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Tamalet C, Devaux C, Dubourg G, Colson P. Resistance to human immunodeficiency virus infection: a rare but neglected state. Ann N Y Acad Sci 2020; 1485:22-42. [PMID: 33009659 DOI: 10.1111/nyas.14452] [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: 04/15/2020] [Revised: 06/25/2020] [Accepted: 07/07/2020] [Indexed: 11/29/2022]
Abstract
The natural history of human immunodeficiency virus (HIV) infection is well understood. In most individuals sexually exposed to HIV, the risk of becoming infected depends on the viral load and on sexual practices and gender. However, a low percentage of individuals who practice frequent unprotected sexual intercourse with HIV-infected partners remain uninfected. Although the systematic study of these individuals has made it possible to identify HIV resistance factors including protective genetic patterns, such epidemiological situations remain paradoxical and not fully understood. In vitro experiments have demonstrated that peripheral blood mononuclear cells (PBMCs) from HIV-free, unexposed blood donors are not equally susceptible to HIV infection; in addition, PBMCs from highly exposed seronegative individuals are generally resistant to infection by primary HIV clinical isolates. We review the literature on permissiveness of PBMCs from healthy blood donors and uninfected hyperexposed individuals to sustained infection and replication of HIV-1 in vitro. In addition, we focus on recent evidence indicating that the gut microbiota may either contribute to natural resistance to or delay replication of HIV infected individuals.
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Affiliation(s)
- Catherine Tamalet
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Gregory Dubourg
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
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2
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Gomes STM, da Silva Graça Amoras E, Gomes ÉR, Queiroz MAF, Júnior ECS, de Vasconcelos Massafra JM, da Silva Lemos P, Júnior JLV, Ishak R, Vallinoto ACR. Immune escape mutations in HIV-1 controllers in the Brazilian Amazon region. BMC Infect Dis 2020; 20:546. [PMID: 32711474 PMCID: PMC7382849 DOI: 10.1186/s12879-020-05268-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/16/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus (HIV-1) infection is characterized by high viral replication and a decrease in CD4+ T cells (CD4+TC), resulting in AIDS, which can lead to death. In elite controllers and viremia controllers, viral replication is naturally controlled, with maintenance of CD4+TC levels without the use of antiretroviral therapy (ART). METHODS The aim of the present study was to describe virological and immunological risk factors among HIV-1-infected individuals according to characteristics of progression to AIDS. The sample included 30 treatment-naive patients classified into three groups based on infection duration (> 6 years), CD4+TC count and viral load: (i) 2 elite controllers (ECs), (ii) 7 viremia controllers (VCs) and (iii) 21 nonviremia controllers (NVCs). Nested PCR was employed to amplify the virus genome, which was later sequenced using the Ion PGM platform for subtyping and analysis of immune escape mutations. RESULTS Viral samples were classified as HIV-1 subtypes B and F. Greater selection pressure on mutations was observed in the group of viremia controllers, with a higher frequency of immunological escape mutations in the genes investigated, including two new mutations in gag. The viral sequences of viremia controllers and nonviremia controllers did not differ significantly regarding the presence of immune escape mutations. CONCLUSION The results suggest that progression to AIDS is not dependent on a single variable but rather on a set of characteristics and pressures exerted by virus biology and interactions with immunogenetic host factors.
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Affiliation(s)
- Samara Tatielle Monteiro Gomes
- Laboratory of Virology, Biological Science Institute, Federal University of Pará (ICB/UFPA), Ananindeua, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Biological Science Institute, Federal University of Pará, Ananindeua, Brazil
| | | | - Érica Ribeiro Gomes
- Laboratory of Virology, Biological Science Institute, Federal University of Pará (ICB/UFPA), Ananindeua, Brazil
| | - Maria Alice Freitas Queiroz
- Laboratory of Virology, Biological Science Institute, Federal University of Pará (ICB/UFPA), Ananindeua, Brazil
| | - Edivaldo Costa Sousa Júnior
- Health Surveillance Department, Ministry of Health (IEC-SVS/MS), Evandro Chagas Institute, Ananindeua, Brazil
| | | | - Poliana da Silva Lemos
- Health Surveillance Department, Ministry of Health (IEC-SVS/MS), Evandro Chagas Institute, Ananindeua, Brazil
| | - João Lídio Vianez Júnior
- Health Surveillance Department, Ministry of Health (IEC-SVS/MS), Evandro Chagas Institute, Ananindeua, Brazil
| | - Ricardo Ishak
- Laboratory of Virology, Biological Science Institute, Federal University of Pará (ICB/UFPA), Ananindeua, Brazil
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Palmer J, Poon AFY. Phylogenetic measures of indel rate variation among the HIV-1 group M subtypes. Virus Evol 2019; 5:vez022. [PMID: 31341641 PMCID: PMC6642732 DOI: 10.1093/ve/vez022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The transmission fitness and pathogenesis of HIV-1 is disproportionately influenced by evolution in the five variable regions (V1–V5) of the surface envelope glycoprotein (gp120). Insertions and deletions (indels) are a significant source of evolutionary change in these regions. However, the rate and composition of indels has not yet been quantified through a large-scale comparative analysis of HIV-1 sequences. Here, we develop and report results from a phylogenetic method to estimate indel rates for the gp120 variable regions across five major subtypes and two circulating recombinant forms (CRFs) of HIV-1 group M. We processed over 26,000 published HIV-1 gp120 sequences, from which we extracted 6,605 sequences for phylogenetic analysis. We reconstructed time-scaled phylogenies by maximum likelihood and fit a binomial-Poisson model to the observed distribution of indels between closely related pairs of sequences in each tree (cherries). By focusing on cherries in each tree, we obtained phylogenetically independent indel reconstructions, and the shorter time scales in cherries reduced the bias due to purifying selection. Rate estimates ranged from 3.0×10−5 to 1.5×10−3 indels/nt/year and varied significantly among variable regions and subtypes. Indel rates were significantly lower in V3 relative to V1, and were also lower in HIV-1 subtype B relative to the 01_AE reference. We also found that V1, V2, and V4 tended to accumulate significantly longer indels. Furthermore, we observed that the nucleotide composition of indels was distinct from the flanking sequence, with higher frequencies of G and lower frequencies of T. Indels affected N-linked glycosylation sites more often in V1 and V2 than expected by chance, consistent with positive selection on glycosylation patterns within these regions. These results represent the first comprehensive measures of indel rates in HIV-1 gp120 across multiple subtypes and CRFs, and identifies novel and unexpected patterns for further research in the molecular evolution of HIV-1.
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Affiliation(s)
- John Palmer
- Department of Pathology & Laboratory Medicine, Western University, London, Canada
| | - Art F Y Poon
- Department of Pathology & Laboratory Medicine, Western University, London, Canada.,Department of Applied Mathematics, Western University, London, Canada.,Department of Microbiology & Immunology, Western University, London, Canada
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Abstract
Viruses are widely used as vectors for heterologous gene expression in cultured cells or natural hosts, and therefore a large number of viruses with exogenous sequences inserted into their genomes have been engineered. Many of these engineered viruses are viable and express heterologous proteins at high levels, but the inserted sequences often prove to be unstable over time and are rapidly lost, limiting heterologous protein expression. Although virologists are aware that inserted sequences can be unstable, processes leading to insert instability are rarely considered from an evolutionary perspective. Here, we review experimental work on the stability of inserted sequences over a broad range of viruses, and we present some theoretical considerations concerning insert stability. Different virus genome organizations strongly impact insert stability, and factors such as the position of insertion can have a strong effect. In addition, we argue that insert stability not only depends on the characteristics of a particular genome, but that it will also depend on the host environment and the demography of a virus population. The interplay between all factors affecting stability is complex, which makes it challenging to develop a general model to predict the stability of genomic insertions. We highlight key questions and future directions, finding that insert stability is a surprisingly complex problem and that there is need for mechanism-based, predictive models. Combining theoretical models with experimental tests for stability under varying conditions can lead to improved engineering of viral modified genomes, which is a valuable tool for understanding genome evolution as well as for biotechnological applications, such as gene therapy.
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Affiliation(s)
- Anouk Willemsen
- Laboratory MIVEGEC (UMR CNRS IRD University of Montpellier), Centre National de la Recherche Scientifique (CNRS), 911 Avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France
| | - Mark P Zwart
- Netherlands Institute of Ecology (NIOO-KNAW), Postbus 50, 6700 AB, Wageningen, The Netherlands
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López-Galíndez C. HIV long-term non-progressors elite controllers: an interplay between host, immune and viral factors. Future Virol 2019. [DOI: 10.2217/fvl-2018-0207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
There is a rare group of HIV-1-infected individuals who show permanent control of clinical progression for over 10 years, maintain CD4+ cells >500 μl and have undetectable viral loads; they are designated long-term non-progressors elite controllers (LTNPs ECs). Multiple studies have demonstrated the necessary contribution of at least two of host, immune and viral factors to the LTNP phenotype. This group of individuals is not homogenous because of the different involvement of these factors. We will review the role of each of these and their combinations to the LTNP EC phenotype. LTNP EC individuals offer an opportunity for the investigation into the mechanisms for the spontaneous control of HIV infection.
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Affiliation(s)
- Cecilio López-Galíndez
- Unidad de Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid 28220, Spain
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Scutari R, Faieta M, D'Arrigo R, Fabeni L, Mussini C, Cossarizza A, Casoli C, Perno CF, Svicher V, Alteri C, Aquaro S. The degree of HIV-1 amino acid variability is strictly related to different disease progression rates. Virus Genes 2018; 54:493-501. [PMID: 29777446 DOI: 10.1007/s11262-018-1571-2] [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: 03/07/2018] [Accepted: 05/10/2018] [Indexed: 11/28/2022]
Abstract
The aim of this study is to evaluate the amino acid variability of HIV-1 Gp41, C2-V3, and Nef in a group of patients characterized by different disease progression rates. HIV-1 sequences were collected from 19 Long term non progressor patients (LTNPs), 9 slow progressors (SPs), and 11 rapid progressors (RPs). Phylogenetic trees were estimated by MEGA 6. Differences in amino acid variability among sequences belonging to the 3 groups have been evaluated by amino acid divergence, Shannon entropy analysis, and the number of amino acid mutations (defined as amino acid variations compared with HxB2). The involvement of amino acid mutations on epitope rich regions was also investigated. The population was mainly composed of males (74.3%) and HIV-1 subtype B strains (B: 92.32%, CRF_12BF, A1, C: 2.56% each). Viral load (log10 copies/mL) and CD4+T cell count (cells/mm3) were 3.9 (3.5-4.2) and 618 (504-857) in LTNPs, 3.3 (2.8-4.7) and 463 (333-627) in SPs, and 4.6 (4.3-5.3) and 201 (110-254) in RPs. Gp41 and C2-V3 amino acid divergence was lower in LTNP and SP strains compared to RPs (median value: 0.085 and 0.091 vs. 0.114, p = 0.005 and 0.042) and a trend of lower variability was observed for Nef (p = 0.198). A lower entropy value was observed at 10, 3, and 7 positions of Gp41, C2-V3, and Nef belonging to LTNPs and at 7, 3, and 1 positions of Gp41, C2-V3, and Nef belonging to SPs compared with RPs (p < 0.05). Focusing on epitope rich regions, again a higher degree of conservation was observed in Gp41 and C2-V3 sequences belonging to LTNPs and SPs compared to those belonging to RPs. This study shows that the extent of amino acid variability correlates with a different HIV-1 progression rate. This variability also involves CTL epitope rich regions, thus suggesting its involvement in the immune escape process modulation.
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Affiliation(s)
- Rossana Scutari
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | | | - Roberta D'Arrigo
- Department of Microbiology and Virology, San Camillo-Forlanini Hospital, Rome, Italy
| | - Lavinia Fabeni
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Cristina Mussini
- Department of Infectious Diseases, University of Modena and Reggio Emilia, Modena, Italy
| | - Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia School of Medicine, Modena, Italy
| | - Claudio Casoli
- GEMIB Laboratory, Centre for Medical Research and Molecular Diagnostic, Parma, Italy
| | | | - Valentina Svicher
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Claudia Alteri
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Stefano Aquaro
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy.
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Martins MA, Tully DC, Shin YC, Gonzalez-Nieto L, Weisgrau KL, Bean DJ, Gadgil R, Gutman MJ, Domingues A, Maxwell HS, Magnani DM, Ricciardi M, Pedreño-Lopez N, Bailey V, Cruz MA, Lima NS, Bonaldo MC, Altman JD, Rakasz E, Capuano S, Reimann KA, Piatak M, Lifson JD, Desrosiers RC, Allen TM, Watkins DI. Rare Control of SIVmac239 Infection in a Vaccinated Rhesus Macaque. AIDS Res Hum Retroviruses 2017; 33:843-858. [PMID: 28503929 DOI: 10.1089/aid.2017.0046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Effector memory T cell (TEM) responses display potent antiviral properties and have been linked to stringent control of simian immunodeficiency virus (SIV) replication. Since recurrent antigen stimulation drives the differentiation of CD8+ T cells toward the TEM phenotype, in this study we incorporated a persistent herpesviral vector into a heterologous prime/boost/boost vaccine approach to maximize the induction of TEM responses. This new regimen resulted in CD8+ TEM-biased responses in four rhesus macaques, three of which controlled viral replication to <1,000 viral RNA copies/ml of plasma for more than 6 months after infection with SIVmac239. Over the course of this study, we made a series of interesting observations in one of these successful controller animals. Indeed, in vivo elimination of CD8αβ+ T cells using a new CD8β-depleting antibody did not abrogate virologic control in this monkey. Only after its CD8α+ lymphocytes were depleted did SIV rebound, suggesting that CD8αα+ but not CD8αβ+ cells were controlling viral replication. By 2 weeks postinfection (PI), the only SIV sequences that could be detected in this animal harbored a small in-frame deletion in nef affecting six amino acids. Deep sequencing of the SIVmac239 challenge stock revealed no evidence of this polymorphism. However, sequencing of the rebound virus following CD8α depletion at week 38.4 PI again revealed only the six-amino acid deletion in nef. While any role for immunological pressure on the selection of this deleted variant remains uncertain, our data provide anecdotal evidence that control of SIV replication can be maintained without an intact CD8αβ+ T cell compartment.
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Affiliation(s)
| | - Damien C. Tully
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
| | - Young C. Shin
- Department of Pathology, University of Miami, Miami, Florida
| | | | - Kim L. Weisgrau
- Wisconsin National Primate Research Center, University of Wisconsin—Madison, Madison, Wisconsin
| | - David J. Bean
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
| | - Rujuta Gadgil
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
| | | | - Aline Domingues
- Department of Pathology, University of Miami, Miami, Florida
| | | | | | | | | | - Varian Bailey
- Department of Pathology, University of Miami, Miami, Florida
| | - Michael A. Cruz
- Department of Pathology, University of Miami, Miami, Florida
| | - Noemia S. Lima
- Laboratório de Biologia Molecular de Flavivirus, Instituto Oswaldo Cruz–FIOCRUZ, Rio de Janeiro, Brazil
| | - Myrna C. Bonaldo
- Laboratório de Biologia Molecular de Flavivirus, Instituto Oswaldo Cruz–FIOCRUZ, Rio de Janeiro, Brazil
| | - John D. Altman
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia
| | - Eva Rakasz
- Wisconsin National Primate Research Center, University of Wisconsin—Madison, Madison, Wisconsin
| | - Saverio Capuano
- Wisconsin National Primate Research Center, University of Wisconsin—Madison, Madison, Wisconsin
| | - Keith A. Reimann
- MassBiologics, University of Massachusetts Medical School, Boston, Massachusetts
| | - Michael Piatak
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | | | - Todd M. Allen
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
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Anti-APOBEC3G activity of HIV-1 Vif protein is attenuated in elite controllers. J Virol 2015; 89:4992-5001. [PMID: 25717111 DOI: 10.1128/jvi.03464-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 01/30/2015] [Indexed: 01/27/2023] Open
Abstract
UNLABELLED HIV-1-infected individuals who control viremia to below the limit of detection without antiviral therapy have been termed elite controllers (EC). Functional attenuation of some HIV-1 proteins has been reported in EC. The HIV-1 accessory protein Vif (virion infectivity factor) enhances viral infectivity through anti-retroviral factor apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3G (APOBEC3G) degradation; however, little is known regarding Vif function in EC. Here, the anti-APOBEC3G activities of clonal, plasma HIV RNA-derived Vif sequences from 46 EC, 46 noncontrollers (NC), and 44 individuals with acute infection (AI) were compared. Vesicular stomatitis virus glycoprotein (VSV-G)-pseudotyped viruses were generated by cotransfecting 293T cells with expression plasmids encoding patient-derived Vif, human APOBEC3G, VSV-G, and a vif/env-deficient luciferase-reporter HIV-1 proviral DNA clone. Viral stocks were used to infect 293T cells, and Vif anti-APOBEC3G activity was quantified in terms of luciferase signal. On average, the anti-APOBEC3G activities of EC-derived Vif sequences (median log10 relative light units [RLU], 4.54 [interquartile range {IQR}, 4.30 to 4.66]) were significantly lower than those of sequences derived from NC (4.75 [4.60 to 4.92], P < 0.0001) and AI (4.74 [4.62 to 4.94], P < 0.0001). Reduced Vif activities were not associated with particular HLA class I alleles expressed by the host. Vif functional motifs were highly conserved in all patient groups. No single viral polymorphism could explain the reduced anti-APOBEC3G activity of EC-derived Vif, suggesting that various combinations of minor polymorphisms may underlie these effects. These results further support the idea of relative attenuation of viral protein function in EC-derived HIV sequences. IMPORTANCE HIV-1 elite controllers (EC) are rare individuals who are able to control plasma viremia to undetectable levels without antiretroviral therapy. Understanding the pathogenesis and mechanisms underpinning this rare phenotype may provide important insights for HIV vaccine design. The EC phenotype is associated with beneficial host immunogenetic factors (such as HLA-B*57) as well as with functions of attenuated viral proteins (e.g., Gag, Pol, and Nef). In this study, we demonstrated that HIV-1 Vif sequences isolated from EC display relative impairments in their ability to counteract the APOBEC3G host restriction factor compared to Vif sequences from normal progressors and acutely infected individuals. This result extends the growing body of evidence demonstrating attenuated HIV-1 protein function in EC and, in particular, supports the idea of the relevance of viral factors in contributing to this rare HIV-1 phenotype.
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Seager I, Travers SA, Leeson MD, Crampin AC, French N, Glynn JR, McCormack GP. Coreceptor usage, diversity, and divergence in drug-naive and drug-exposed individuals from Malawi, infected with HIV-1 subtype C for more than 20 years. AIDS Res Hum Retroviruses 2014; 30:975-83. [PMID: 24925099 DOI: 10.1089/aid.2013.0240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
There are few cohorts of individuals who have survived infection with HIV-1 for more than 20 years, reported and followed in the literature, and even fewer from Africa. Here we present data on a cohort of subtype C-infected individuals from rural northern Malawi. By sequencing multiple clones from long-term survivors at different time points, and using multiple genotyping approaches, we show that 5 of the 11 individuals are predicted as CXCR4 using (by ≥3/5 predictors) but only one individual is predicted as CXCR4 using by all five algorithms. Using any one genotyping approach overestimates the number of predicted CXCR4 sequences. Patterns of diversity and divergence were variable between the HIV-1 long-term survivors with some individuals showing very small amounts of variation and change, and others showing a greater amount; both patterns are consistent with what has been described in the literature.
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Affiliation(s)
- Ishla Seager
- Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Simon A. Travers
- Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
- South African National Bioinformatics Institute, SA Medical Research Council Bioinformatics Unit, University of the Western Cape, Bellville, South Africa
| | - Michael D. Leeson
- Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Amelia C. Crampin
- Karonga Prevention Study, Chilumba, Malawi
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Neil French
- Karonga Prevention Study, Chilumba, Malawi
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Institute of Infection & Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Judith R. Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Grace P. McCormack
- Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
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HLA-B*57 elite suppressor and chronic progressor HIV-1 isolates replicate vigorously and cause CD4+ T cell depletion in humanized BLT mice. J Virol 2014; 88:3340-52. [PMID: 24390323 DOI: 10.1128/jvi.03380-13] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Elite controllers or suppressors (ES) are HIV-1-infected patients who maintain undetectable viral loads without antiretroviral therapy. The mechanism of control remains unclear, but the HLA-B*57 allele is overrepresented in cohorts of these patients. However, many HLA-B*57 patients develop progressive disease, and some studies have suggested that infection with defective viruses may be the cause of the lack of high levels of virus replication and disease progression in ES. We therefore performed a comprehensive comparative in vivo and in vitro characterization of viruses isolated from well-defined ES. For this purpose, we first performed full-genome sequence analysis and in vitro fitness assays on replication-competent isolates from HLA-B*57 ES and HLA-B*57 chronic progressors (CPs). Under our experimental conditions, we found that isolates from ES and CPs can replicate in vitro. However, since inherently these assays involve the use of unnaturally in vitro-activated cells, we also investigated the replication competence and pathogenic potential of these HIV isolates in vivo using humanized BLT mice. The results from these analyses demonstrate that virus isolates from ES are fully replication competent in vivo and can induce peripheral and systemic CD4 T cell depletion. These results provide the first direct in vivo evidence that viral fitness does not likely determine clinical outcome in HLA-B*57 patients and that elite suppressors can control replication-competent, fully pathogenic viruses. A better understanding of the immunological bases of viral suppression in ES will serve to inform novel approaches to preventive and therapeutic HIV vaccine design. IMPORTANCE Elite suppressors are HIV-1-infected patients who have undetectable levels of viremia despite not being on antiviral drugs. One of the most fundamental questions about this phenomenon involves the mechanism of control. To address this question, we isolated virus from elite suppressors and from HIV-1-infected patients who have the usual progressive disease course. We compared how well the isolates from the two groups of patients replicated in culture and in humanized mice. Our results suggest that elite suppressors are capable of controlling HIV-1 due to the possession of unique host factors rather than infection with defective virus.
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Slow immunological progression in HIV-1 CRF07_BC-infected injecting drug users. Emerg Microbes Infect 2013; 2:e83. [PMID: 26038447 PMCID: PMC3880871 DOI: 10.1038/emi.2013.83] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/21/2013] [Accepted: 11/14/2013] [Indexed: 01/03/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) circulating recombinant form (CRF) 07_BC has caused serious HIV-1 epidemics among injecting drug users (IDUs) in East Asia. Little is known about the characteristics of the virus and its impact on disease progression among the infected individuals. In this study, we compared immunological progression between 423 IDUs infected with CRF07_BC and 194 men who have sex with men (MSM) with primary subtype B infection, and a representative full-length CRF07_BC molecular clone, pCRF07_BC, was constructed to characterize the virus. We found that IDUs infected with CRF07_BC had significantly slower immunological progression in the Cox proportional hazards model (hazard ratio: 0.30; 95% confidence interval: 0.13–0.69; P=0.004). The constructed recombinant CRF07_BC viruses had a reduced processing of the Gag/Gag-Pol polyproteins, a decreased incorporation of Vpr in the virus particle, tethering of virus particles on the plasma membrane and decreased virus growth kinetics. These phenotypes are related to the unique 7-amino acid deletion in the p6 of CRF07_BC, since complementation of the 7-amino acid in pCRF07_BC could improve the defective phenotypes. In summary, compared with MSM infected with HIV-1 subtype B, IDUs infected with CRF07_BC had slower immunological progression, which is likely correlated with interference of virus particle maturation by the 7-amino acid deletion in p6.
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Effects of Korean Red Ginseng and HAART on vif Gene in 10 Long-Term Slow Progressors over 20 Years: High Frequency of Deletions and G-to-A Hypermutation. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2013; 2013:871648. [PMID: 24319487 PMCID: PMC3844231 DOI: 10.1155/2013/871648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 09/03/2013] [Indexed: 01/08/2023]
Abstract
To investigate if Korean red ginseng (KRG) affects vif gene, we determined vif gene over 20 years in 10 long-term slowly progressing patients (LTSP) who were treated with KRG alone and then KRG plus HAART. We also compared these data with those of 21 control patients who did not receive KRG. Control patient group harbored only one premature stop codon (PSC) (0.9%), whereas the 10 LTSP revealed 78 defective genes (18.1%) (P < 0.001). The frequency of small in-frame deletions was found to be significantly higher in patients who received KRG alone (10.5%) than 0% in the pre-KRG or control patients (P < 0.01). Regarding HAART, vif genes containing PSCs were more frequently detected in patients receiving KRG plus HAART than patients receiving KRG alone or control patients (P < 0.01). In conclusion, our current data suggest that the high frequency of deletions and PSC in the vif gene is associated with KRG intake and HAART, respectively.
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De Maio FA, Rocco CA, Aulicino PC, Bologna R, Mangano A, Sen L. Unusual substitutions in HIV-1 vif from children infected perinatally without progression to AIDS for more than 8 years without therapy. J Med Virol 2013; 84:1844-52. [PMID: 23080486 DOI: 10.1002/jmv.23261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The HIV-1 vif gene encodes for an accessory protein that is central for virus replication due mainly to its capacity to counteract the antiviral action of host APOBEC3 restriction factors. In order to evaluate whether HIV-1 vif alterations account for a delayed progression to AIDS in children infected perinatally, the vif genes from a group of 11 patients who exhibited an extremely slow disease progression (slow progressors) were studied by direct sequencing. In addition, the vif genes from a group of 93 children with typical disease progression (typical progressors) were analyzed for comparison. Phylogenetic analysis indicated that sequences from slow progressors did not have a common origin, discarding a shared ancestor of reduced virulence. There were no differences in the diversity between the vif genes from slow and typical progressors. No gross defects showing a clear distinction among sequences from both groups of children were found. However, in the deduced Vif proteins, changes V13I, V55T, and L81M were observed only in sequences from slow progressors. By analyzing sequences stored in databases, these mutations were determined as unusual substitutions occurring at highly conserved Vif sites across different HIV-1 clades, but were observed with an increased frequency in sequences from elite controllers. These mutations were in the Vif regions reported as relevant for protein activity. These findings suggest that the Vif sequences from slow progressors carry unusual substitutions, which may alter the protein function and may contribute to viral attenuation.
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Affiliation(s)
- Federico A De Maio
- Cellular Biology and Retroviruses Laboratory-CONICET, Juan P. Garrahan, Pediatric Hospital, Buenos Aires, Argentina
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Buckheit III RW, Salgado M, Martins KO, Blankson JN. The implications of viral reservoirs on the elite control of HIV-1 infection. Cell Mol Life Sci 2013; 70:1009-19. [PMID: 22864624 PMCID: PMC11113402 DOI: 10.1007/s00018-012-1101-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 07/02/2012] [Accepted: 07/17/2012] [Indexed: 01/24/2023]
Abstract
The mechanisms by which a small percentage of HIV-1 infected individuals known as elite suppressors or controllers are able to control viral replication are not fully understood. Early cases of viremic control were attributed to infection with defective virus, but subsequent work has demonstrated that infection with a defective virus is not the exclusive cause of control. Replication-competent virus has been isolated from patients who control viral replication, and studies have demonstrated that evolution occurs in plasma virus but not in virus isolates from the latent reservoir. Additionally, transmission pair studies have demonstrated that patients infected with similar viruses can have dramatically different outcomes of infection. An increased understanding of the viral factors associated with control is important to understand the interplay between viral replication and host control, and has implications for the design of an effective therapeutic vaccine that can lead to a functional cure of HIV-1 infection.
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Affiliation(s)
- Robert W. Buckheit III
- Department of Medicine, Johns Hopkins University School of Medicine, 733 N. Broadway, BRB 880, Baltimore, MD 21205 USA
| | - Maria Salgado
- Department of Medicine, Johns Hopkins University School of Medicine, 733 N. Broadway, BRB 880, Baltimore, MD 21205 USA
- Institut de Recerca de La SIDA (IrsiCaixa), Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Karen O. Martins
- Department of Integrated Toxicology, USAMRIID, Frederick, MD 21702 USA
| | - Joel N. Blankson
- Department of Medicine, Johns Hopkins University School of Medicine, 733 N. Broadway, BRB 880, Baltimore, MD 21205 USA
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Cruz NVG, Amorim R, Oliveira FE, Speranza FAC, Costa LJ. Mutations in the nef and vif genes associated with progression to AIDS in elite controller and slow-progressor patients. J Med Virol 2013; 85:563-74. [PMID: 23417613 DOI: 10.1002/jmv.23512] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2012] [Indexed: 11/07/2022]
Abstract
Progression towards AIDS can vary from 5 to 10 years from the establishment of the primary infection by HIV-1 to more than 10 years in the complete absence of antiretroviral therapy. Several factors can contribute to the outcome of HIV infection, including host genetic and viral replicating characteristics. Historically, nef-deleted viral genomes have been associated with disease progression. Therefore, the lentiviral Nef protein is regarded as a progression factor. The objective of this work was to characterize the nef gene from a group of treatment naive patients infected with HIV-1 for more than 10 years. These patients were classified as long-term non-progressors, elite controller, and slow-progressors according to clinical and laboratorial data. A premature stop codon within the nef gene leading to the expression of a truncated peptide was observed on samples from the elite controller patient. For the slow-progressor patients, several degrees of deletions at the C-terminal of Nef were observed predicting a loss of function of this protein. The vif gene was characterized for these patients and a rare mutation that predicts a miss localization of the Vif protein to the nucleus of infected cells that could prevent its function as an APOBEC neutralization factor was also observed. These data indicate the importance of the HIV accessory proteins as factors that contribute to the outcome of AIDS.
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Affiliation(s)
- Nadia V G Cruz
- Department of Virology, Institute of Microbiology Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Münk C, Jensen BEO, Zielonka J, Häussinger D, Kamp C. Running loose or getting lost: how HIV-1 counters and capitalizes on APOBEC3-induced mutagenesis through its Vif protein. Viruses 2012; 4:3132-61. [PMID: 23202519 PMCID: PMC3509687 DOI: 10.3390/v4113132] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 10/29/2012] [Accepted: 11/05/2012] [Indexed: 12/24/2022] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) dynamics reflect an intricate balance within the viruses’ host. The virus relies on host replication factors, but must escape or counter its host’s antiviral restriction factors. The interaction between the HIV-1 protein Vif and many cellular restriction factors from the APOBEC3 protein family is a prominent example of this evolutionary arms race. The viral infectivity factor (Vif) protein largely neutralizes APOBEC3 proteins, which can induce in vivo hypermutations in HIV-1 to the extent of lethal mutagenesis, and ensures the production of viable virus particles. HIV-1 also uses the APOBEC3-Vif interaction to modulate its own mutation rate in harsh or variable environments, and it is a model of adaptation in a coevolutionary setting. Both experimental evidence and the substantiation of the underlying dynamics through coevolutionary models are presented as complementary views of a coevolutionary arms race.
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Affiliation(s)
- Carsten Münk
- Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany; (C.M.); (B.-E.O.J.); (J.Z.); (D.H.)
| | - Björn-Erik O. Jensen
- Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany; (C.M.); (B.-E.O.J.); (J.Z.); (D.H.)
| | - Jörg Zielonka
- Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany; (C.M.); (B.-E.O.J.); (J.Z.); (D.H.)
- Roche Glycart AG, Schlieren 8952, Switzerland
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany; (C.M.); (B.-E.O.J.); (J.Z.); (D.H.)
| | - Christel Kamp
- Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Paul-Ehrlich-Straße 51-59, 63225 Langen, Germany
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17
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De Maio FA, Rocco CA, Aulicino PC, Bologna R, Mangano A, Sen L. APOBEC3-mediated editing in HIV type 1 from pediatric patients and its association with APOBEC3G/CUL5 polymorphisms and Vif variability. AIDS Res Hum Retroviruses 2012; 28:619-27. [PMID: 22145963 DOI: 10.1089/aid.2011.0291] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The APOBEC3 proteins are cytidine deaminases that can introduce G→A mutations in the HIV-1 plus DNA strand. This editing process may inhibit virus replication through lethal mutagenesis (hypermutation), but could also contribute to viral diversification leading to the emergence of escape forms. The HIV-1 Vif protein has the capacity to counteract APOBEC3 factors by recruiting a CUL5-based ubiquitin ligase complex that determines their proteasomal degradation. In this work, we analyzed the APOBEC3-mediated editing in proviral HIV-1 from perinatally infected children (n=93) in order to explore its association with polymorphisms of APOBEC3G and CUL5 genes (APOBEC3G H186R, APOBEC3G C40693T, and CUL5 SNP6), the Vif protein variability, and also the time to AIDS development. To calculate the level of editing, we have developed an index exploiting the properties of a region within the HIV-1 pol gene that includes the central polypurine tract (cPPT). We detected a reduced editing associated with the CUL5 SNP6 minor allele and also with certain Vif variants (mutations at sites 46, 122, and 160), although we found no evidence supporting an impact of APOBEC3 activity on disease progression. Thus, our findings suggest that APOBEC3-mediated editing of HIV-1 could be modulated by host and virus genetic characteristics in the context of pediatric infection.
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Affiliation(s)
- Federico A. De Maio
- Laboratorio de Biología Celular y Retrovirus–CONICET, Hospital de Pediatría “Prof. Dr. Juan P. Garrahan,” Ciudad de Buenos Aires, Argentina
| | - Carlos A. Rocco
- Laboratorio de Biología Celular y Retrovirus–CONICET, Hospital de Pediatría “Prof. Dr. Juan P. Garrahan,” Ciudad de Buenos Aires, Argentina
| | - Paula C. Aulicino
- Laboratorio de Biología Celular y Retrovirus–CONICET, Hospital de Pediatría “Prof. Dr. Juan P. Garrahan,” Ciudad de Buenos Aires, Argentina
| | - Rosa Bologna
- Servicio de Epidemiología e Infectología, Hospital de Pediatría “Prof. Dr. Juan P. Garrahan,” Ciudad de Buenos Aires, Argentina
| | - Andrea Mangano
- Laboratorio de Biología Celular y Retrovirus–CONICET, Hospital de Pediatría “Prof. Dr. Juan P. Garrahan,” Ciudad de Buenos Aires, Argentina
| | - Luisa Sen
- Laboratorio de Biología Celular y Retrovirus–CONICET, Hospital de Pediatría “Prof. Dr. Juan P. Garrahan,” Ciudad de Buenos Aires, Argentina
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Kourteva Y, De Pasquale M, Allos T, McMunn C, D'Aquila RT. APOBEC3G expression and hypermutation are inversely associated with human immunodeficiency virus type 1 (HIV-1) burden in vivo. Virology 2012; 430:1-9. [PMID: 22579353 DOI: 10.1016/j.virol.2012.03.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 03/12/2012] [Accepted: 03/24/2012] [Indexed: 12/01/2022]
Abstract
APOBEC3G (A3G) and APOBEC3F (A3F) reduce Vif-negative HIV-1 provirus formation and cause disabling provirus G-to-A hypermutation in vitro. However, evidence conflicts about whether they negatively impact Vif-positive HIV-1, or only enhance virus genetic diversity, in vivo. We studied peripheral blood mononuclear cells (PBMC) from 19 antiretroviral-naïve, HIV-infected adults: 12 long-term non-progressors (LTNP) and 7 non-controllers (NC). Cells from LTNP had higher A3G and A3F mRNA levels, lower provirus burden, and more A3G-hypermutated positions in provirus sequence than cells from NC. A3G mRNA level was directly associated with its Hypermutation Index (HI) and inversely associated with provirus burden. Plasma HIV-1 RNA levels were inversely associated with A3G expression levels and with HI only among subjects who had HI>1. A3G HI was not associated with provirus burden. These results indicate that A3G deaminase-dependent activity above a threshold level, and its deaminase-independent functions, contribute to decreasing Vif-positive virus replication in vivo.
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Affiliation(s)
- Yordanka Kourteva
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University, Nashville, TN 37232, USA
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19
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Buckheit RW, Allen TG, Alme A, Salgado M, O’Connell KA, Huculak S, Falade-Nwulia O, Williams TM, Gallant JE, Siliciano RF, Blankson JN. Host factors dictate control of viral replication in two HIV-1 controller/chronic progressor transmission pairs. Nat Commun 2012; 3:716. [PMID: 22395607 PMCID: PMC3549550 DOI: 10.1038/ncomms1697] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 01/23/2012] [Indexed: 02/07/2023] Open
Abstract
Viremic controllers and elite controllers/suppressors maintain control over HIV-1 replication. Some studies have suggested that control is a result of infection with a defective viral strain, while others suggested host immune factors have a key role. Here we document two HIV-1 transmission pairs: one consisting of a patient with progressive disease and an individual who became an elite suppressor, and the second consisting of a patient with progressive disease and a viremic controller. In contrast to another elite suppressor transmission pair, virus isolated from all patients was fully competent. These data suggest that some viremic controllers and elite suppressors are infected with HIV-1 isolates that replicate vigorously in vitro and are able to cause progressive disease in vivo. These data suggest that host factors have a dominant role in the control of HIV-1 infection, thus it may be possible to control fully pathogenic HIV-1 isolates with therapeutic vaccination.
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Affiliation(s)
- Robert W. Buckheit
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
| | - Tracy G. Allen
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
| | - Angela Alme
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
| | - Maria Salgado
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
| | - Karen A. O’Connell
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
| | - Sarah Huculak
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
| | - Oluwaseun Falade-Nwulia
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
| | - Thomas M. Williams
- Department of Pathology, School of Medicine and Tricore Reference Laboratories, University of New Mexico, Albuquerque, New Mexico
| | - Joel E. Gallant
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
- Howard Hughes Medical Institute. Johns Hopkins University School of Medicine. 733 N. Broadway, Baltimore MD 21205, USA
| | - Joel N. Blankson
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
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20
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De Maio FA, Rocco CA, Aulicino PC, Bologna R, Mangano A, Sen L. Effect of HIV-1 Vif variability on progression to pediatric AIDS and its association with APOBEC3G and CUL5 polymorphisms. INFECTION GENETICS AND EVOLUTION 2011; 11:1256-62. [PMID: 21571098 DOI: 10.1016/j.meegid.2011.04.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 03/31/2011] [Accepted: 04/14/2011] [Indexed: 10/18/2022]
Abstract
The APOBEC3G protein is a restriction factor that can inhibit the replication of HIV-1. The virus has the capacity to counteract this antiviral activity through the expression of the Vif accessory protein, which recruits a CUL5-based ubiquitin ligase complex that determines APOBEC3G proteasomal degradation. In this work we evaluated in a large pediatric cohort (i) whether single nucleotide polymorphisms of APOBEC3G and CUL5 genes (APOBEC3G H186R, APOBEC3G C40693T and CUL5 SNP6) can alter the risk of HIV-1 vertical transmission and/or the rate of progression to AIDS, (ii) the effect of HIV-1 Vif variants on the clinical course of disease, and (iii) whether the patient genotype for the studied polymorphisms could have an impact on Vif characteristics. We found no effect of the studied APOBEC3G or CUL5 genetic variants on vertical transmission or progression to pediatric AIDS. However, we detected an association of certain Vif alterations (a one amino acid insertion at position 61 and the substitutions A62D/N/S and Q136P) with an accelerated AIDS outcome. Additionally, we observed that the APOBEC3G C40693T and CUL5 SNP6 minor alleles were correlated with substitutions in Vif motifs that are involved in the interaction with APOBEC3G and CUL5 proteins, respectively. Our results suggest that Vif alterations may contribute to a rapid AIDS onset and that Vif variability could be influenced by APOBEC3G and CUL5 polymorphisms in children.
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Affiliation(s)
- Federico A De Maio
- Laboratorio de Biología Celular y Retrovirus - CONICET, Hospital de Pediatría Juan P. Garrahan, Ciudad de Buenos Aires, Argentina
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21
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Poropatich K, Sullivan DJ. Human immunodeficiency virus type 1 long-term non-progressors: the viral, genetic and immunological basis for disease non-progression. J Gen Virol 2010; 92:247-68. [PMID: 21106806 DOI: 10.1099/vir.0.027102-0] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A small subset of human immunodeficiency virus type 1 (HIV-1)-infected, therapy-naive individuals--referred to as long-term non-progressors (LTNPs)--maintain a favourable course of infection, often being asymptomatic for many years with high CD4(+) and CD8(+) T-cell counts (>500 cells μl(-1)) and low plasma HIV-RNA levels (<10 ,000 copies ml(-1)). Research in the field has undergone considerable development in recent years and LTNPs offer a piece of the puzzle in understanding the ways that persons can naturally control HIV-1 infection. Their method of control is based on viral, genetic and immunological components. With respect to virological features, genomic sequencing has shown that some LTNPs are infected with attenuated strains of HIV-1 and harbour mutant nef, vpr, vif or rev genes that contain single nuclear polymorphisms, or less frequently, large deletions, in conserved domains. Studies have also shown that some LTNPs have unique genetic advantages, including heterozygosity for the CCR5-Δ32 polymorphism, and have been found with excitatory mutations that upregulate the production of the chemokines that competitively inhibit HIV-1 binding to CCR5 or CXCR4. Lastly, immunological factors are crucial for providing LTNPs with a natural form of control, the most important being robust HIV-specific CD4(+) and CD8(+) T-cell responses that correlate with lower viral loads. Many LTNPs carry the HLA class I B57 allele that enhances presentation of antigenic peptides on the surface of infected CD4(+) cells to cytotoxic CD8(+) T cells. For these reasons, LTNPs serve as an ideal model for HIV-1 vaccine development due to their natural control of HIV-1 infection.
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Affiliation(s)
- Kate Poropatich
- The George Washington School of Medicine and Health Sciences, Washington, DC, USA
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22
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Abstract
Multiple APOBEC3 proteins are expressed in HIV-1 target cells, but their individual contributions to viral suppression when expressed at endogenous levels remain largely unknown. We used an HIV NL4-3 mutant that selectively counteracts APOBEC3G (A3G) but not APOBEC3F (A3F) to dissect the relative contribution of A3F to the inhibition of HIV-1 replication in primary human lymphocytes (peripheral blood mononuclear cells [PBMCs]). This HIV Vif mutant replicated similarly to wild-type virus in PBMCs, suggesting that the effect of A3F on HIV restriction in these cells is limited. The different A3F variants found in PMBC donors displayed either comparable activity or less activity than wild-type A3F. Lastly, the endogenous A3F mRNA and protein expression levels in PBMCs were considerably lower than those of A3G. Our results suggest that A3F neutralization is dispensable for HIV-1 replication in primary human T-lymphocytes.
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Tzitzivacos D, Tiemessen C, Stevens W, Papathanasopoulos M. Viral genetic determinants of nonprogressive HIV type 1 subtype C infection in antiretroviral drug-naive children. AIDS Res Hum Retroviruses 2009; 25:1141-8. [PMID: 19895210 DOI: 10.1089/aid.2009.0080] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Characterization of HIV-1 from slow progressors is important to facilitate vaccine and antiviral drug development. To identify virus attenuations that may contribute to slower rates of disease progression, the full-length viral genomes from primary isolates of six slow progressing HIV-positive children were sequenced. Proviral DNA was extracted from cocultured peripheral blood mononuclear cells and used to PCR amplify, sequence, and extensively analyze the near full-length genomes and LTR regions. All primary HIV-1 isolates were HIV-1 subtype C throughout their genome, and amino acid (AA) sequence analysis revealed open reading frames for all genes. However, all isolates had at least one unusual gene/protein. For example, isolate LT5 had a 2AA insertion in the Vpr mitochondriotoxic domain. Isolate LT21 contained an additional 5AA in the C-terminus of tat exon 2, while integrase in isolate LT39 had an additional 4AA at the C-terminus. Rev from isolates LT45 and LT46 did not have the characteristic subtype C 16AA truncation, and in addition, had a further 3AA. Furthermore, altered functional domains were noted in several isolates, such as the cAMP-dependent kinase PKA phosphorylation site in Nef (LT5), a Vpr mutation involved in decreased proapoptotic activity (all isolates), and the Nef ExxxLL motif involved in the interaction with AP-1 and AP-2 (LT46). The slower HIV-1 disease progression in these six children may be attributed to altered protein functions. For example, LT46 Nef is unable to bind AP-1 and AP-2 and therefore is inactive on CD4 endocytosis. The biological relevance of these findings requires further investigation.
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Affiliation(s)
- D.B. Tzitzivacos
- HIV Pathogenesis Research Laboratory, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, Parktown, Johannesburg 2193, South Africa
| | - C.T. Tiemessen
- Cell Biology, AIDS Virus Research Unit, National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - W.S. Stevens
- HIV Pathogenesis Research Laboratory, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, Parktown, Johannesburg 2193, South Africa
| | - M.A. Papathanasopoulos
- HIV Pathogenesis Research Laboratory, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, Parktown, Johannesburg 2193, South Africa
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24
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Blankson JN. Effector mechanisms in HIV-1 infected elite controllers: highly active immune responses? Antiviral Res 2009; 85:295-302. [PMID: 19733595 DOI: 10.1016/j.antiviral.2009.08.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 07/30/2009] [Accepted: 08/30/2009] [Indexed: 10/20/2022]
Abstract
Elite controllers (EC) are HIV-1 infected patients control viral replication to a level of <50 copies/ml without antiretroviral therapy. These patients are also known as elite suppressors, or HIV controllers, and they differ from traditional long-term non-progressors (LTNPs) who maintain stable CD4 counts and are asymptomatic without antiretroviral therapy. Recent studies suggest that many EC are infected with replication-competent virus. Thus it appears that host factors such as innate immunity, the humoral immune response, and the cellular immune response are involved in the suppression of viral replication in EC. This article will review the effector mechanisms that are thought to play a role in the remarkable control of viral replication seen in these patients. This article forms part of a special issue of Antiviral Research marking the 25th anniversary of antiretroviral drug discovery and development, Vol 85, issue 1, 2010.
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Affiliation(s)
- Joel N Blankson
- Broadway Research Bldg, Rm 880, Johns Hopkins University School of Medicine, 722 N. Broadway, Baltimore, MD 21205, United States.
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25
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Tumultuous relationship between the human immunodeficiency virus type 1 viral infectivity factor (Vif) and the human APOBEC-3G and APOBEC-3F restriction factors. Microbiol Mol Biol Rev 2009; 73:211-32. [PMID: 19487726 DOI: 10.1128/mmbr.00040-08] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The viral infectivity factor (Vif) is dispensable for human immunodeficiency virus type 1 (HIV-1) replication in so-called permissive cells but is required for replication in nonpermissive cell lines and for pathogenesis. Virions produced in the absence of Vif have an aberrant morphology and an unstable core and are unable to complete reverse transcription. Recent studies demonstrated that human APOBEC-3G (hA3G) and APOBEC-3F (hA3F), which are selectively expressed in nonpermissive cells, possess strong anti-HIV-1 activity and are sufficient to confer a nonpermissive phenotype. Vif induces the degradation of hA3G and hA3F, suggesting that its main function is to counteract these cellular factors. Most studies focused on the hypermutation induced by the cytidine deaminase activity of hA3G and hA3F and on their Vif-induced degradation by the proteasome. However, recent studies suggested that several mechanisms are involved both in the antiviral activity of hA3G and hA3F and in the way Vif counteracts these antiviral factors. Attempts to reconcile the studies involving Vif in virus assembly and stability with these recent findings suggest that hA3G and hA3F partially exert their antiviral activity independently of their catalytic activity by destabilizing the viral core and the reverse transcription complex, possibly by interfering with the assembly and/or maturation of the viral particles. Vif could then counteract hA3G and hA3F by excluding them from the viral assembly intermediates through competition for the viral genomic RNA, by regulating the proteolytic processing of Pr55(Gag), by enhancing the efficiency of the reverse transcription process, and by inhibiting the enzymatic activities of hA3G and hA3F.
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Genetic characterization of human immunodeficiency virus type 1 in elite controllers: lack of gross genetic defects or common amino acid changes. J Virol 2008; 82:8422-30. [PMID: 18562530 DOI: 10.1128/jvi.00535-08] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite reports of viral genetic defects in persons who control human immunodeficiency virus type 1 (HIV-1) in the absence of antiviral therapy, the extent to which such defects contribute to the long-term containment of viremia is not known. Most previous studies examining for such defects have involved small numbers of subjects, primarily focused on subjects expressing HLA-B57, or have examined single viral genes, and they have focused on cellular proviral DNA rather than plasma viral RNA sequences. Here, we attempted viral sequencing from 95 HIV-1 elite controllers (EC) who maintained plasma viral loads of <50 RNA copies/ml in the absence of therapy, the majority of whom did not express HLA-B57. HIV-1 gene fragments were obtained from 94% (89/95) of the EC, and plasma viral sequences were obtained from 78% (61/78), the latter indicating the presence of replicating virus in the majority of EC. Of 63 persons for whom nef was sequenced, only three cases of nef deletions were identified, and gross genetic defects were rarely observed in other HIV-1 coding genes. In a codon-by-codon comparison between EC and persons with progressive infection, correcting for HLA bias and coevolving secondary mutations, a significant difference was observed at only three codons in Gag, all three of which represented the historic population consensus amino acid at the time of infection. These results indicate that the spontaneous control of HIV replication is not attributable to shared viral genetic defects or shared viral polymorphisms.
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Gorry PR, McPhee DA, Verity E, Dyer WB, Wesselingh SL, Learmont J, Sullivan JS, Roche M, Zaunders JJ, Gabuzda D, Crowe SM, Mills J, Lewin SR, Brew BJ, Cunningham AL, Churchill MJ. Pathogenicity and immunogenicity of attenuated, nef-deleted HIV-1 strains in vivo. Retrovirology 2007; 4:66. [PMID: 17888184 PMCID: PMC2075523 DOI: 10.1186/1742-4690-4-66] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Accepted: 09/23/2007] [Indexed: 11/10/2022] Open
Abstract
In efforts to develop an effective vaccine, sterilizing immunity to primate lentiviruses has only been achieved by the use of live attenuated viruses carrying major deletions in nef and other accessory genes. Although live attenuated HIV vaccines are unlikely to be developed due to a myriad of safety concerns, opportunities exist to better understand the correlates of immune protection against HIV infection by studying rare cohorts of long-term survivors infected with attenuated, nef-deleted HIV strains such as the Sydney blood bank cohort (SBBC). Here, we review studies of viral evolution, pathogenicity, and immune responses to HIV infection in SBBC members. The studies show that potent, broadly neutralizing anti-HIV antibodies and robust CD8+ T-cell responses to HIV infection were not necessary for long-term control of HIV infection in a subset of SBBC members, and were not sufficient to prevent HIV sequence evolution, augmentation of pathogenicity and eventual progression of HIV infection in another subset. However, a persistent T-helper proliferative response to HIV p24 antigen was associated with long-term control of infection. Together, these results underscore the importance of the host in the eventual outcome of infection. Thus, whilst generating an effective antibody and CD8+ T-cell response are an essential component of vaccines aimed at preventing primary HIV infection, T-helper responses may be important in the generation of an effective therapeutic vaccine aimed at blunting chronic HIV infection.
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Affiliation(s)
- Paul R Gorry
- Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Medicine, Monash University, Melbourne, Victoria, Australia
| | - Dale A McPhee
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology, Monash University, Melbourne, Victoria, Australia
- National Serology Reference Laboratory, St. Vincent's Institute for Medical Research, Fitzroy, Victoria, Australia
| | - Erin Verity
- Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia
- Department of Microbiology, Monash University, Melbourne, Victoria, Australia
- National Serology Reference Laboratory, St. Vincent's Institute for Medical Research, Fitzroy, Victoria, Australia
| | - Wayne B Dyer
- Australian Red Cross Blood Service, Sydney, New South Wales, Australia
- Faculty of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Steven L Wesselingh
- Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Medicine, Monash University, Melbourne, Victoria, Australia
| | - Jennifer Learmont
- Australian Red Cross Blood Service, Sydney, New South Wales, Australia
| | - John S Sullivan
- Australian Red Cross Blood Service, Sydney, New South Wales, Australia
- Faculty of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Michael Roche
- Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia
| | - John J Zaunders
- Center for Immunology, St. Vincent's Hospital, Sydney, New South Wales, Australia
| | - Dana Gabuzda
- Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Suzanne M Crowe
- Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia
- Department of Medicine, Monash University, Melbourne, Victoria, Australia
| | - John Mills
- Department of Medicine, Monash University, Melbourne, Victoria, Australia
- Department of Microbiology, Monash University, Melbourne, Victoria, Australia
- Department of Epidemiology & Community Medicine, Monash University, Melbourne, Victoria, Australia
| | - Sharon R Lewin
- Department of Medicine, Monash University, Melbourne, Victoria, Australia
- Infectious Diseases Unit, Alfred Hospital, Melbourne, Victoria, Australia
| | - Bruce J Brew
- Department of Neurology, St. Vincent's Hospital, Sydney, New South Wales, Australia
| | | | - Melissa J Churchill
- Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia
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Lama J, Planelles V. Host factors influencing susceptibility to HIV infection and AIDS progression. Retrovirology 2007; 4:52. [PMID: 17651505 PMCID: PMC1978541 DOI: 10.1186/1742-4690-4-52] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Accepted: 07/25/2007] [Indexed: 12/21/2022] Open
Abstract
Transmission of HIV first results in an acute infection, followed by an apparently asymptomatic period that averages ten years. In the absence of antiretroviral treatment, most patients progress into a generalized immune dysfunction that culminates in death. The length of the asymptomatic period varies, and in rare cases infected individuals never progress to AIDS. Other individuals whose behavioral traits put them at high-risk of HIV transmission, surprisingly appear resistant and never succumb to infection. These unique cases highlight the fact that susceptibility to HIV infection and progression to disease are complex traits modulated by environmental and genetic factors. Recent evidence has indicated that natural variations in host genes can influence the outcome of HIV infection and its transmission. In this review we summarize the available literature on the roles of cellular factors and their genetic variation in modulating HIV infection and disease progression.
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Affiliation(s)
- Juan Lama
- La Jolla Institute for Molecular Medicine, 4570 Executive Drive, Suite 100, San Diego, California 92121, USA
- RetroVirox, Inc. 4570 Executive Drive, Suite 100, San Diego, California 92121, USA
| | - Vicente Planelles
- Department of Pathology, University of Utah School of Medicine, 15 North Medical Drive East #2100 – Room 2520, Salt Lake City, Utah 84112, USA
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Churchill MJ, Chiavaroli L, Wesselingh SL, Gorry PR. Persistence of attenuated HIV-1 rev alleles in an epidemiologically linked cohort of long-term survivors infected with nef-deleted virus. Retrovirology 2007; 4:43. [PMID: 17601342 PMCID: PMC1933581 DOI: 10.1186/1742-4690-4-43] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Accepted: 07/01/2007] [Indexed: 11/10/2022] Open
Abstract
Background The Sydney blood bank cohort (SBBC) of long-term survivors consists of multiple individuals infected with nef-deleted, attenuated strains of human immunodeficiency virus type 1 (HIV-1). Although the cohort members have experienced differing clinical courses and now comprise slow progressors (SP) as well as long-term nonprogressors (LTNP), longitudinal analysis of nef/long-terminal repeat (LTR) sequences demonstrated convergent nef/LTR sequence evolution in SBBC SP and LTNP. Thus, the in vivo pathogenicity of attenuated HIV-1 strains harboured by SBBC members is dictated by factors other than nef/LTR. Therefore, to determine whether defects in other viral genes contribute to attenuation of these HIV-1 strains, we characterized dominant HIV-1 rev alleles that persisted in 4 SBBC subjects; C18, C64, C98 and D36. Results The ability of Rev derived from D36 and C64 to bind the Rev responsive element (RRE) in RNA binding assays was reduced by approximately 90% compared to Rev derived from HIV-1NL4-3, C18 or C98. D36 Rev also had a 50–60% reduction in ability to express Rev-dependent reporter constructs in mammalian cells. In contrast, C64 Rev had only marginally decreased Rev function despite attenuated RRE binding. In D36 and C64, attenuated RRE binding was associated with rare amino acid changes at 3 highly conserved residues; Gln to Pro at position 74 immediately N-terminal to the Rev activation domain, and Val to Leu and Ser to Pro at positions 104 and 106 at the Rev C-terminus, respectively. In D36, reduced Rev function was mapped to an unusual 13 amino acid extension at the Rev C-terminus. Conclusion These findings provide new genetic and mechanistic insights important for Rev function, and suggest that Rev function, not Rev/RRE binding may be rate limiting for HIV-1 replication. In addition, attenuated rev alleles may contribute to viral attenuation and long-term survival of HIV-1 infection in a subset of SBBC members.
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Affiliation(s)
- Melissa J Churchill
- The Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia
| | - Lisa Chiavaroli
- The Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia
| | - Steven L Wesselingh
- The Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Medicine, Monash University, Melbourne, Victoria, Australia
| | - Paul R Gorry
- The Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Medicine, Monash University, Melbourne, Victoria, Australia
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Blankson JN, Bailey JR, Thayil S, Yang HC, Lassen K, Lai J, Gandhi SK, Siliciano JD, Williams TM, Siliciano RF. Isolation and characterization of replication-competent human immunodeficiency virus type 1 from a subset of elite suppressors. J Virol 2006; 81:2508-18. [PMID: 17151109 PMCID: PMC1865922 DOI: 10.1128/jvi.02165-06] [Citation(s) in RCA: 226] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Elite suppressors (ES) are untreated human immunodeficiency virus type 1 (HIV-1)-infected individuals who control viremia to levels below the limit of detection of current assays. The mechanisms involved in this control have not been fully elucidated. Several studies have demonstrated that some ES are infected with defective viruses, but it remains unclear whether others are infected with replication-competent HIV-1. To answer this question, we used a sensitive coculture assay in an attempt to isolate replication-competent virus from a cohort of 10 ES. We successfully cultured six replication-competent isolates from 4 of the 10 ES. The frequency of latently infected cells in these patients was more than a log lower than that seen in patients on highly active antiretroviral therapy with undetectable viral loads. Full-length sequencing of all six isolates revealed no large deletions in any of the genes. A few mutations and small insertions and deletions were found in some isolates, but phenotypic analysis of the affected genes suggested that their function remained intact. Furthermore, all six isolates replicated as well as standard laboratory strains in vitro. The results suggest that some ES are infected with HIV-1 isolates that are fully replication competent and that long-term immunologic control of replication-competent HIV-1 is possible.
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Affiliation(s)
- Joel N Blankson
- Department of Medicine, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
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Zhang H, Hoffmann F, He J, He X, Kankasa C, West JT, Mitchell CD, Ruprecht RM, Orti G, Wood C. Characterization of HIV-1 subtype C envelope glycoproteins from perinatally infected children with different courses of disease. Retrovirology 2006; 3:73. [PMID: 17054795 PMCID: PMC1635063 DOI: 10.1186/1742-4690-3-73] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Accepted: 10/20/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The causal mechanisms of differential disease progression in HIV-1 infected children remain poorly defined, and much of the accumulated knowledge comes from studies of subtype B infected individuals. The applicability of such findings to other subtypes, such as subtype C, remains to be substantiated. In this study, we longitudinally characterized the evolution of the Env V1-V5 region from seven subtype C HIV-1 perinatally infected children with different clinical outcomes. We investigated the possible influence of viral genotype and humoral immune response on disease progression in infants. RESULTS Genetic analyses revealed that rapid progressors (infants that died in the first year of life) received and maintained a genetically homogeneous viral population throughout the disease course. In contrast, slow progressors (infants that remained clinically asymptomatic for up to four years) also exhibited low levels variation initially, but attained higher levels of diversity over time. Genetic assessment of variation, as indicated by dN/dS, showed that particular regions of Env undergo selective changes. Nevertheless, the magnitude and distribution of these changes did not segregate slow and rapid progressors. Longitudinal trends in Env V1-V5 length and the number of potential N-glycosylation sites varied among patients but also failed to discriminate between fast and slow progressors. Viral isolates from rapid progressors and slow progressors displayed no significant growth properties differences in vitro. The neutralizing activity in maternal and infant baseline plasma also varied in its effectiveness against the initial virus from the infants but did not differentiate rapid from slow progressors. Quantification of the neutralization susceptibility of the initial infant viral isolates to maternal baseline plasma indicated that both sensitive and resistant viruses were transmitted, irrespective of disease course. We showed that humoral immunity, whether passively acquired or developed de novo in the infected children, varied but was not predictive of disease progression. CONCLUSION Our data suggest that neither genetic variation in env, or initial maternal neutralizing activity, or the level of passively acquired neutralizing antibody, or the level of the de novo neutralization response appear to be linked to differences in disease progression in subtype C HIV-1 infected children.
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Affiliation(s)
- Hong Zhang
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Federico Hoffmann
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Jun He
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Xiang He
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Chipepo Kankasa
- Department of Pediatrics, University Teaching Hospital, Lusaka, Zambia
| | - John T West
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Charles D Mitchell
- Department of Pediatrics, University of Miami School of Medicine, Miami, FL, USA
| | - Ruth M Ruprecht
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Guillermo Orti
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Charles Wood
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
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Alexander L, Cuchura L, Simpson BJ, Andiman WA. Virologic and host characteristics of human immunodeficiency virus type 1-infected pediatric long term survivors. Pediatr Infect Dis J 2006; 25:135-41. [PMID: 16462290 DOI: 10.1097/01.inf.0000199299.00345.83] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND There are limited data concerning determinants of varying clinical progression rates in human immunodeficiency virus type 1 (HIV-1)-infected children. Therefore, we sought to determine whether viral or host factors associated with nonprogressive HIV-1 infection in adults play a role in limiting progression of infection in 5 vertically infected youths, ages 12-18 years, who have displayed no signs of advanced HIV-1 disease or acquired immunodeficiency syndrome despite having received minimal treatment with antiretroviral drugs. RESULTS The 5 individuals, whom we characterize as long term survivors, have maintained low loads of HIV-1 RNA in plasma when compared to many of their peers, and have also maintained normal and stable CD4 T-lymphocyte numbers and percentages throughout their lives. Determination of their predominant HIV-1 sequences revealed that 4 of 5 patients harbor virus with markers of resistance to their therapy (one was never treated). Furthermore 2 harbored viral isolates that contained insertions in Gag or Vif that inhibit HIV-1 replication. Moreover, 2 were found to be heterozygous for the CCR2 polymorphism 64I, a genotype associated with slower progression to acquired immunodeficiency syndrome in adults. All 5 expressed the histocompatibility leukocyte antigen DQ1 and 2 had unusual DR/DQ1 phenotypes. CONCLUSIONS We believe that the limited antiretroviral therapy received by the long term survivors cannot solely account for their benign clinical status. Therefore, we conclude that other factors, including gene polymorphisms that affect viral replicative capacity, account for the long term survival in some, and deduce that, as in adults, no single factor (virologic or host) can account for this clinical phenotype in all cases.
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Affiliation(s)
- Louis Alexander
- Department of Epidemiology and Public Health, Yale University School of Medicine, 60 College Street, New Haven, CT 06520, USA.
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33
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Tolstrup M, Laursen AL, Gerstoft J, Pedersen FS, Ostergaard L, Duch M. Cysteine 138 mutation in HIV-1 Nef from patients with delayed disease progression. Sex Health 2006; 3:281-6. [PMID: 17112441 DOI: 10.1071/sh06002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2006] [Accepted: 04/10/2006] [Indexed: 11/23/2022]
Abstract
Background: The nef gene from HIV-1 has been shown to be an important pathogenic factor when considering development of AIDS. Detection of nef variants with an effect on immune modulation is important to understand HIV-1 pathogenesis and has possible impact on treatment strategies. Methods: The nef gene of HIV-1 isolates from patients in a long-term non-progressor (LTNP) cohort and a slow-progressor (SP) cohort (n = 11) was analysed and compared with isolates from a control patient group of progressors (n = 18). Most of the patients with delayed disease progression had extensive medical records, providing an insight into the LTNP disease profile and allowing for the stratification of patients based on their CD4 cell decline. Results: In sequences from nine patients, most of the functional domains of HIV-1 Nef appeared intact, and no major deletions were observed to possibly account for an effect on the delayed disease status. However, the results demonstrate a high incidence of a single amino acid polymorphism (cysteine 138) in HIV-1 Nef. The allelic frequency of cysteine 138 between the delayed disease progression group and the progressor group was found to be statistically significant (P = 0.0139). The phylogeny of isolates was investigated and the variants harbouring the cysteine 138 mutation clustered independently. Conclusion: The present study describes a viral genetic polymorphism related to AIDS disease progression. The polymorphism (cysteine 138) has previously been reported to confer decreased viral replication (Premkumar DR, et al. AIDS Res Hum Retroviruses 1996; 12(4): 337–45). A sequence database search for comparative mutations revealed a high frequency of cysteine 138 in patients with reported SP AIDS.
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Affiliation(s)
- Martin Tolstrup
- Department of Infectious Diseases, Skejby Hospital, 8200 Aarhus, Denmark.
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Winters MA, Merigan TC. Insertions in the human immunodeficiency virus type 1 protease and reverse transcriptase genes: clinical impact and molecular mechanisms. Antimicrob Agents Chemother 2005; 49:2575-82. [PMID: 15980322 PMCID: PMC1168704 DOI: 10.1128/aac.49.7.2575-2582.2005] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Mark A Winters
- Division of Infectious Diseases and Geographic Medicine, Stanford University, 300 Pasteur Drive, Room S-146, Stanford, California 94305-5107, USA.
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Farrow MA, Somasundaran M, Zhang C, Gabuzda D, Sullivan JL, Greenough TC. Nuclear localization of HIV type 1 Vif isolated from a long-term asymptomatic individual and potential role in virus attenuation. AIDS Res Hum Retroviruses 2005; 21:565-74. [PMID: 15989462 DOI: 10.1089/aid.2005.21.565] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recent reports have determined that HIV-1 Vif counteracts an innate antiviral cellular factor, Apobec3G. However, the function of Vif during HIV-1 pathogenesis remains poorly understood. To gain a better understanding of Vif function, the viral isolate from an HIV-1-infected long-term nonprogressor (LTNP) that displayed a Vif-mutant replication phenotype was studied. This LTNP has been infected since before 1983 and has no HIV-related disease in the absence of antiretroviral therapy. From separate samples, obtained on more than one study visit, virus grew in cocultures of LTNP cells with Vif-complementing T cell lines, but not the parental T cell lines. An unusual amino acid motif (KKRK) was found in the Vif sequence at positions 90 to 93. Since this motif commonly functions as a nuclear localization sequence, experiments were performed to determine the ability of this KKRK motif to mediate nuclear localization of Vif. Wild-type Vif displayed a predominantly cytoplasmic distribution. In contrast, the KKRK Vif showed a predominantly nuclear localization. The effect of the KKRK mutation on virus production and infectivity was also studied. The KKRK motif that mislocalizes Vif to the nucleus also reduces viral replication and infectivity in nonpermissive cells. Our data highlight the importance of Vif in HIV-1 pathogenesis and also provide a unique tool to investigate the interaction of Vif and Apobec3G.
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Affiliation(s)
- Melissa A Farrow
- Program in Molecular Medicine and Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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36
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Kristbjörnsdóttir HB, Andrésdóttir V, Svansson V, Torsteinsdóttir S, Matthíasdóttir S, Andrésson OS. The vif gene of maedi-visna virus is essential for infectivity in vivo and in vitro. Virology 2004; 318:350-9. [PMID: 14972560 DOI: 10.1016/j.virol.2003.09.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2003] [Revised: 09/25/2003] [Accepted: 09/29/2003] [Indexed: 11/17/2022]
Abstract
We have investigated the role of vif in maedi-visna virus (MVV), a lentivirus of sheep, by studying in vitro replication of vif-deleted MVV in several cell types, and the effects of vif deletion on in vivo infection. By measuring RT activity, we found that in comparison to wild-type MVV, growth of vif-deleted MVV was similar in fetal ovine synovial (FOS) cells, highly attenuated in sheep choroid plexus (SCP) cells, and not detectable in macrophages, natural target cells of MVV. Productive infection by vif-deleted MVV could not be demonstrated in sheep. An increased mutation frequency was observed in DNA produced by endogenous reverse transcription of viral RNA in vif-deleted virions, indicating the existence of a factor comparable in action to human APOBEC3G. These results suggest that the vif gene of MVV is essential for infectivity and that the Vif protein protects the viral genome from enpackaged mutagenic activities.
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Papathanasopoulos MA, Patience T, Meyers TM, McCutchan FE, Morris L. Full-length genome characterization of HIV type 1 subtype C isolates from two slow-progressing perinatally infected siblings in South Africa. AIDS Res Hum Retroviruses 2003; 19:1033-7. [PMID: 14686322 DOI: 10.1089/088922203322588396] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Isolation and characterization of HIV-1 from asymptomatic, slow-progressing individuals are important in studying viral pathogenesis and facilitate the development of vaccines and antivirals. In this study we identified two slow-progressing HIV-1-infected siblings, isolated viruses, and sequenced the full-length genome, to identify virus attenuations that may contribute to their altered rate of disease progression. Proviral DNA from strains 99ZATM10 and 01ZATM45 was isolated from peripheral blood mononuclear cells (PBMC) coculture.Virtually full-length genomes and long terminal repeat (LTR) regions were polymerase chain reaction (PCR) amplified, sequenced, and assembled to generate the complete genomes. Phylogenetic analysis confirmed that both isolates were subtype C throughout their genome. Predicted amino acid sequence analysis for all the HIV-1 proteins showed that both viruses had open reading frames for all genes, and encoded proteins of the expected length, except for the rev gene. The 3' end of rev exon 2 did not have the 16-amino acid (aa) truncation characteristic of subtype C viruses, and in addition, had a three-aa extension (GlyCysCys). Rev is a necessary regulatory factor for HIV expression, and changes in the protein may affect viral replication. These results suggest that slower HIV disease progression in these children may be attributed, at least in part, to an altered Rev protein.
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Affiliation(s)
- M A Papathanasopoulos
- AIDS Virus Research Unit, National Institute of Communicable Diseases, Sandringham, Johannesburg, South Africa.
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Abstract
We propose that retroviruses exploit a cell-encoded pathway of intercellular vesicle traffic, exosome exchange, for both the biogenesis of retroviral particles and a low-efficiency but mechanistically important mode of infection. This Trojan exosome hypothesis reconciles current paradigms of retrovirus-directed transmission with the unique lipid composition of retroviral particles, the host cell proteins present in retroviral particles, the complex cell biology of retroviral release, and the ability of retroviruses to infect cells independently of Envelope protein-receptor interactions. An exosomal origin also predicts that retroviruses pose an unsolvable paradox for adaptive immune responses, that retroviral antigen vaccines are unlikely to provide prophylactic protection, and that alloimmunity is a central component of antiretroviral immunity. Finally, the Trojan exosome hypothesis has important implications for the fight against HIV and AIDS, including how to develop new antiretroviral therapies, assess the risk of retroviral infection, and generate effective antiretroviral vaccines.
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Affiliation(s)
- Stephen J Gould
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Abstract
Antiretroviral therapy, where available, has transformed HIV-1 disease into a treatable and somewhat chronic infection. This article summarizes the accomplishments thus far and what lies ahead in our struggle to improve the treatment of, and possibly eliminate, HIV-1 infection.
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Affiliation(s)
- Roger J Pomerantz
- Center for Human Virology and Biodefense, Division of Infectious Diseases and Environmental Medicine, Department of Medicine, Jefferson Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.
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