1
|
Saag M. Wonder of wonders, miracle of miracles: the unprecedented speed of COVID-19 science. Physiol Rev 2022; 102:1569-1577. [PMID: 35446679 PMCID: PMC9169823 DOI: 10.1152/physrev.00010.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 12/15/2022] Open
Affiliation(s)
- Michael Saag
- University of Alabama at Birmingham, Birmingham, Alabama
| |
Collapse
|
2
|
Lorenzo-Redondo R, Ozer EA, Achenbach CJ, D'Aquila RT, Hultquist JF. Molecular epidemiology in the HIV and SARS-CoV-2 pandemics. Curr Opin HIV AIDS 2021; 16:11-24. [PMID: 33186230 PMCID: PMC7723008 DOI: 10.1097/coh.0000000000000660] [Citation(s) in RCA: 3] [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] [Indexed: 12/20/2022]
Abstract
PURPOSE OF REVIEW The aim of this review was to compare and contrast the application of molecular epidemiology approaches for the improved management and understanding of the HIV versus SARS-CoV-2 epidemics. RECENT FINDINGS Molecular biology approaches, including PCR and whole genome sequencing (WGS), have become powerful tools for epidemiological investigation. PCR approaches form the basis for many high-sensitivity diagnostic tests and can supplement traditional contact tracing and surveillance strategies to define risk networks and transmission patterns. WGS approaches can further define the causative agents of disease, trace the origins of the pathogen, and clarify routes of transmission. When coupled with clinical datasets, such as electronic medical record data, these approaches can investigate co-correlates of disease and pathogenesis. In the ongoing HIV epidemic, these approaches have been effectively deployed to identify treatment gaps, transmission clusters and risk factors, though significant barriers to rapid or real-time implementation remain critical to overcome. Likewise, these approaches have been successful in addressing some questions of SARS-CoV-2 transmission and pathogenesis, but the nature and rapid spread of the virus have posed additional challenges. SUMMARY Overall, molecular epidemiology approaches offer unique advantages and challenges that complement traditional epidemiological tools for the improved understanding and management of epidemics.
Collapse
Affiliation(s)
- Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | | | | | | | | |
Collapse
|
3
|
Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing. mSphere 2020; 5:5/5/e00551-20. [PMID: 33055255 PMCID: PMC7565892 DOI: 10.1128/msphere.00551-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The highly recombinogenic nature of human immunodeficiency virus type 1 (HIV-1) leads to recombination and emergence of quasispecies. It is important to reliably identify subpopulations to understand the complexity of a viral population for drug resistance surveillance and vaccine development. High-throughput sequencing (HTS) provides improved resolution over Sanger sequencing for the analysis of heterogeneous viral subpopulations. However, current methods of analysis of HTS reads are unable to fully address accurate population reconstruction. Hence, there is a dire need for a more sensitive, accurate, user-friendly, and cost-effective method to analyze viral quasispecies. For this purpose, we have improved the HIVE-hexahedron algorithm that we previously developed with in silico short sequences to analyze raw HTS short reads. The significance of this study is that our standalone algorithm enables a streamlined analysis of quasispecies, subtype, and recombination patterns from long HIV-1 genome regions without the need of additional sequence analysis tools. Distinct viral populations and recombination patterns identified by HIVE-hexahedron are further validated by comparison with sequences obtained by single genome sequencing (SGS). High-throughput sequencing (HTS) has been widely used to characterize HIV-1 genome sequences. There are no algorithms currently that can directly determine genotype and quasispecies population using short HTS reads generated from long genome sequences without additional software. To establish a robust subpopulation, subtype, and recombination analysis workflow, we amplified the HIV-1 3′-half genome from plasma samples of 65 HIV-1-infected individuals and sequenced the entire amplicon (∼4,500 bp) by HTS. With direct analysis of raw reads using HIVE-hexahedron, we showed that 48% of samples harbored 2 to 13 subpopulations. We identified various subtypes (17 A1s, 4 Bs, 27 Cs, 6 CRF02_AGs, and 11 unique recombinant forms) and defined recombinant breakpoints of 10 recombinants. These results were validated with viral genome sequences generated by single genome sequencing (SGS) or the analysis of consensus sequence of the HTS reads. The HIVE-hexahedron workflow is more sensitive and accurate than just evaluating the consensus sequence and also more cost-effective than SGS. IMPORTANCE The highly recombinogenic nature of human immunodeficiency virus type 1 (HIV-1) leads to recombination and emergence of quasispecies. It is important to reliably identify subpopulations to understand the complexity of a viral population for drug resistance surveillance and vaccine development. High-throughput sequencing (HTS) provides improved resolution over Sanger sequencing for the analysis of heterogeneous viral subpopulations. However, current methods of analysis of HTS reads are unable to fully address accurate population reconstruction. Hence, there is a dire need for a more sensitive, accurate, user-friendly, and cost-effective method to analyze viral quasispecies. For this purpose, we have improved the HIVE-hexahedron algorithm that we previously developed with in silico short sequences to analyze raw HTS short reads. The significance of this study is that our standalone algorithm enables a streamlined analysis of quasispecies, subtype, and recombination patterns from long HIV-1 genome regions without the need of additional sequence analysis tools. Distinct viral populations and recombination patterns identified by HIVE-hexahedron are further validated by comparison with sequences obtained by single genome sequencing (SGS).
Collapse
|
4
|
The Determination of HIV-1 RT Mutation Rate, Its Possible Allosteric Effects, and Its Implications on Drug Resistance. Viruses 2020; 12:v12030297. [PMID: 32182845 PMCID: PMC7150816 DOI: 10.3390/v12030297] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 12/31/2022] Open
Abstract
The high mutation rate of the human immunodeficiency virus type 1 (HIV-1) plays a major role in treatment resistance, from the development of vaccines to therapeutic drugs. In addressing the crux of the issue, various attempts to estimate the mutation rate of HIV-1 resulted in a large range of 10−5–10−3 errors/bp/cycle due to the use of different types of investigation methods. In this review, we discuss the different assay methods, their findings on the mutation rates of HIV-1 and how the locations of mutations can be further analyzed for their allosteric effects to allow for new inhibitor designs. Given that HIV is one of the fastest mutating viruses, it serves as a good model for the comprehensive study of viral mutations that can give rise to a more horizontal understanding towards overall viral drug resistance as well as emerging viral diseases.
Collapse
|
5
|
Ray K, Mengistu M, Orlandi C, Pazgier M, Lewis GK, DeVico AL. Concurrent Exposure of Neutralizing and Non-neutralizing Epitopes on a Single HIV-1 Envelope Structure. Front Immunol 2019; 10:1512. [PMID: 31338095 PMCID: PMC6628914 DOI: 10.3389/fimmu.2019.01512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 01/14/2023] Open
Abstract
The trimeric envelope spikes on the HIV-1 virus surface initiate infection and comprise key targets for antiviral humoral responses. Circulating virions variably present intact envelope spikes, which react with neutralizing antibodies; and altered envelope structures, which bind non-neutralizing antibodies. Once bound, either type of antibody can enable humoral effector mechanisms with the potential to control HIV-1 infection in vivo. However, it is not clear how the presentation of neutralizing vs. non-neutralizing epitopes defines distinct virus populations and/or envelope structures on single particles. Here we used single-virion fluorescence correlation spectroscopy (FCS), fluorescence resonance energy transfer (FRET), and two-color coincidence FCS approaches to examine whether neutralizing and non-neutralizing antibodies are presented by the same envelope structure. Given the spatial requirements for donor-acceptor energy transfer (≤10 nm), FRET signals generated by paired neutralizing and non-neutralizing fluorescent Fabs should occur via proximal binding to the same target antigen. Fluorescent-labeled Fabs of the neutralizing anti-gp120 antibodies 2G12 and b12 were combined with Fabs of the non-neutralizing anti-gp41 antibody F240, previously thought to mainly bind gp41 "stumps." We find that both 2G12-F240 and/or b12-F240 Fab combinations generate FRET signals on multiple types of virions in solution. FRET efficiencies position the neutralizing and non-neutralizing epitopes between 7.1 and 7.8 nm apart; potentially fitting within the spatial dimensions of a single trimer-derived structure. Further, the frequency of FRET detection suggests that at least one of such structures occurs on the majority of particles in a virus population. Thus, there is frequent, overlapping presentation of non-neutralizing and neutralizing epitope on freely circulating HIV-1 surfaces. Such information provides a broader perspective of how anti-HIV humoral immunity interfaces with circulating virions.
Collapse
Affiliation(s)
- Krishanu Ray
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, United States,*Correspondence: Krishanu Ray
| | - Meron Mengistu
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Chiara Orlandi
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Marzena Pazgier
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - George K. Lewis
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Anthony L. DeVico
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| |
Collapse
|
6
|
Tolbert WD, Sherburn RT, Van V, Pazgier M. Structural Basis for Epitopes in the gp120 Cluster A Region that Invokes Potent Effector Cell Activity. Viruses 2019; 11:v11010069. [PMID: 30654465 PMCID: PMC6357199 DOI: 10.3390/v11010069] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 12/28/2022] Open
Abstract
While a number of therapeutic options to control the progression of human immunodeficiency virus (HIV-1) now exist, a broadly effective preventive vaccine is still not available. Through detailed structural analysis of antibodies able to induce potent effector cell activity, a number of Env epitopes have been identified which have the potential to be considered vaccine candidates. These antibodies mainly target the gp120 Cluster A region which is only exposed upon viral binding to the target cell with epitopes becoming available for antibody binding during viral entry and fusion and, therefore, after the effective window for neutralizing antibody activity. This review will discuss recent advances in the structural characterization of these important targets with a special focus on epitopes that are involved in Fc-mediated effector function without direct viral neutralizing activities.
Collapse
Affiliation(s)
- William D Tolbert
- Infectious Diseases Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
| | - Rebekah T Sherburn
- Infectious Diseases Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
| | - Verna Van
- Department of Biochemistry and Molecular Biology of University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Marzena Pazgier
- Infectious Diseases Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
| |
Collapse
|
7
|
Abstract
Chemoprophylaxis may be a prevention strategy for the sexual transmission of human immunodeficiency virus (HIV). Evidence suggests that condom use has waned with the availability of antiretroviral medication, at least in some resource-rich settings. Barrier methods of HIV prevention have inherent problems, and the potential for failure. Microbicide research has focused primarily on male-to-female transmission. Analogous to post-exposure prophylaxis, HIV prevention may be achieved by pre-exposure prophylaxis in some settings. Research in this potential strategy may be rewarding.
Collapse
Affiliation(s)
- Mike Youle
- Royal Free Centre for HIV Medicine, Royal Free Hospital, Pond Street, London NW3 2QG.
| | | |
Collapse
|
8
|
DiClemente RJ. The Emergence of Adolescents as a Risk Group for Human Immunodeficiency Virus Infection. JOURNAL OF ADOLESCENT RESEARCH 2016. [DOI: 10.1177/074355489051003] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Adolesceents have only recently been identified as a risk group for human immunodeficiencv, virus inifectioni. Limited data suggest that the prevalence of HIV infection among selected adolescent populatiotns is considerable. These data, however, are not generalizable because of the unrepresentative nature of the adolescent populations studied. Surrogate epidemiologic markers for projecting the potential spread of HIV in the adolescent populationi are idenitified. These markers include the prevalence of contraceptive behavior, rate of untinttetided pregnancy, and the prevalence of sexually transmitted diseases. Adolescetits kniowledge, attitudes, atid clanges in AIDS-preventive behavior are described. Psychosocial factors that may influence the adoption and maintenance of AIDS-prev entitie behav iors are identified and discussed. To increase the potentialfor developing the most effective HIV prevention programs, there is a need for greater understanding of the psxychosocial determinants motivating behavior change among adolescents.
Collapse
|
9
|
Schols D, Pauwels R, Witvrouw M, Desmyter J, De Clercq E. Differential Activity of Polyanionic Compounds and Castanospermine against HIV Replication and HIV-Induced Syncytium Formation Depending on Virus Strain and Cell Type. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029200300104] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Polyanionic compounds [i.e. pentosan polysulphate, dextran sulphate, heparin, suramin, and aurintricarboxylic acid (ATA)] and castanospermine were examined for their inhibitory effect on human immunodeficiency virus (HIV) strains (HIV-1IIIB, HIV-1RF, HIV-2ROD and HIV-2EHO) in two different assays (HIV cytopathicity in MT-4 cells and HIV antigen expression in CEM cells). In the MT-4 assay dextran sulphate and pentosan polysulphate were more active against HIV-2ROD, suramin was more active against HIV-1RF, and ATA more active against HIV-2EHO-Heparin was less, but castanospermine was more, active against the two HIV-2 strains. In the CEM assay dextran sulphate and suramin were equally active against all HIV strains, pentosan polysulphate was more active against both HIV-2 strains, whereas heparin was less active against HIV-2ROD and ATA again was more active against HIV-2EHO. The compounds and soluble CD4 (sCD4) were also tested in the HIV-induced syncytium formation assay, where chronically infected HUT-78 cells were mixed with uninfected MOLT-4 or CEM cells. The inhibitory effect of suramin and ATA on syncytium formation was independent of the virus strain or cell type. For dextran sulphate and pentosan polysulphate, it was dependent on virus strain, and for heparin, castanospermine, and sCD4, it was dependent on both the virus strain and cell type.
Collapse
Affiliation(s)
- D. Schols
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - R. Pauwels
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - M. Witvrouw
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - J. Desmyter
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - E. De Clercq
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| |
Collapse
|
10
|
Medeiros SDO, Abreu CM, Delvecchio R, Ribeiro AP, Vasconcelos Z, Brindeiro RDM, Tanuri A. Follow-up on long-term antiretroviral therapy for cats infected with feline immunodeficiency virus. J Feline Med Surg 2015; 18:264-72. [PMID: 25855689 DOI: 10.1177/1098612x15580144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVES Feline immunodeficiency virus (FIV) is a lentivirus that induces AIDS-like disease in cats. Some of the antiretroviral drugs available to treat patients with HIV type 1 are used to treat FIV-infected cats; however, antiretroviral therapy (ART) is not used in cats as a long-term treatment. In this study, the effects of long-term ART were evaluated in domestic cats treated initially with the nucleoside transcriptase reverse inhibitor (NTRI) zidovudine (AZT) over a period ranging from 5-6 years, followed by a regimen of the NTRI lamivudine (3TC) plus AZT over 3 years. METHODS Viral load, sequencing of pol (reverse transcriptase [RT]) region and CD4:CD8 lymphocyte ratio were evaluated during and after treatment. Untreated cats were evaluated as a control group. RESULTS CD4:CD8 ratios were lower, and uncharacterized resistance mutations were found in the RT region in the group of treated cats. A slight increase in viral load was observed in some cats after discontinuing treatment. CONCLUSIONS AND RELEVANCE The data strongly suggest that treated cats were resistant to therapy, and uncharacterized resistance mutations in the RT gene of FIV were selected for by AZT. Few studies have been conducted to evaluate the effect of long-term antiretroviral therapy in cats. To date, resistance mutations have not been described in vivo.
Collapse
Affiliation(s)
- Sheila de Oliveira Medeiros
- Laboratory of Molecular Virology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Celina Monteiro Abreu
- Laboratory of Molecular Virology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rodrigo Delvecchio
- Laboratory of Molecular Virology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Rodrigo de Moraes Brindeiro
- Laboratory of Molecular Virology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amilcar Tanuri
- Laboratory of Molecular Virology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
11
|
Mestecky J, Wei Q, Alexander R, Raska M, Novak J, Moldoveanu Z. Humoral immune responses to HIV in the mucosal secretions and sera of HIV-infected women. Am J Reprod Immunol 2014; 71:600-7. [PMID: 24494997 PMCID: PMC4024328 DOI: 10.1111/aji.12203] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 12/17/2013] [Indexed: 12/16/2022] Open
Abstract
Although sera and all external secretions contain antibodies to human immunodeficiency virus (HIV), their levels, specificity, isotypes, and relevant effector functions display a great degree of variability. Antibodies that bind HIV antigens and neutralize the virus are predominantly associated with the IgG isotype in sera and in all external secretions, even where total levels of IgG are much lower than those of IgA. Rectal fluid that contains high IgA, but low IgG levels, displayed low neutralizing activity independent of antibodies. Therefore, external secretions should be evaluated before and after selective depletion of Ig. At the systemic level, HIV-specific IgA may interfere with the effector functions of IgG, as suggested by recent studies of individuals systemically immunized with an experimental HIV vaccine. Although HIV-specific IgG and IgA antibodies may exhibit their protective activities at mucosal surfaces through interference with viral entry and local neutralization at the systemic level, such antibodies may display discordant effector functions.
Collapse
Affiliation(s)
- Jiri Mestecky
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
- Institute of Immunology and Microbiology, Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Qing Wei
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rashada Alexander
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
- Office of the Director, National Institutes of Health, Bethesda, MD
| | - Milan Raska
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Immunology, Faculty of Medicine, Palacky University, Olomouc, Czech Republic
| | - Jan Novak
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Zina Moldoveanu
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| |
Collapse
|
12
|
Epstein-Barr virus latent membrane protein 1 genetic variability in peripheral blood B cells and oropharyngeal fluids. J Virol 2014; 88:3744-55. [PMID: 24429365 DOI: 10.1128/jvi.03378-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED We report the diversity of latent membrane protein 1 (LMP1) gene founder sequences and the level of Epstein-Barr virus (EBV) genome variability over time and across anatomic compartments by using virus genomes amplified directly from oropharyngeal wash specimens and peripheral blood B cells during acute infection and convalescence. The intrahost nucleotide variability of the founder virus was 0.02% across the region sequences, and diversity increased significantly over time in the oropharyngeal compartment (P = 0.004). The LMP1 region showing the greatest level of variability in both compartments, and over time, was concentrated within the functional carboxyl-terminal activating regions 2 and 3 (CTAR2 and CTAR3). Interestingly, a deletion in a proline-rich repeat region (amino acids 274 to 289) of EBV commonly reported in EBV sequenced from cancer specimens was not observed in acute infectious mononucleosis (AIM) patients. Taken together, these data highlight the diversity in circulating EBV genomes and its potential importance in disease pathogenesis and vaccine design. IMPORTANCE This study is among the first to leverage an improved high-throughput deep-sequencing methodology to investigate directly from patient samples the degree of diversity in Epstein-Barr virus (EBV) populations and the extent to which viral genome diversity develops over time in the infected host. Significant variability of circulating EBV latent membrane protein 1 (LMP1) gene sequences was observed between cellular and oral wash samples, and this variability increased over time in oral wash samples. The significance of EBV genetic diversity in transmission and disease pathogenesis are discussed.
Collapse
|
13
|
Small ruminant lentiviruses: genetic variability, tropism and diagnosis. Viruses 2013; 5:1175-207. [PMID: 23611847 PMCID: PMC3705272 DOI: 10.3390/v5041175] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 04/09/2013] [Accepted: 04/12/2013] [Indexed: 02/05/2023] Open
Abstract
Small ruminant lentiviruses (SRLV) cause a multisystemic chronic disease affecting animal production and welfare. SRLV infections are spread across the world with the exception of Iceland. Success in controlling SRLV spread depends largely on the use of appropriate diagnostic tools, but the existence of a high genetic/antigenic variability among these viruses, the fluctuant levels of antibody against them and the low viral loads found in infected individuals hamper the diagnostic efficacy. SRLV have a marked in vivo tropism towards the monocyte/macrophage lineage and attempts have been made to identify the genome regions involved in tropism, with two main candidates, the LTR and env gene, since LTR contains primer binding sites for viral replication and the env-encoded protein (SU ENV), which mediates the binding of the virus to the host’s cell and has hypervariable regions to escape the humoral immune response. Once inside the host cell, innate immunity may interfere with SRLV replication, but the virus develops counteraction mechanisms to escape, multiply and survive, creating a quasi-species and undergoing compartmentalization events. So far, the mechanisms of organ tropism involved in the development of different disease forms (neurological, arthritic, pulmonary and mammary) are unknown, but different alternatives are proposed. This is an overview of the current state of knowledge on SRLV genetic variability and its implications in tropism as well as in the development of alternative diagnostic assays.
Collapse
|
14
|
Haaland RE, Sullivan ST, Evans-Strickfaden T, Lennox JL, Hart CE. Female genital tract shedding of CXCR4-tropic HIV Type 1 is associated with a majority population of CXCR4-tropic HIV Type 1 in blood and declining CD4(+) cell counts. AIDS Res Hum Retroviruses 2012; 28:1524-32. [PMID: 22369497 PMCID: PMC5555632 DOI: 10.1089/aid.2012.0004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study compared HIV-1 genotypes shed over time (≤3.5 years) in the vaginal secretions (VS) and blood plasma (BP) of 15 chronically infected women. Analysis of predicted coreceptor tropism (CCR5=R5, CXCR4=X4) for quasispecies shedding revealed three patterns: (1) viral quasispecies shed in both VS and BP were restricted to R5-tropism at all time points, (2) quasispecies shed in VS were restricted to R5-tropism at all time points but X4 quasispecies were identified in the BP at one or more time points, and (3) quasispecies shed in matched VS and BP both contained X4-tropic viruses. Overall, the frequency of X4 quasispecies circulation in VS was 2-fold less than in BP and detection of X4 virus in VS was more likely to occur when X4 quasispecies comprised more than 50% of BP viruses (p=0.01) and when declines in blood CD4(+) lymphocyte levels were the greatest (p=0.038). Additionally, the mean number of predicted N-glycosylation sites between matched VS and BP samples was strongly correlated (r=0.86, p<0.0001) with glycosylation densities in the following order (VS R5=BP R5 > BP X4 > VS X4). The X4 glycosylation densities may result from compartmentalization pressures in the female genital tract or the delayed appearance of these viruses in VS. Our results suggest that the presence of X4 virus in VS is associated with a threshold population of X4 quasispecies in BP, which are increasing during the HIV-induced failure of the human immune system.
Collapse
Affiliation(s)
- Richard E Haaland
- Laboratory Branch, Division of HIV and AIDS Prevention, National Center for HIV, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, Georgia 30333, USA.
| | | | | | | | | |
Collapse
|
15
|
Saidi H, Jenabian MA, Belec L. Understanding factors that modulate HIV infection at the female genital tract mucosae for the rationale design of microbicides. AIDS Res Hum Retroviruses 2012; 28:1485-97. [PMID: 22867060 DOI: 10.1089/aid.2012.0049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Women are now becoming the pivot of the epidemiological spread of HIV infection worldwide, especially in developing countries. Therefore, research to develop an efficient microbicide is now a priority for the prevention of HIV-1 acquisition in exposed women. However, recent disappointing failures in microbicide clinical trials revealed major gaps in basic and applied knowledge that hinder the development of effective microbicide formulations. Indeed, the inhibitory power of microbicide molecules may be affected by several physiological and immunological factors present in male and female genital tracts. Furthermore, mucosal crossing of HIV-1 to increase the ability to reach the submucosal target cells (macrophages, lymphocytes, and dendritic cells) may be modulated by supraepithelial factors such as seminal complement components (opsonized HIV-1), by epithelial factors released in the submucosal microenvironment such as antimicrobial soluble factors, cytokines, and chemokines, and by potent intraepithelial and submucosal innate immunity. The design of vaginal microbicide formulations should take into account an understanding of the intimate mechanisms involved in the crossing of HIV through the female genital mucosae, in the context of a mixture of both male and female genital fluids.
Collapse
Affiliation(s)
- Hela Saidi
- Division of Immuno-Virology, Institute of Emerging Diseases and Innovative Therapies, Commissariat à l'Energie Atomique, Fontenay-aux-Roses, France
| | - Mohammad-Ali Jenabian
- Chronic Viral Illnesses Service of the McGill University Health Centre, and Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Laurent Belec
- Assistance Publique–Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Laboratoire de Virologie, and Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| |
Collapse
|
16
|
Preventing the formation of positive transcription elongation factor b by human cyclin T1-binding RNA aptamer for anti-HIV transcription. AIDS 2012; 26:1599-605. [PMID: 22569018 DOI: 10.1097/qad.0b013e3283554f7d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Development of an innovative antitranscriptional technique for HIV. DESIGN Systematic evolution of ligands by exponential enrichment (SELEX) technique that can characterize target-specific aptamer was employed to synthesize an aptamer that binds human cyclin T1 (CycT1). When CycT1-binding aptamer interferes the binding of cyclin-dependent kinase 9 (Cdk9) to CycT1, HIV transcription is likely to be discouraged. METHODS Throughout SELEX steps, RNA aptamers having high specific affinity toward CycT1 were characterized. The binding interaction between selected aptamers and CycT1 was analyzed via various techniques. RESULTS Both qualitative and quantitative analyses revealed Apt4 aptamer, among four candidates, has the highest specific affinity to CycT1. In the presence of Apt4, Cdk9 protein was unable to make interaction with CycT1. CONCLUSION A specific RNA aptamer that identifies and binds to CycT1 with high affinity was successfully characterized. As CycT1 plays an important role in HIV transcription, this novel method that interferes and inhibits the transcription of HIV has the potential of being exploited in extended research fields, such as clinical therapy.
Collapse
|
17
|
Beloukas A, Magiorkinis E, Magiorkinis G, Zavitsanou A, Karamitros T, Hatzakis A, Paraskevis D. Assessment of phylogenetic sensitivity for reconstructing HIV-1 epidemiological relationships. Virus Res 2012; 166:54-60. [DOI: 10.1016/j.virusres.2012.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Revised: 03/02/2012] [Accepted: 03/04/2012] [Indexed: 12/27/2022]
|
18
|
De Crignis E, Guglietta S, Foley BT, Negroni M, Di Narzo AF, Waelti Da Costa V, Cavassini M, Bart PA, Pantaleo G, Graziosi C. Nonrandom distribution of cryptic repeating triplets of purines and pyrimidines (RNY)(n) in gp120 of HIV Type1. AIDS Res Hum Retroviruses 2012; 28:493-504. [PMID: 21902591 DOI: 10.1089/aid.2011.0208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have analyzed purine (R) and pyrimidine (Y) codon patterns in variable and constant regions of HIV-1 gp120 in seven patients infected with different HIV-1 subtypes and naive to antiretroviral therapy. We have calculated the relative frequency of each in-frame codon RNY, YNR, RNR, and YNY (N=any nucleotide) in variable and constant regions of gp120, in the sequence within indels and at indels' flanking sites. Our data show that hypervariable regions V1, V2, V4, and V5 are characterized by the presence of long stretches of RNY codons constituting the majority of the sequence portion within insertions/deletions. In full-length gp120 and within inserted/deleted fragments the number of AVT (V=A, C, G) codons did not exceed 50% of the total RNY codons. RNY strings in variable regions spanned up to 21 codons and were always in frame. In contrast, RNY strings in constant regions were mostly out of frame and their length was limited to five codons. The frequency of the codon RNY was found to be significantly higher in variable regions (p<0.0001; t-test), within indels, and at indels' flanking sites (p<0.0001; χ(2) test). Analysis of the distribution of RNY strings equal to or longer than five codons in the full genome of HXB2 also shows that these sequences are mostly out of frame, unless they contain a potential N-glycosylation site or an asparagine. These data suggest that cryptic repeats of RNY may play a role in the genesis of multiple base insertions and deletions in hypervariable regions of gp120.
Collapse
Affiliation(s)
- Elisa De Crignis
- Laboratory of AIDS Immunopathogenesis, Division of Immunology and Allergy, Department of Medicine, CHUV, Lausanne, Switzerland
| | - Silvia Guglietta
- Laboratory of AIDS Immunopathogenesis, Division of Immunology and Allergy, Department of Medicine, CHUV, Lausanne, Switzerland
| | - Brian T. Foley
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratories, Los Alamos, New Mexico
| | - Matteo Negroni
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | | | | | - Matthias Cavassini
- Division of Infectious Diseases, Department of Medicine, CHUV, Lausanne, Switzerland
| | - Pierre-Alexandre Bart
- Laboratory of AIDS Immunopathogenesis, Division of Immunology and Allergy, Department of Medicine, CHUV, Lausanne, Switzerland
| | - Giuseppe Pantaleo
- Laboratory of AIDS Immunopathogenesis, Division of Immunology and Allergy, Department of Medicine, CHUV, Lausanne, Switzerland
| | - Cecilia Graziosi
- Laboratory of AIDS Immunopathogenesis, Division of Immunology and Allergy, Department of Medicine, CHUV, Lausanne, Switzerland
| |
Collapse
|
19
|
Wilen CB, Tilton JC, Doms RW. Molecular mechanisms of HIV entry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 726:223-42. [PMID: 22297516 DOI: 10.1007/978-1-4614-0980-9_10] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human immunodeficiency virus (HIV) entry is a complex and intricate process that facilitates delivery of the viral genome to the host cell. The only viral surface protein, Envelope (Env), is composed of a trimer of gp120 and gp41 heterodimers. It is essentially a fusion machine cloaked in a shroud of carbohydrate structures and variable loops of amino acids that enable it to evade the humoral immune response. For entry to occur gp120 sequentially engages the host protein CD4 and then one of two chemokine coreceptors, either CCR5 or CXCR4. CD4 binding facilitates exposure and formation of the coreceptor-binding site, and coreceptor binding then triggers the membrane fusion machinery in the gp41 subunit. Our understanding of HIV entry has led to the development of successful small molecule inhibitors for the clinical treatment of HIV infection as well as insights into viral tropism and pathogenesis.
Collapse
Affiliation(s)
- Craig B Wilen
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | |
Collapse
|
20
|
Wainberg MA, Moisi D, Oliveira M, Toni TD, Brenner BG. Transmission dynamics of the M184V drug resistance mutation in primary HIV infection. J Antimicrob Chemother 2011; 66:2346-9. [PMID: 21750100 DOI: 10.1093/jac/dkr291] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES M184V in HIV-1 reverse transcriptase is among the most common mutations in patients failing antiretroviral therapy but is found only rarely in cases of transmitted drug resistance. METHODS To investigate this apparent paradox, we developed an allele-specific real-time PCR (AS-PCR) assay to determine the transmission of M184V in newly infected individuals. RESULTS M184V transmission may occur to a greater extent than previously thought. Persistence of M184V may commonly involve linkage to other drug resistance mutations. The presence of M184V as a single substitution in newly infected individuals was shown to wane over time, as a likely consequence of reversion and overgrowth by more fit wild-type viruses. CONCLUSIONS The M184V mutation can be documented in newly infected individuals, and the alternative hypothesis that this substitution might impact on the ability of HIV to be transmitted is unfounded.
Collapse
Affiliation(s)
- Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada.
| | | | | | | | | |
Collapse
|
21
|
Bixby JG, Laur O, Johnson WE, Desrosiers RC. Diversity of envelope genes from an uncloned stock of SIVmac251. AIDS Res Hum Retroviruses 2010; 26:1115-31. [PMID: 20836705 DOI: 10.1089/aid.2010.0029] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
AIDS vaccine and pathogenesis research will benefit from a more diverse array of cloned SIV challenge stocks from which to choose. Toward this end, 20 envelope genes were cloned from an extensively used, primary stock of uncloned SIVmac251. Each of the 20 clones had a unique sequence. Their translated sequences differed by as many as 26 amino acids from one another and by as many as 45 amino acids from the commonly used clone SIVmac239. Envelope sequences up to and including the membrane-spanning domain were exchanged into the infectious pathogenic SIVmac239 clone and virus stocks were produced by HEK293T cell transfection. Seventeen of the 20 recombinants were replication competent. The infectivities per ng p27 of the 17 new replication-competent recombinants in C8166-SEAP cells and in TZM-bl cells ranged from minus 32-fold to plus 7.6-fold relative to SIVmac239. A range of sensitivities to neutralization by sCD4 and by sera from SIV-infected macaques was observed but none was as sensitive to these neutralizing agents as SIVmac316, the highly macrophage-competent derivative of SIVmac239. Four strains that were most sensitive to sCD4 inhibition were also among the most sensitive to antibody-mediated neutralization. None of the new recombinant viruses replicated as well as SIVmac316 in primary alveolar macrophage cultures from rhesus monkeys but three of the strains did exhibit significant levels of delayed replication in these primary macrophages, reaching peak levels of virus production of ≥50 ng/ml p27 compared to 600-800 ng/ml p27 with SIVmac316. These new SIV clones are being contributed to the NIH AIDS Reagent Repository and are available to the scientific community.
Collapse
Affiliation(s)
- Jacqueline G. Bixby
- New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts
| | - Olga Laur
- New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts
| | - Welkin E. Johnson
- New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts
| | - Ronald C. Desrosiers
- New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts
| |
Collapse
|
22
|
HIV-1 Entry, Inhibitors, and Resistance. Viruses 2010; 2:1069-1105. [PMID: 21994672 PMCID: PMC3187606 DOI: 10.3390/v2051069] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 04/16/2010] [Accepted: 04/18/2010] [Indexed: 02/07/2023] Open
Abstract
Entry inhibitors represent a new class of antiretroviral agents for the treatment of infection with HIV-1. While resistance to other HIV drug classes has been well described, resistance to this new class is still ill defined despite considerable clinical use. Several potential mechanisms have been proposed: tropism switching (utilization of CXCR4 instead of CCR5 for entry), increased affinity for the coreceptor, increased rate of virus entry into host cells, and utilization of inhibitor-bound receptor for entry. In this review we will address the development of attachment, fusion, and coreceptor entry inhibitors and explore recent studies describing potential mechanisms of resistance.
Collapse
|
23
|
Ceballos A, Andreani G, Ripamonti C, Dilernia D, Mendez R, Rabinovich RD, Cárdenas PC, Zala C, Cahn P, Scarlatti G, Peralta LM. Lack of viral selection in human immunodeficiency virus type 1 mother-to-child transmission with primary infection during late pregnancy and/or breastfeeding. J Gen Virol 2009; 89:2773-2782. [PMID: 18931075 DOI: 10.1099/vir.0.83697-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mother-to-child transmission (MTCT) of human immunodeficiency virus type 1 (HIV-1) as described for women with an established infection is, in most cases, associated with the transmission of few maternal variants. This study analysed virus variability in four cases of maternal primary infection occurring during pregnancy and/or breastfeeding. Estimated time of seroconversion was at 4 months of pregnancy for one woman (early seroconversion) and during the last months of pregnancy and/or breastfeeding for the remaining three (late seroconversion). The C2V3 envelope region was analysed in samples of mother-child pairs by molecular cloning and sequencing. Comparisons of nucleotide and amino acid sequences as well as phylogenetic analysis were performed. The results showed low variability in the virus population of both mother and child. Maximum-likelihood analysis showed that, in the early pregnancy seroconversion case, a minor viral variant with further evolution in the child was transmitted, which could indicate a selection event in MTCT or a stochastic event, whereas in the late seroconversion cases, the mother's and child's sequences were intermingled, which is compatible with the transmission of multiple viral variants from the mother's major population. These results could be explained by the less pronounced selective pressure exerted by the immune system in the early stages of the mother's infection, which could play a role in MTCT of HIV-1.
Collapse
Affiliation(s)
- Ana Ceballos
- National Reference Center for AIDS, Department of Microbiology, University of Buenos Aires School of Medicine, Buenos Aires, Argentina
| | - Guadalupe Andreani
- National Reference Center for AIDS, Department of Microbiology, University of Buenos Aires School of Medicine, Buenos Aires, Argentina
| | - Chiara Ripamonti
- Viral Evolution and Transmission Unit, DIBIT - San Raffaele Scientific Institute, Milan, Italy
| | - Dario Dilernia
- National Reference Center for AIDS, Department of Microbiology, University of Buenos Aires School of Medicine, Buenos Aires, Argentina
| | - Ramiro Mendez
- National Reference Center for AIDS, Department of Microbiology, University of Buenos Aires School of Medicine, Buenos Aires, Argentina
| | - Roberto D Rabinovich
- National Reference Center for AIDS, Department of Microbiology, University of Buenos Aires School of Medicine, Buenos Aires, Argentina
| | | | - Carlos Zala
- Hospital Juan Fernández, Buenos Aires, Argentina
| | - Pedro Cahn
- Hospital Juan Fernández, Buenos Aires, Argentina
| | - Gabriella Scarlatti
- Viral Evolution and Transmission Unit, DIBIT - San Raffaele Scientific Institute, Milan, Italy
| | - Liliana Martínez Peralta
- National Reference Center for AIDS, Department of Microbiology, University of Buenos Aires School of Medicine, Buenos Aires, Argentina
| |
Collapse
|
24
|
Sahu GK, Paar D, Frost SDW, Smith MM, Weaver S, Cloyd MW. Low-level plasma HIVs in patients on prolonged suppressive highly active antiretroviral therapy are produced mostly by cells other than CD4 T-cells. J Med Virol 2008; 81:9-15. [PMID: 19031450 DOI: 10.1002/jmv.21366] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The cellular source(s) and the clinical significance of persistent low-level viremia, below 50 HIV RNA copies per ml of plasma, achieved in many patients with high adherence to highly active antiretroviral therapy (HAART) remain unclear. Also, it is not clear if residual plasma HIVs during HAART can become predominant populations in the rebounding plasma viral loads after therapy interruption. Since, different HIV quasispecies tend to compartmentalize in various cell types and tissue locations in patients during chronic infection, the phylogenetic relationships between HIV sequences amplified from residual plasma viruses and CD4 T cells of five patients on long-term suppressive therapy were examined. Three of these patients stopped therapy voluntarily for 3 weeks, but only one of them demonstrated viral load rebound in plasma. In phylogenetic analyses, the residual plasma viruses were found to be distinct genetically from the majority of CD4 T cell-associated virus populations in four of five patients. The compartmental analyses revealed that in all patients, plasma- and CD4 T cell-derived viral sequences were compartmentalized separately. Interestingly, the plasma sequences obtained before and after HAART-off in two patients were produced apparently from the same compartment, which was different from the circulating CD4 T cell-compartment. These results suggest the possibility that residual plasma viruses in patients on long-term suppressive HAART may be produced persistently from a cellular source yet to be identified, and are capable of spreading quickly in vivo, accounting for the rapid rebound of viral loads in plasma after therapy interruption.
Collapse
Affiliation(s)
- Gautam K Sahu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555, USA.
| | | | | | | | | | | |
Collapse
|
25
|
Liu S, Xing H, He X, Xin R, Zhang Y, Zhu J, Shao Y. Dynamic analysis of genetic diversity of gag and env regions of HIV-1 CRF07_BC recombinant in intravenous drug users in Xinjiang Uvghur Autonomous Region, China. Arch Virol 2008; 153:1233-40. [PMID: 18504522 DOI: 10.1007/s00705-008-0107-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Accepted: 03/31/2008] [Indexed: 12/30/2022]
Abstract
The aim of this study was to investigate the genetic variation of HIV-1 CRF07_BC, the most prevalent circulating strain in intravenous drug users (IDUs) in China. We studied the diversity in the C2-V5 region of the HIV-1 env gene and in the p17-p24 region of the HIV-1 gag gene from the same samples in 12 IDUs who were divided into two groups according to the length of infection time. Two IDUs were longitudinally monitored from the time of seroconversion for 2-2.5 years. The viral divergence from the founder strain and the viral population diversity between sequential time points were analyzed in two men. The data show that the divergence of the env gene is higher than that of gag in general, while the diversity of the gag gene is sometimes higher than that of env during the course of HIV evolution. In addition, env and gag gene diversity increased over time. The observed patterns and associations may enhance our understanding of HIV-1 evolution.
Collapse
Affiliation(s)
- Shengya Liu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Center for AIDS/STD Control and Prevention, Beijing, China.
| | | | | | | | | | | | | |
Collapse
|
26
|
Abstract
Summary We report a case of HIV-1 infection transmission caused by a fist fight between brothers. A 30-year-old Caucasian UK resident man developed ‘flu-like illness with symptoms of lethargy and weakness. Persistent lymphadenopathy six months later lead to HIV antibody testing, which was positive. Of note, his 37-year-old brother, who was HIV antibody-positive since August 2000, was taking HAART (combivir and nevaripine) with CD4 350 × 106/L (16%) with viral load 4800 copies/mL (log 2.58). A bloody fight had occurred between them four weeks prior to onset of symptoms. Phylogenetic analysis was undertaken. Analysis of the pol gene region indicated that samples from both brothers belonged to the subtype C clade of HIV-1, and that the sequences were closely related to one another. Exposure risk data are extremely useful in helping counsel patients prior to HIV-testing but, as this case illustrates, does not cover all situations.
Collapse
Affiliation(s)
- C R Emerson
- Genitourinary Medicine Department, Royal Victoria Hospital, Belfast, BT12 6BA, UK
| | - S P Quah
- Genitourinary Medicine Department, Royal Victoria Hospital, Belfast, BT12 6BA, UK
| |
Collapse
|
27
|
Zárate S, Pond SLK, Shapshak P, Frost SDW. Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1. J Virol 2007; 81:6643-51. [PMID: 17428864 PMCID: PMC1900087 DOI: 10.1128/jvi.02268-06] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus (HIV) infects different organs and tissues. During these infection events, subpopulations of HIV type 1 (HIV-1) develop and, if viral trafficking is restricted between subpopulations, the viruses can follow independent evolutionary histories, i.e., become compartmentalized. This phenomenon is usually detected via comparative sequence analysis and has been reported for viruses isolated from the central nervous system (CNS) and the genital tract. Several approaches have been proposed to study the compartmentalization of HIV sequences, but to date, no rigorous comparison of the most commonly employed methods has been made. In this study, we systematically compared inferences made by six different methods for detecting compartmentalization based on three data sets: (i) a sample of 45 patients with sequences gathered from the CNS, (ii) sequences from the female genital tract of 18 patients, and (iii) a set of simulated sequences. We found that different methods often reached contradictory conclusions. Methods based on the topology of a phylogenetic tree derived from clonal sequences were generally more sensitive in detecting compartmentalization than those that relied solely upon pairwise genetic distances between sequences. However, as the branching structure in a phylogenetic tree is often uncertain, especially for short, low-diversity, or recombinant sequences, tree-based approaches may need to be modified to take phylogenetic uncertainty into account. Given the frequently discordant predictions of different methods and the strengths and weaknesses of each particular methodology, we recommend that a suite of several approaches be used for reliable inference of compartmentalized population structure.
Collapse
Affiliation(s)
- Selene Zárate
- Antiviral Research Center, 150 W Washington St., Ste. 100, San Diego, CA 92103, USA.
| | | | | | | |
Collapse
|
28
|
Abstract
Dr. Robert C. Gallo provides a personal reflection on the 25 year history of AIDS.
Collapse
Affiliation(s)
- Robert C Gallo
- Institute of Human Virology, University of Maryland Biotechnology Institute and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
| |
Collapse
|
29
|
Sullivan ST, Mandava U, Evans-Strickfaden T, Lennox JL, Ellerbrock TV, Hart CE. Diversity, divergence, and evolution of cell-free human immunodeficiency virus type 1 in vaginal secretions and blood of chronically infected women: associations with immune status. J Virol 2005; 79:9799-809. [PMID: 16014941 PMCID: PMC1181596 DOI: 10.1128/jvi.79.15.9799-9809.2005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Most human immunodeficiency virus type 1 (HIV-1) infections are believed to be the result of exposure to the virus in genital secretions. However, prevention and therapeutic strategies are usually based on characterizations of HIV-1 in blood. To understand better the dynamics between HIV-1 quasispecies in the genital tract and blood, we performed heteroduplex assays on amplified env products from cell-free viral RNA in paired vaginal secretion (VS) and blood plasma (BP) samples of 14 women followed for 1.5 to 3.5 years. Diversity and divergence were less in VS than in BP (P = 0.03 and P < 0.01, respectively), and divergence at both sites was correlated with blood CD4(+) cell levels (VS, P = 0.05; BP, P = 0.01). Evolution of quasispecies was observed in 58% of the women; the loss or gain of quasispecies in VS or BP was always accompanied by such changes at the other site. In addition, sustained compartmentalization of quasispecies in VS was found for four women, even as CD4(+) cell levels decreased to low levels (<50 cells/microl). Quasispecies changes over time were associated with fluctuations in CD4(+) cell levels; concordant increases or decreases in VS and BP divergence had greater CD4(+) cell level changes than intervals with discordant changes (P = 0.05), and women with evolving quasispecies had greater decreases in CD4(+) cell levels compared to that for women who maintained the same quasispecies (P < 0.05). Thus, diversity, divergence, and evolution of cell-free HIV-1 in VS can be different from that in BP, and dynamics between their respective quasispecies are associated with changes in CD4(+) cell levels.
Collapse
Affiliation(s)
- Sharon T Sullivan
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for HIV, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | | | | | | | | | | |
Collapse
|
30
|
Dey AK, Griffiths C, Lea SM, James W. Structural characterization of an anti-gp120 RNA aptamer that neutralizes R5 strains of HIV-1. RNA (NEW YORK, N.Y.) 2005; 11:873-84. [PMID: 15923374 PMCID: PMC1370772 DOI: 10.1261/rna.7205405] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We recently described the isolation of 2'-fluoropyrimidine-substituted RNA aptamers that bind specifically to the surface glycoprotein (gp 120) of the R5 strain, HIV-1(Ba-L), as presented in a previous study. These aptamers potently neutralize HIV-1 infectivity in human peripheral blood mononuclear cells of both tissue culture lab-adapted strains and diverse R5 clinical isolates from multiple clades. Here, we report a detailed structural characterization of one such neutralizing aptamer, B40, using enzymatic and chemical probing methods. We identify the minimal region of the aptamer essential for binding gp120 and accordingly design a 77-nucleotide truncated aptamer, B40t77. We then quantitatively analyze the binding affinity and neutralization potency of the parental and truncated (minimal) aptamer, and show them to be comparable. Furthermore, using results from secondary structure analysis, RNA mutagenesis and BIAcore surface plasmon resonance (SPR) binding assays, we hypothesize that a folded RNA structure is required to present specific nucleotide sequences to allow gp120-recognition and binding. The information gained from this study may provide leads for development of novel anti-HIV-1 therapies and can be used to extend our understanding of the molecular interactions between the virus and its host cell.
Collapse
Affiliation(s)
- Antu K Dey
- Sir William Dunn School of Pathology, University of Oxford, UK
| | | | | | | |
Collapse
|
31
|
Martinez-Picado J, Morales-Lopetegi K, Villena C, Gutiérrez C, Izquierdo N, Marfil S, Clotet B, Ruiz L. Evidence for preferential genotyping of a minority human immunodeficiency virus population due to primer-template mismatching during PCR-based amplification. J Clin Microbiol 2005; 43:436-8. [PMID: 15635008 PMCID: PMC540107 DOI: 10.1128/jcm.43.1.436-438.2005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) genotyping assays have come to be widely used for monitoring antiretroviral drug resistance. We report a case in which primer-template mismatches during nested PCR-based amplification biased the composition of the original viral population in the sample, magnifying a distinct minority HIV-1 population. This observation might help to explain some unexpected HIV-1 genotypes.
Collapse
Affiliation(s)
- Javier Martinez-Picado
- IrsiCaixa Foundation, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Stürmer M, Preiser W, Gute P, Nisius G, Doerr HW. Phylogenetic analysis of HIV-1 transmission: pol gene sequences are insufficient to clarify true relationships between patient isolates. AIDS 2004; 18:2109-13. [PMID: 15577643 DOI: 10.1097/00002030-200411050-00002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Martin Stürmer
- J.W. Goethe University Hospital, Institute for Medical Virology, Frankfurt, Germany.
| | | | | | | | | |
Collapse
|
33
|
Bhattacharya B, Weiss RA, Davis C, Holmes H, Hockley D, Fassati A. Detection and quantitation of human immunodeficiency virus type-1 particles by confocal microscopy. J Virol Methods 2004; 120:13-21. [PMID: 15234805 DOI: 10.1016/j.jviromet.2004.03.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2004] [Accepted: 03/23/2004] [Indexed: 10/26/2022]
Abstract
A method is described to visualise directly human immunodeficiency virus type-1 (HIV-1) particles. HIV-1 containing samples were adsorbed onto a plastic surface and doubly labeled with antibodies specific for viral proteins and sensitive nucleic acids dyes. Laser scanning confocal microscopy detected co-localization of viral proteins and nucleic acids, thus allowing specific identification of HIV. Using this technique, we have quantified eight different HIV-1 sub-types and three HIV-1 groups in tissue culture supernatants from infected peripheral blood mononuclear cells (PBMCs). Confocal counts correlated well with electron microscopy (EM) counts and HIV-1 RNA loads as determined by quantitative PCR. Confocal microscopy may prove to be a simple alternative to electron microscopy for virus identification and quantitation.
Collapse
Affiliation(s)
- Bishnupriya Bhattacharya
- Department of Immunology and Molecular Pathology, Windeyer Institute of Medical Sciences, Medical School, Royal Free and University College London, 46 Cleveland Street, London W1T 4JF, UK
| | | | | | | | | | | |
Collapse
|
34
|
Zelmer DA, Seed JR. A Patch Hath Smaller Patches: Delineating Ecological Neighborhoods for Parasites. COMP PARASITOL 2004. [DOI: 10.1654/4136] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
35
|
Abstract
Our laboratory is interested in the properties of proteins that render them immunogenic, and how such immunogenicity may be modulated in vivo. We are attempting to enhance the immune response in the design of more effective vaccines against viral diseases, such as HIV, and against tumor antigens expressed on breast, ovarian, and cervical cancer and B cell lymphomas. Our main approach is to use a facultative intracellular bacterium, Listeria monocytogenes, which has the unusual ability to live and grow in the cytoplasm of the cell and is thus an excellent vector for targeting passenger antigens to the major histocompatibility complex (MHC) class I pathway of antigen processing with the generation of authentic cytotoxic T lymphocytes (CTL) epitopes. In the field of tumor immunotherapy, we are also developing nonliving vaccine vectors for tumor antigens.
Collapse
Affiliation(s)
- Yvonne Paterson
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
| |
Collapse
|
36
|
Gao F, Chen Y, Levy DN, Conway JA, Kepler TB, Hui H. Unselected mutations in the human immunodeficiency virus type 1 genome are mostly nonsynonymous and often deleterious. J Virol 2004; 78:2426-33. [PMID: 14963138 PMCID: PMC369203 DOI: 10.1128/jvi.78.5.2426-2433.2004] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Mutation rates of human immunodeficiency virus type 1 (HIV-1) genomes have been estimated using purified reverse transcriptase or single-round infection system. Since small sequences were used as templates, the overall mutation rates could only be extrapolated and the biological significance of mutations is unknown. For direct estimation of HIV-1 mutation rates and understanding of the potential biological influences of mutations, we obtained 19 complete or nearly full-length proviral genomes from single-round-infected adherent cells of lymphocytes by using a lambda phage library method and a long-range PCR technique. Analysis of 160,000 bp of sequences showed that the overall mutation rate of HIV-1 genomes was 5.4 x 10(-5) per base per replication cycle. On average, 1.1 mutations (range, 0 to 3) were generated in each viral genome during one infection cycle. Inspection of the mutations in the HIV-1 genome revealed that all site mutations within protein-coding regions were nonsynonymous mutations. Among all mutations, half were deleterious (premature stop codon and deletions) and would result in defective genomes. By applying the same system to an HIV-1 genome with a G262A mutation in the thumb region of the reverse transcriptase, a significant increase was observed in deletion and insertion mutation rates but no increase in the overall mutation rate in viral genomes was found.
Collapse
Affiliation(s)
- Feng Gao
- Department of Medicine, Duke University Medical Center, Duke University, Durham, North Carolina 27710, USA.
| | | | | | | | | | | |
Collapse
|
37
|
Plumelle Y. HIV, 'an evolving species'. Roles of cellular activation and co-infections. Med Hypotheses 2003; 61:136-57. [PMID: 12781657 DOI: 10.1016/s0306-9877(03)00147-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Each small variation of the genome of a species can be preserved if it is useful for the survival of the species in a given environment. Within this framework, the finality of the biological cycle of HIV consists in a search for harmony (biological coherence) with man, which is to say a stable condition. Cellular activation appears to be the strategy developed by HIV in order to achieve this coherence. The price of this strategy is the AIDS. The first contact between HIV and immune system appears to determine the subsequent clinical outcome and the future of HIV. Lymphocytic activation varies during the course of the vital cycle of HIV. For each individual, this lymphocytic activation depends on both the HLA repertoire acquired during thymic ontogenesis and the antigenic experience before and after HIV infection. Thus intercurrent infections alter the immune condition of the organism and influence the outcome of HIV. We described a synthetic analysis of the effects of HIV on the surface protein expression and the cellular activation pathways which should provide insights in the evolutionary relationship between HIV and man and should permit to do a more physiological therapeutic approach.
Collapse
Affiliation(s)
- Yves Plumelle
- Department of Hematobiology, University Hospital, France.
| |
Collapse
|
38
|
Youle M, Wainberg MA. Could chemoprophylaxis be used as an HIV prevention strategy while we wait for an effective vaccine? AIDS 2003; 17:937-8. [PMID: 12660549 DOI: 10.1097/00002030-200304110-00027] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
39
|
Abstract
Ebola virus and HIV present challenges for vaccine development because natural immunity to these viruses is difficult to find, and there are no immune correlates of protection in humans. Modern molecular genetic, virologic and immune analyses have been used to rationally identify promising approaches based on animal model and human clinical studies. Improved vaccine candidates have been defined for HIV, and a promising Ebola vaccine have conferred protection in non-human primates. Further evaluation in humans will allow an assessment of their potential efficacy and point the way to the development of more successful vaccines.
Collapse
Affiliation(s)
- Gary J Nabel
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892-3005, USA.
| |
Collapse
|
40
|
Verhofstede C, Demecheleer E, De Cabooter N, Gaillard P, Mwanyumba F, Claeys P, Chohan V, Mandaliya K, Temmerman M, Plum J. Diversity of the human immunodeficiency virus type 1 (HIV-1) env sequence after vertical transmission in mother-child pairs infected with HIV-1 subtype A. J Virol 2003; 77:3050-7. [PMID: 12584330 PMCID: PMC149764 DOI: 10.1128/jvi.77.5.3050-3057.2003] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although several virologic and immunologic factors associated with an increased risk of perinatal human immunodeficiency virus type 1 (HIV-1) transmission have been described, the mechanism of mother-to-child transmission is still unclear. More specifically, the question of whether selective pressures influence the transmission remains unanswered. The aim of this study was to assess the genetic diversity of the transmitted virus after in utero transmission and after peripartum transmission and to compare the viral heterogeneity in the child with the viral heterogeneity in the mother. To allow a very accurate characterization of the viral heterogeneity in a single sample, limiting-dilution sequencing of a 1016-bp fragment of the env gene was performed. Thirteen children were tested, including 6 with in utero infections and 7 with peripartum infections. Samples were taken the day after birth and at the ages of 6 and 14 weeks. A homogeneous virus population was seen in six (46.2%) infants, of whom two were infected in utero and four were infected peripartum. A more heterogeneous virus population was detected in seven infants (53.8%), four infected in utero and three infected peripartum. The phylogenetic trees of the mother-child pairs presented a whole range of different tree topologies and showed infection of the child by one or more maternal variants. In conclusion, after HIV-1 transmission from mother to child a heterogeneous virus population was detected in approximately one-half of the children examined. Heterogeneous virus populations were found after peripartum infection as well as after in utero infection. Phylogenetic tree topologies argue against selection processes as the major mechanism driving mother-to-child transmission but support the hypothesis that virus variability is mainly driven by the inoculum level and/or exposure time.
Collapse
Affiliation(s)
- Chris Verhofstede
- AIDS Reference Laboratory, Ghent University Hospital, Ghent, Belgium.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Quiñones-Mateu ME, Gao Y, Ball SC, Marozsan AJ, Abraha A, Arts EJ. In vitro intersubtype recombinants of human immunodeficiency virus type 1: comparison to recent and circulating in vivo recombinant forms. J Virol 2002; 76:9600-13. [PMID: 12208939 PMCID: PMC136488 DOI: 10.1128/jvi.76.19.9600-9613.2002] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The increased prevalence of human immunodeficiency virus type 1 (HIV-1) intersubtype recombinants (ISRs) is shaping HIV-1 evolution throughout the world and will have an impact on both therapeutic and vaccine strategies. This study was designed to generate and compare in vitro ISRs to those isolated from HIV-infected individuals throughout the world. Human peripheral blood mononuclear cells were dually infected with seven pairs of HIV-1 isolates from different subtypes (i.e., A to F). Recombinant crossover sites were mapped to specific regions in the envelope (env) gene by using a cloning-hybridization technique and subtype-specific probes. In vitro intersubtype recombination was at least twofold more frequent in the V1-to-V3 region than in any other env fragment, i.e., C1 to V1, V3 to V5, or V5 to gp41. Sequence and recombination site analyses suggested the C2 env domain as a "hot region" for recombination and selection of replication-competent ISRs during the 15-day incubation. In addition to these regional preferences for env recombination, homopolymeric nucleotide tracts, i.e., sequences known to pause reverse transcriptase and promote template switching, were found in most in vitro crossover sites. ISRs, originating from recent dual infections and limited transmission events, partly retained this in vitro regional or sequence preference for recombination sites. However, a shift to crossover sites flanking the gp120-coding sequence was evident in the stable circulating recombinant forms of HIV-1. Based on these findings, HIV-1 recombinants generated from these dual infections may be used as a model for in vivo intersubtype recombination and for the design of various diagnostic assays and vaccine constructs.
Collapse
Affiliation(s)
- Miguel E Quiñones-Mateu
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | | | | | | | | | | |
Collapse
|
42
|
Abstract
Fifteen years after the first, definitive reports of HIV-1-specific, CD8+ T cells [147,148], there is ample evidence for the importance of these cells in control of HIV-1 infection. As much is known of their role in the natural history of HIV-1 infection and their cellular and molecular mechanisms of reactivity than of T-cell responses to any other human virus. Indeed, HIV-1-related research has led the scientific field in revealing many new, fundamental principles of cellular immunity in the last 15 years. From these data, there are multiple, posited mechanisms for loss of CD8+ T-cell control of HIV-1 infection. These include both intrinsic defects in T-cell function and loss of T-cell recognition of HIV-1 because of its extraordinary genetic diversity and disruption of antigen presentation. Efforts have begun on devising approaches to reverse these immune defects in infected individuals and develop vaccines that induce T-cell immunity for protection from infection. Combination antiretroviral drug regimens now provide exceptional, long-lasting control of HIV-1 infection, even though they do not restore anti-HIV-1 T-cell immunity fully in persons with chronic HIV-1 infection. Very encouraging results show that such treatment can maintain normal T-cell reactivity specific for this virus in some persons with early HIV-1 infection. Unfortunately, the antiviral treatment does not cure the host of this persistent, latent virus. This has led to new strategies for immunotherapeutic intervention to enhance the level and breadth of the T-cell repertoire specific for the host's residual virus in persons with chronic HIV-1 infection. Although the principles of immunotherapy stem from early in the last century, modern era approaches are integrating highly sophisticated, molecular and cell biology reagents and methods for control of HIV-1 infection. The most promising immunotherapies are autologous virus activated in vivo by STI or administered in autologous DC that have been engineered ex vivo. There are also compelling rationales supported by animal models and early clinical trials for use of cytokines and chemokines as recombinant proteins or DNA to augment anti-HIV-1 T-cell reactivity and trafficking of T cells and APC to tissue sites of infection. For prevention of HIV-1 infection, the discouragingly poor results of vaccine development in the late 1980s and early 1990s have led to very encouraging, recent studies in monkeys that show partially protective and possibly sterilizing immunity. Finally, clinical trials of new-generation DNA and live vector vaccines already have indications of improved induction of HIV-1-specific T-cell responses. Knowledge of HIV-1-specific T-cell immunity and its role in protection from HIV-1 infection and disease must continue to expand until the goal of complete control of HIV-1 infection is accomplished.
Collapse
Affiliation(s)
- Paolo Piazza
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, 425 Parran Hall, Pittsburgh, PA 15261, USA.
| | | | | |
Collapse
|
43
|
Boutonnet N, Janssens W, Boutton C, Verschelde JL, Heyndrickx L, Beirnaert E, van der Groen G, Lasters I. Comparison of predicted scaffold-compatible sequence variation in the triple-hairpin structure of human imunodeficiency virus type 1 gp41 with patient data. J Virol 2002; 76:7595-606. [PMID: 12097573 PMCID: PMC136393 DOI: 10.1128/jvi.76.15.7595-7606.2002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It has been proposed that the ectodomain of human immunodeficiency virus type 1 (HIV-1) gp41 (e-gp41), involved in HIV entry into the target cell, exists in at least two conformations, a pre-hairpin intermediate and a fusion-active hairpin structure. To obtain more information on the structure-sequence relationship in e-gp41, we performed in silico a full single-amino-acid substitution analysis, resulting in a Fold Compatible Database (FCD) for each conformation. The FCD contains for each residue position in a given protein a list of values assessing the energetic compatibility (ECO) of each of the 20 natural amino acids at that position. Our results suggest that FCD predictions are in good agreement with the sequence variation observed for well-validated e-gp41 sequences. The data show that at a minECO threshold value of 5 kcal/mol, about 90% of the observed patient sequence variation is encompassed by the FCD predictions. Some inconsistent FCD predictions at N-helix positions packing against residues of the C helix suggest that packing of both peptides may involve some flexibility and may be attributed to an altered orientation of the C-helical domain versus the N-helical region. The permissiveness of sequence variation in the C helices is in agreement with FCD predictions. Comparison of N-core and triple-hairpin FCDs suggests that the N helices may impose more constraints on sequence variation than the C helices. Although the observed sequences of e-gp41 contain many multiple mutations, our method, which is based on single-point mutations, can predict the natural sequence variability of e-gp41 very well.
Collapse
|
44
|
Fisher TS, Prasad VR. Substitutions of Phe61 located in the vicinity of template 5'-overhang influence polymerase fidelity and nucleoside analog sensitivity of HIV-1 reverse transcriptase. J Biol Chem 2002; 277:22345-52. [PMID: 11948182 DOI: 10.1074/jbc.m200282200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human immunodeficiency virus type 1 reverse transcriptase (RT) is an error-prone DNA polymerase. Structural determinants of its fidelity are incompletely understood. RT/template primer contacts have been shown to influence its fidelity and sensitivity to nucleoside analog inhibitors. The Phe(61) residue, located within the beta 3 sheet of the finger subdomain, is highly conserved among retroviral RTs. The crystal structure of a ternary complex revealed that Phe(61) contacts the first and second bases of the 5'-template overhang. To determine whether such contacts influence the dNTP-binding pocket, we performed a limited vertical scanning mutagenesis (Phe --> Ala, Leu, Trp, or Tyr) at Phe(61). The F61A mutant displayed the highest increase in fidelity, followed by the F61L and F61W variants, which had intermediate phenotypes. F61Y RT had a minimal effect. The increase in fidelity of the F61A mutant was corroborated by a 12-fold decrease in its forward mutation rate. The Phe(61) mutant RTs also displayed large reductions in sensitivity to 2',3'-dideoxythymidine triphosphate and 2',3'-dideoxy,2'3'-didehydrothymidine triphosphate. Mutants displaying the largest increase in fidelity (F61A and F61L) were also the most resistant. These results suggest that contacts between the finger subdomain of human immunodeficiency virus type 1 RT and the template 5'-overhang are important determinants of the geometry of the dNTP-binding pocket.
Collapse
Affiliation(s)
- Timothy S Fisher
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | | |
Collapse
|
45
|
Machuca R, Bøgh M, Salminen M, Gerstoft J, Kvinesdal B, Pedersen C, Obel N, Nielsen H, Nielsen C. HIV-1 subtypes in Denmark. SCANDINAVIAN JOURNAL OF INFECTIOUS DISEASES 2002; 33:697-701. [PMID: 11669229 DOI: 10.1080/00365540110026863] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The objective of this study was to investigate the presence of non-subtype B HIV-1 in Denmark. The C2-V3-C3 region of the env gene from proviral DNA obtained from patients suspected of being infected with non-subtype B virus was PCR-amplified and directly sequenced. The DNA sequences were aligned with full-length HIV-1 reference strains from each subtype and analysed using the phylogenetic package PHYLIP 3.1. The neighbour-joining method was used with 100 bootstraps. Of the 144 patients included in this study C2-V3-C3 sequences were obtained from 129 patients (90%). The phylogenetic analyses showed that virus from 49 patients (38%) was subtype A, 39 (30%) subtype C, 9 (7%) subtype D, 14 (11%) subtype CRF01_AE, 16 (12%) subtype B, 1 (1%) subtype F and 1 (1%) subtype J. This study demonstrates that almost all subtypes can be detected in Denmark; all non-subtype B infections could be traced to countries with a high prevalence of non-subtype B virus.
Collapse
Affiliation(s)
- R Machuca
- Department of Virology, Statens Serum Institut, Copenhagen, Denmark
| | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Jansson M, Backström E, Scarlatti G, Björndal A, Matsuda S, Rossi P, Albert J, Wigzell H. Length variation of glycoprotein 120 V2 region in relation to biological phenotypes and coreceptor usage of primary HIV type 1 isolates. AIDS Res Hum Retroviruses 2001; 17:1405-14. [PMID: 11679153 DOI: 10.1089/088922201753197079] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Conflicting data have been published concerning the correlation between the length of the second variable region (V2) in the HIV-1 envelope and the biological phenotype of the virus. Here the V2 region length of primary HIV-1 isolates was compared with biological phenotype and coreceptor usage. The V2 region variation was determined by DNA fragment length analysis, virus biological phenotype by the MT-2 cell assay, and coreceptor usage by infection of U87.CD4 cells expressing CCR3, CCR5, or CXCR4. Ninety-three primary virus isolates from 40 patients were analyzed. This panel of viruses included sequential isolates obtained from patients who progressed to AIDS with or without a virus phenotypic switch. We found that NSI MT-2-negative isolates had significantly shorter V2 regions than SI MT-2-positive isolates. However, when V2 region lengths of viruses were analyzed in more detail, we observed that NSI isolates obtained from patients shortly before the phenotypic switch had V2 region lengths similar to those of SI isolates. V2 regions of NSI isolates obtained from patients who progressed to AIDS without a virus phenotypic switch had, in contrast, shorter V2 region than isolates obtained just before virus phenotypic switch. Coreceptor analysis revealed that CCR5-using (R5) isolates generally had shorter V2 regions than virus isolates with the ability to enter CXCR4-expressing cells. Moreover, no significant difference in V2 region length was observed between monotropic SI isolates, that is, X4 isolates, and multitropic SI isolates, that is, R3R5X4 or R5X4 isolates. Thus, we conclude that R5 NSI isolates obtained from patients with stable virus phenotype through the whole disease course display shorter V2 regions than isolates obtained from patients at switch of virus phenotype, suggesting that V2 region length may influence virus coreceptor usage.
Collapse
Affiliation(s)
- M Jansson
- Microbiology and Tumor Biology Center, Karolinska Institute, 171 77 Stockholm, Sweden.
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Abstract
▪ Abstract This review examines the current state of knowledge about HIV/AIDS in terms of its origins, pathogenesis, genetic variation, and evolutionary biology. The HIV virus damages the host's immune system, resulting in AIDS, which is characterized by immunodeficiency, opportunistic infections, neoplasms, and neurological problems. HIV is a complex retrovirus with a high mutation rate. This mutation rate allows the virus to evade host immune responses, and evidence indicates that selection favors more virulent strains with rapid replication. While a number of controversial theories attempt to explain the origin of HIV/AIDS, phylogenetic evidence suggests a zoonotic transmission of HIV to humans and implicates the chimpanzee (Pan troglodytes troglodytes) as the source of HIV-1 infection and the sooty mangabey as the source of HIV-2 infection in human populations. New therapies provide hope for increased longevity among people living with AIDS, but the biology of HIV presents significant obstacles to finding a cure and/or vaccine. HIV continues to be a threat to the global population because of its fast mutation rate, recombinogenic effect, and its use of human defenses to replicate itself.
Collapse
|
48
|
Brossette T, Klein E, Créminon C, Grassi J, Mioskowski C, Lebeau L. Synthesis of haptens for the development of immunoassays for the monitoring of intracellular anti-HIV nucleosides and nucleotides. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(01)00800-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
49
|
Jayan GC, Cordelier P, Patel C, BouHamdan M, Johnson RP, Lisziewicz J, Pomerantz RJ, Strayer DS. SV40-derived vectors provide effective transgene expression and inhibition of HIV-1 using constitutive, conditional,and pol III promoters. Gene Ther 2001; 8:1033-42. [PMID: 11438838 DOI: 10.1038/sj.gt.3301481] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2001] [Accepted: 03/19/2001] [Indexed: 11/09/2022]
Abstract
Vectors based on recombinant SV40 viruses (rSV40) are highly effective in delivering transgene expression driven by constitutive promoters. We tested here whether these vectors could be used with conditional promoters and promoters using RNA polymerase III transcription, with inhibition of HIV-1 by Tat activation response (TAR) decoys as a functional measure of effective transgene delivery and activity. TAR decoys inhibit HIV-1 Tat, a trans-activator of HIV-1 transcription. Tat acts early in the viral replicative cycle and is essential for efficient viral replication. We evaluated rSV40 gene delivery using two different inhibitors of Tat. One was a dual function polyTAR gene encoding 25 sequential TAR elements (TAR(25)), plus an antisense tat, driven either by HIV-1 long terminal repeat (HIV-LTR) as a conditional promoter, or by cytomegalovirus immediate-early promoter (CMV-IEP) as a constitutive promoter. The other inhibitor was a single TAR decoy, driven by the U6 small nuclear RNA promoter (U6-P). These decoys were delivered to unselected cells in two different human T lymphocyte lines and to unstimulated primary human peripheral blood mononuclear cells (pbmc). Gene delivery was confirmed by PCR, and expression by RT-PCR. By in situ hybridization analysis, >95% of cells were transduced. These transgene constructs protected all cell types tested from HIV-1, as measured by syncytia formation and p24 antigen release. Somewhat better inhibition of HIV-1 replication was achieved with HIV-1 long terminal repeat (HIV-1 LTR) as a conditional promoter than with the constitutive CMV-IEP. The U6-P was also very effective, driving a TAR(1) transcript. Cell viability was not detectably affected by TAR decoy expression. Thus, rSV40 vectors effectively deliver HIV-1-inhibitory RNAs using either constitutive or conditional pol II promoters, or using a pol III promoter. The versatility of this gene delivery system may prove to be useful in anti-HIV-1 therapeutics.
Collapse
Affiliation(s)
- G C Jayan
- Department of Pathology, Jefferson Medical College, Philadelphia, PA 19107, USA
| | | | | | | | | | | | | | | |
Collapse
|
50
|
de Mendoza C, Lu W, Machuca A, Sainz M, Castilla J, Soriano V. Monitoring the response to antiretroviral therapy in HIV-1 group O infected patients using two new RT-PCR assays. J Med Virol 2001; 64:217-22. [PMID: 11424107 DOI: 10.1002/jmv.1039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Failure to recognise infection caused by human immunodeficiency virus type 1 (HIV-1) group O variants has been described using both serological and genetic procedures. Moreover, monitoring the response to antiretroviral therapy is a difficult task in patients infected with HIV-1 group O since commercial tests are not available so far for the quantitation of this virus. In this study, the virological response to antiretroviral therapy were assessed in five HIV-1 group O-infected patients living in Spain by using two new and different RT-PCR methods (MUPROVAMA and LCx). Twenty-four plasma samples belonging to these five patients were selected. As reference, p24 antigenaemia levels and CD4+ cell counts were used. All samples yielded positive viral load values using MUPROVAMA (range: 138 to 595,500 HIV-RNA copies/ml) and 23 of 24 using LCx (range: < 178 to 98,356 HIV-RNA copies/ml). Overall, the results obtained using both assays showed a good correlation among themselves, and in respect to p24 antigenaemia and CD4+ cell counts. However, the values provided by LCx were significantly lower (0.33 logs on average) than those provided by MUPROVAMA. In conclusion, both the highly sensitive MUPROVAMA and LCx Quantitative assays might represent an useful tool for guiding the decision on when start treatment and for monitoring the response to antiretroviral therapy in HIV-1 group O-infected patients.
Collapse
Affiliation(s)
- C de Mendoza
- Service of Infectious Diseases, Hospital Carlos III, Instituto de Salud Carlos III, Madrid, Spain
| | | | | | | | | | | |
Collapse
|