1
|
Lungu C, Overmars RJ, Grundeken E, Boers PHM, van der Ende ME, Mesplède T, Gruters RA. Genotypic and Phenotypic Characterization of Replication-Competent HIV-2 Isolated from Controllers and Progressors. Viruses 2023; 15:2236. [PMID: 38005913 PMCID: PMC10675771 DOI: 10.3390/v15112236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Although some individuals with HIV-2 develop severe immunodeficiency and AIDS-related complications, most may never progress to AIDS. Replication-competent HIV-2 isolated from asymptomatic long-term non-progressors (controllers) have lower replication rates than viruses from individuals who progress to AIDS (progressors). To investigate potential retroviral factors that correlate with disease progression in HIV-2, we sequenced the near full-length genomes of replication-competent viruses previously outgrown from controllers and progressors and used phylogeny to seek genotypic correlates of disease progression. We validated the integrity of all open reading frames and used cell-based assays to study the retroviral transcriptional activity of the long terminal repeats (LTRs) and Tat proteins of HIV-2 from controllers and progressors. Overall, we did not identify genotypic defects that may contribute to HIV-2 non-progression. Tat-induced, LTR-mediated transcription was comparable between viruses from controllers and progressors. Our results were obtained from a small number of participants and should be interpreted accordingly. Overall, they suggest that progression may be determined before or during integration of HIV-2.
Collapse
Affiliation(s)
- Cynthia Lungu
- Viroscience Department, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (C.L.); (R.J.O.); (E.G.); (P.H.M.B.)
| | - Ronald J. Overmars
- Viroscience Department, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (C.L.); (R.J.O.); (E.G.); (P.H.M.B.)
| | - Esmée Grundeken
- Viroscience Department, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (C.L.); (R.J.O.); (E.G.); (P.H.M.B.)
| | - Patrick H. M. Boers
- Viroscience Department, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (C.L.); (R.J.O.); (E.G.); (P.H.M.B.)
| | - Marchina E. van der Ende
- Department of Internal Medicine, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands;
| | - Thibault Mesplède
- Viroscience Department, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (C.L.); (R.J.O.); (E.G.); (P.H.M.B.)
| | - Rob A. Gruters
- Viroscience Department, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (C.L.); (R.J.O.); (E.G.); (P.H.M.B.)
| |
Collapse
|
2
|
Esbjörnsson J, Jansson M, Jespersen S, Månsson F, Hønge BL, Lindman J, Medina C, da Silva ZJ, Norrgren H, Medstrand P, Rowland-Jones SL, Wejse C. HIV-2 as a model to identify a functional HIV cure. AIDS Res Ther 2019; 16:24. [PMID: 31484562 PMCID: PMC6727498 DOI: 10.1186/s12981-019-0239-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/27/2019] [Indexed: 12/15/2022] Open
Abstract
Two HIV virus types exist: HIV-1 is pandemic and aggressive, whereas HIV-2 is confined mainly to West Africa and less pathogenic. Despite the fact that it has been almost 40 years since the discovery of AIDS, there is still no cure or vaccine against HIV. Consequently, the concepts of functional vaccines and cures that aim to limit HIV disease progression and spread by persistent control of viral replication without life-long treatment have been suggested as more feasible options to control the HIV pandemic. To identify virus-host mechanisms that could be targeted for functional cure development, researchers have focused on a small fraction of HIV-1 infected individuals that control their infection spontaneously, so-called elite controllers. However, these efforts have not been able to unravel the key mechanisms of the infection control. This is partly due to lack in statistical power since only 0.15% of HIV-1 infected individuals are natural elite controllers. The proportion of long-term viral control is larger in HIV-2 infection compared with HIV-1 infection. We therefore present the idea of using HIV-2 as a model for finding a functional cure against HIV. Understanding the key differences between HIV-1 and HIV-2 infections, and the cross-reactive effects in HIV-1/HIV-2 dual-infection could provide novel insights in developing functional HIV cures and vaccines.
Collapse
|
3
|
Prediction of HIV-1 and HIV-2 proteins by using Chou's pseudo amino acid compositions and different classifiers. Sci Rep 2018; 8:2359. [PMID: 29402983 PMCID: PMC5799304 DOI: 10.1038/s41598-018-20819-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/24/2018] [Indexed: 01/02/2023] Open
Abstract
Human immunodeficiency virus (HIV) is the retroviral agent that causes acquired immune deficiency syndrome (AIDS). The number of HIV caused deaths was about 4 million in 2016 alone; it was estimated that about 33 million to 46 million people worldwide living with HIV. The HIV disease is especially harmful because the progressive destruction of the immune system prevents the ability of forming specific antibodies and to maintain an efficacious killer T cell activity. Successful prediction of HIV protein has important significance for the biological and pharmacological functions. In this study, based on the concept of Chou’s pseudo amino acid (PseAA) composition and increment of diversity (ID), support vector machine (SVM), logisitic regression (LR), and multilayer perceptron (MP) were presented to predict HIV-1 proteins and HIV-2 proteins. The results of the jackknife test indicated that the highest prediction accuracy and CC values were obtained by the SVM and MP were 0.9909 and 0.9763, respectively, indicating that the classifiers presented in this study were suitable for predicting two groups of HIV proteins.
Collapse
|
4
|
Hollenbaugh JA, Montero C, Schinazi RF, Munger J, Kim B. Metabolic profiling during HIV-1 and HIV-2 infection of primary human monocyte-derived macrophages. Virology 2016; 491:106-14. [PMID: 26895248 DOI: 10.1016/j.virol.2016.01.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/26/2016] [Accepted: 01/29/2016] [Indexed: 12/14/2022]
Abstract
We evaluated cellular metabolism profiles of HIV-1 and HIV-2 infected primary human monocyte-derived macrophages (MDMs). First, HIV-2 GL-AN displays faster production kinetics and greater amounts of virus as compared to HIV-1s: YU-2, 89.6 and JR-CSF. Second, quantitative LC-MS/MS metabolomics analysis demonstrates very similar metabolic profiles in glycolysis and TCA cycle metabolic intermediates between HIV-1 and HIV-2 infected macrophages, with a few notable exceptions. The most striking metabolic change in MDMs infected with HIV-2 relative to HIV-1-infected MDMs was the increased levels of quinolinate, a metabolite in the tryptophan catabolism pathway that has been linked to HIV/AIDS pathogenesis. Third, both HIV-1 and HIV-2 infected MDMs showed elevated levels of ribose-5-phosphate, a key metabolic component in nucleotide biosynthesis. Finally, HIV-2 infected MDMs display increased dNTP concentrations as predicted by Vpx-mediated SAMHD1 degradation. Collectively, these data show differential metabolic changes during HIV-1 and HIV-2 infection of macrophages.
Collapse
Affiliation(s)
- Joseph A Hollenbaugh
- Center for Drug Discovery, Department of Pediatrics, Health Sciences Research Building, Emory University, 1760 Haygood Drive, Atlanta, GA 30322, USA
| | - Catherine Montero
- Center for Drug Discovery, Department of Pediatrics, Health Sciences Research Building, Emory University, 1760 Haygood Drive, Atlanta, GA 30322, USA
| | - Raymond F Schinazi
- Center for Drug Discovery, Department of Pediatrics, Health Sciences Research Building, Emory University, 1760 Haygood Drive, Atlanta, GA 30322, USA
| | - Joshua Munger
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14627, USA
| | - Baek Kim
- Center for Drug Discovery, Department of Pediatrics, Health Sciences Research Building, Emory University, 1760 Haygood Drive, Atlanta, GA 30322, USA; Department of Pharmacy, Kyung-Hee University, Seoul, South Korea; Children's Healthcare of Atlanta, Emory University, Atlanta, GA 30322, USA.
| |
Collapse
|
5
|
Menéndez-Arias L, Alvarez M. Antiretroviral therapy and drug resistance in human immunodeficiency virus type 2 infection. Antiviral Res 2013; 102:70-86. [PMID: 24345729 DOI: 10.1016/j.antiviral.2013.12.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 12/02/2013] [Accepted: 12/06/2013] [Indexed: 12/19/2022]
Abstract
One to two million people worldwide are infected with the human immunodeficiency virus type 2 (HIV-2), with highest prevalences in West African countries, but also present in Western Europe, Asia and North America. Compared to HIV-1, HIV-2 infection undergoes a longer asymptomatic phase and progresses to AIDS more slowly. In addition, HIV-2 shows lower transmission rates, probably due to its lower viremia in infected individuals. There is limited experience in the treatment of HIV-2 infection and several antiretroviral drugs used to fight HIV-1 are not effective against HIV-2. Effective drugs against HIV-2 include nucleoside analogue reverse transcriptase (RT) inhibitors (e.g. zidovudine, tenofovir, lamivudine, emtricitabine, abacavir, stavudine and didanosine), protease inhibitors (saquinavir, lopinavir and darunavir), and integrase inhibitors (raltegravir, elvitegravir and dolutegravir). Maraviroc, a CCR5 antagonist blocking coreceptor binding during HIV entry, is active in vitro against CCR5-tropic HIV-2 but more studies are needed to validate its use in therapeutic treatments against HIV-2 infection. HIV-2 strains are naturally resistant to a few antiretroviral drugs developed to suppress HIV-1 propagation such as nonnucleoside RT inhibitors, several protease inhibitors and the fusion inhibitor enfuvirtide. Resistance selection in HIV-2 appears to be faster than in HIV-1. In this scenario, the development of novel drugs specific for HIV-2 is an important priority. In this review, we discuss current anti-HIV-2 therapies and mutational pathways leading to drug resistance.
Collapse
Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Mar Alvarez
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
6
|
HIV-2 A-subtype gp125c₂-v₃-c₃ mutations and their association with CCR5 and CXCR4 tropism. Arch Virol 2011; 156:1943-51. [PMID: 21814863 DOI: 10.1007/s00705-011-1075-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 07/11/2011] [Indexed: 10/17/2022]
Abstract
The early events of the HIV replication cycle involve the interaction between viral envelope glycoproteins and their cellular CD4-chemokine (CCR5/CXCR4) receptor complex. In this study, for the first time, the HIV-2 A-subtype gp125(C2-V3-C3) mutations and their tropism association were characterized by analyzing 149 HIV-2 sequences from the Los Alamos database. The analysis has strengthened the importance of C2-V3-C3 region as a determinant factor for co-receptor selection. Moreover, statistically significant correlations were observed between C2-V3-C3 mutations, and several correlated mutations were associated with CXCR4 and CCR5 co-receptor usage. A dendrogram showed two distinct clusters, with numerous associated mutations grouped, thus dividing CCR5- and CXCR4-tropic viruses. Fourteen X4-tropic virus mutations, all in V3 and C3 domains and forming highly significant subclusters, were found. Finally, R5 associations, two strong subclusters were observed, grouping several C2-V3-C3 mutated positions. These data indicate the possible contribution of C2-V3-C3 mutational patterns in regulating HIV-2 tropism.
Collapse
|
7
|
Evolutionary and structural features of the C2, V3 and C3 envelope regions underlying the differences in HIV-1 and HIV-2 biology and infection. PLoS One 2011; 6:e14548. [PMID: 21283793 PMCID: PMC3024314 DOI: 10.1371/journal.pone.0014548] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 12/10/2010] [Indexed: 11/21/2022] Open
Abstract
Background Unlike in HIV-1 infection, the majority of HIV-2 patients produce broadly reactive neutralizing antibodies, control viral replication and survive as elite controllers. The identification of the molecular, structural and evolutionary footprints underlying these very distinct immunological and clinical outcomes may lead to the development of new strategies for the prevention and treatment of HIV infection. Methodology/Principal Findings We performed a side-by-side molecular, evolutionary and structural comparison of the C2, V3 and C3 envelope regions from HIV-1 and HIV-2. These regions contain major antigenic targets and are important for receptor binding. In HIV-2, these regions also have immune modulatory properties. We found that these regions are significantly more variable in HIV-1 than in HIV-2. Within each virus, C3 is the most entropic region followed by either C2 (HIV-2) or V3 (HIV-1). The C3 region is well exposed in the HIV-2 envelope and is under strong diversifying selection suggesting that, like in HIV-1, it may harbour neutralizing epitopes. Notably, however, extreme diversification of C2 and C3 seems to be deleterious for HIV-2 and prevent its transmission. Computer modelling simulations showed that in HIV-2 the V3 loop is much less exposed than C2 and C3 and has a retractile conformation due to a physical interaction with both C2 and C3. The concealed and conserved nature of V3 in the HIV-2 is consistent with its lack of immunodominancy in vivo and with its role in preventing immune activation. In contrast, HIV-1 had an extended and accessible V3 loop that is consistent with its immunodominant and neutralizing nature. Conclusions/Significance We identify significant structural and functional constrains to the diversification and evolution of C2, V3 and C3 in the HIV-2 envelope but not in HIV-1. These studies highlight fundamental differences in the biology and infection of HIV-1 and HIV-2 and in their mode of interaction with the human immune system and may inform new vaccine and therapeutic interventions against these viruses.
Collapse
|
8
|
Envelope-specific antibody response in HIV-2 infection: C2V3C3-specific IgG response is associated with disease progression. AIDS 2008; 22:2257-65. [PMID: 18981765 DOI: 10.1097/qad.0b013e3283155546] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
OBJECTIVE To examine the unspecific and envelope-specific IgA and IgG responses in acute and chronic HIV-2 infection. METHODS Twenty-eight chronically infected adults and two children with perinatal infection were studied. Total plasma concentrations of IgA and IgG were determined by nephelometry. IgA and IgG reactivity against the immunodominant region in gp36 and the C2V3C3 region in gp125 was tested with the enzyme-linked immunosorbent assay (ELISA)-HIV-2 assay. Clonal sequences of the C2V3C3 env region were obtained for most patients. RESULTS Total plasma IgG concentration, but not IgA, was significantly higher than normal in HIV-2 patients and correlated inversely with CD4 T-cell counts. Seroconversion to gp36 occurred during the first year of life in both infants. The infant with rapid disease progression did not elicit C2V3C3-specific antibodies. Most chronically infected patients produced plasma IgG1, IgG3 and IgA antibodies against gp36 and C2V3C3. Lack of C2V3C3-specific IgG response in two patients was associated with a major antigenic change in the V3 region. In longitudinal analysis, there was a significant inverse association between the C2V3C3-specific IgG antibody response and the number of CD4 T cells. CONCLUSION HIV-2 promotes an early, strong and broad gp36 and C2V3C3-specific IgG and IgA response. Increase in the IgG response against the envelope C2V3C3 region is associated with increased loss of CD4 T cells in chronically infected patients. These results provide further support for the immune protective role of the C2V3C3 envelope region during HIV-2 infection and have direct implications for HIV-2 diagnosis, clinical management and pathogenesis.
Collapse
|
9
|
de Silva TI, Cotten M, Rowland-Jones SL. HIV-2: the forgotten AIDS virus. Trends Microbiol 2008; 16:588-95. [PMID: 18964021 DOI: 10.1016/j.tim.2008.09.003] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 09/16/2008] [Accepted: 09/18/2008] [Indexed: 10/21/2022]
Abstract
HIV type 2 (HIV-2), a closely related retrovirus discovered a few years after HIV type 1, causes AIDS in only a minority of infected individuals. Determining why HIV-2 causes asymptomatic infection in most patients could further our understanding of HIV immunopathogenesis. Studies to date have suggested that both enhanced immune responses and lower viral replication could play a role. We summarize the important findings to date and highlight areas that warrant further exploration.
Collapse
Affiliation(s)
- Thushan I de Silva
- Medical Research Council Laboratories, Atlantic Road, PO Box 273, Fajara, The Gambia, West Africa.
| | | | | |
Collapse
|