but distinct HIV-1 variants to two individuals on the same evening. We confirm that the clustering of viral genetic sequences, present within each recipient, is consistent with the history of a single donor across the viral env, gag and pol genes by maximum likelihood and Bayesian Markov Chain Monte Carlo based phylogenetic analyses. Based on an uncorrelated, lognormal relaxed clock of env gene evolution calibrated with other datasets, the time since the most recent common ancestor is estimated as 2.86 years prior to transmission (95% confidence interval 1.28 to 4.54 years). Conclusion Our results show that an effective design for a preventative vaccine will need to anticipate extensive HIV-1 diversity within an individual donor as well as diversity at the population level.
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Affiliation(s)
- Suzanne English
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, Oxford University, South Parks Road, Oxford, OX1 3SY, UK
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Collins-Fairclough AM, Charurat M, Nadai Y, Pando M, Avila MM, Blattner WA, Carr JK. Significantly longer envelope V2 loops are characteristic of heterosexually transmitted subtype B HIV-1 in Trinidad. PLoS One 2011; 6:e19995. [PMID: 21698149 PMCID: PMC3117786 DOI: 10.1371/journal.pone.0019995] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 04/08/2011] [Indexed: 11/19/2022] Open
Abstract
Background In Trinidad and the wider Caribbean, subtype B Human Immunodeficiency Virus-type 1 (HIV-1B) overwhelmingly accounts for HIV infection among heterosexuals; this contrasts with the association of HIV-1B with homosexual transmission and injecting drug use globally. The HIV envelope contains genetic determinants of cell tropism and evasion from immune attack. In this study we investigate the genetic properties of the env V1-C4 of HIV-1B soon after transmission to Trinidadian heterosexuals. This will reveal distinctive genetic features of the strains that cause the HIV-1B epidemic in Trinidad and generate insights to better understand their properties. Methodology/Principal Findings Quasispecies sampling was performed on the env V1-C4 of HIV-1B strains soon after transmission to heterosexual Trinidadians in a cohort of seroconverters. Phylogenetic relationships were determined for these quasispecies and the length and number of asparagine (N) linked glycosylation sites (NLGS) in their variable loops compared to that for HIV-1B globally. Signature amino acids within the constant domains of the env V1-C4 were identified for heterosexually transmitted HIV-1B from Trinidad relative to HIV-1B globally. HIV-1B obtained from Trinidadian heterosexuals soon after seroconversion had significantly longer V2 loops with one more glycosylation site, shorter V3 loops and no significant difference in V1 or V4 when compared to HIV-1B obtained soon after seroconversion from infected individuals in the rest of the world. HIV-1B soon after seroconversion and during chronic infection of Trinidadians was not significantly different, suggesting that distinctly long V2 loops are characteristic of HIV-1B in Trinidad. A threonine deletion at position 319 (T319-) along with the substitutions R315K and S440R were found to be distinctly associated with HIV-1B from Trinidad compared to HIV-1B globally. Conclusions This finding of distinctive genetic features that are characteristic of HIV-1B strains from Trinidad is consistent with the Trinidad epidemic being established by a founder strain or closely related founder strains of HIV-1B.
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Characterization of glycosylation profiles of HIV-1 transmitted/founder envelopes by mass spectrometry. J Virol 2011; 85:8270-84. [PMID: 21653661 DOI: 10.1128/jvi.05053-11] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The analysis of HIV-1 envelope carbohydrates is critical to understanding their roles in HIV-1 transmission as well as in binding of envelope to HIV-1 antibodies. However, direct analysis of protein glycosylation by glycopeptide-based mass mapping approaches involves structural simplification of proteins with the use of a protease followed by an isolation and/or enrichment step before mass analysis. The successful completion of glycosylation analysis is still a major analytical challenge due to the complexity of samples, wide dynamic range of glycopeptide concentrations, and glycosylation heterogeneity. Here, we use a novel experimental workflow that includes an up-front complete or partial enzymatic deglycosylation step before trypsin digestion to characterize the glycosylation patterns and maximize the glycosylation coverage of two recombinant HIV-1 transmitted/founder envelope oligomers derived from clade B and C viruses isolated from acute infection and expressed in 293T cells. Our results show that both transmitted/founder Envs had similar degrees of glycosylation site occupancy as well as similar glycan profiles. Compared to 293T-derived recombinant Envs from viruses isolated from chronic HIV-1, transmitted/founder Envs displayed marked differences in their glycosylation site occupancies and in their amounts of complex glycans. Our analysis reveals that the glycosylation patterns of transmitted/founder Envs from two different clades (B and C) are more similar to each other than they are to the glycosylation patterns of chronic HIV-1 Envs derived from their own clades.
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50
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Rusert P, Krarup A, Magnus C, Brandenberg OF, Weber J, Ehlert AK, Regoes RR, Günthard HF, Trkola A. Interaction of the gp120 V1V2 loop with a neighboring gp120 unit shields the HIV envelope trimer against cross-neutralizing antibodies. ACTA ACUST UNITED AC 2011; 208:1419-33. [PMID: 21646396 PMCID: PMC3135368 DOI: 10.1084/jem.20110196] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Structure–function analysis and mathematical modeling reveal insight into the mechanisms through which conserved HIV-1 gp120 epitopes are masked in the HIV-1 envelope trimer. The HIV-1 envelope trimer adopts a quaternary conformation that effectively shields neutralization-sensitive domains and thus represents a major obstacle for natural and vaccine-elicited antibody responses. By using a structure–function analysis based on a specifically devised mathematical model, we demonstrate in this study that protection from neutralization is enforced by intersubunit contact between the variable loops 1 and 2 (V1V2) and domains of neighboring gp120 subunits in the trimer encompassing the V3 loop. Our data are consistent with an interaction of the V1V2 and V3 loop at the spike apex as proposed by cryoelectron tomography experiments. By defining the orientation of the V1V2 loop within the trimer toward the neighboring gp120 subunit’s V3 loop, our data close an important gap in the understanding of the architecture of the trimeric spike. Knowledge on how the V1V2 barrier functions in the context of the trimer to mask conserved epitopes on gp120 may aid future vaccine design.
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Affiliation(s)
- Peter Rusert
- Institute of Medical Virology, University Hospital Zurich; University of Zurich, 8006 Zurich, Switzerland
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