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Tebit DM, Patel H, Ratcliff A, Alessandri E, Liu J, Carpenter C, Plantier JC, Arts EJ. HIV-1 Group O Genotypes and Phenotypes: Relationship to Fitness and Susceptibility to Antiretroviral Drugs. AIDS Res Hum Retroviruses 2016; 32:676-88. [PMID: 26861573 DOI: 10.1089/aid.2015.0318] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Despite only 30,000 group O HIV-1 infections, a similar genetic diversity is observed among the O subgroups H (head) and T (tail) (previously described as subtypes A, B) as in the 9 group M subtypes (A-K). Group O isolates bearing a cysteine at reverse transcriptase (RT) position 181, predominantly the H strains are intrinsically resistant to non-nucleoside reverse transcriptase inhibitors (NNRTIs). However, their susceptibility to newer antiretroviral drugs such as etravirine, maraviroc, raltegravir (RAL), and elvitegravir (EVG) remains relatively unknown. We tested a large collection of HIV-1 group O strains for their susceptibility to four classes of antiretroviral drugs namely nucleoside RT, non-nucleoside RT, integrase, and entry inhibitors knowing in advance the intrinsic resistance to NNRTIs. Drug target regions were sequenced to determine various polymorphisms and were phylogenetically analyzed. Replication kinetics and fitness assays were performed in U87-CD4(+)CCR5 and CXCR4 cells and peripheral blood mononuclear cells. With all antiretroviral drugs, group O HIV-1 showed higher variability in IC50 values than group M HIV-1. The mean IC50 values for entry and nucleoside reverse transcriptase inhibitor (NRTI) were similar for group O and M HIV-1 isolates. Despite similar susceptibility to maraviroc, the various phenotypic algorithms failed to predict CXCR4 usage based on the V3 Env sequences of group O HIV-1 isolates. Decreased sensitivity of group O HIV-1 to integrase or NNRTIs had no relation to replicative fitness. Group O HIV-1 isolates were 10-fold less sensitive to EVG inhibition than group M HIV-1. These findings suggest that in regions where HIV-1 group O is endemic, first line treatment regimens combining two NRTIs with RAL may provide more sustained virologic responses than the standard regimens involving an NNRTI or protease inhibitors.
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Affiliation(s)
- Denis M. Tebit
- Division of Infectious Diseases, Case Western Reserve University, Cleveland, Ohio
| | - Hamish Patel
- Division of Infectious Diseases, Case Western Reserve University, Cleveland, Ohio
| | - Annette Ratcliff
- Division of Infectious Diseases, Case Western Reserve University, Cleveland, Ohio
| | | | - Joseph Liu
- Division of Infectious Diseases, Case Western Reserve University, Cleveland, Ohio
| | - Crystal Carpenter
- Division of Infectious Diseases, Case Western Reserve University, Cleveland, Ohio
| | | | - Eric J. Arts
- Division of Infectious Diseases, Case Western Reserve University, Cleveland, Ohio
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2
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Tongo M, Burgers WA. Challenges in the design of a T cell vaccine in the context of HIV-1 diversity. Viruses 2014; 6:3968-90. [PMID: 25341662 PMCID: PMC4213573 DOI: 10.3390/v6103968] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 10/15/2014] [Accepted: 10/18/2014] [Indexed: 12/27/2022] Open
Abstract
The extraordinary variability of HIV-1 poses a major obstacle to vaccine development. The effectiveness of a vaccine is likely to vary dramatically in different populations infected with different HIV-1 subtypes, unless innovative vaccine immunogens are developed to protect against the range of HIV-1 diversity. Immunogen design for stimulating neutralizing antibody responses focuses on “breadth” – the targeting of a handful of highly conserved neutralizing determinants on the HIV-1 Envelope protein that can recognize the majority of viruses across all HIV-1 subtypes. An effective vaccine will likely require the generation of both broadly cross-neutralizing antibodies and non-neutralizing antibodies, as well as broadly cross-reactive T cells. Several approaches have been taken to design such broadly-reactive and cross-protective T cell immunogens. Artificial sequences have been designed that reduce the genetic distance between a vaccine strain and contemporary circulating viruses; “mosaic” immunogens extend this concept to contain multiple potential T cell epitope (PTE) variants; and further efforts attempt to focus T cell immunity on highly conserved regions of the HIV-1 genome. Thus far, a number of pre-clinical and early clinical studies have been performed assessing these new immunogens. In this review, the potential use of these new immunogens is explored.
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Affiliation(s)
- Marcel Tongo
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa.
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa.
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4
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TB and HIV in the Central African region: current knowledge and knowledge gaps. Infection 2013; 42:281-94. [PMID: 24311148 DOI: 10.1007/s15010-013-0568-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/27/2013] [Indexed: 12/12/2022]
Abstract
PURPOSE Reliable and comprehensive data on the HIV/AIDS and TB co-pandemics from Central Africa remain scarce. This systematic review provides a comprehensive overview on current and past research activities in the region and provides a basis for future research work to close knowledge gaps. METHODS The scientific literature was searched for publications meeting the following search terms: "tuberculosis" or "HIV" or "acquired immunodeficiency syndrome", combined with "Central Africa", or the names of individual countries within the region. Original studies, reviews and case series were included, and a selection of relevant articles was made. RESULTS Most research in the field of HIV and TB has been conducted in Cameroon, where the epidemics have been described fairly well. The Democratic Republic of Congo ranked second on the amount of publications, despite the civil wars over the past several decades. Very little has been published on HIV and TB in the other countries, possibly due to the poor infrastructure of health care systems, lack of scientific capacity building or shortage of laboratory equipment. CONCLUSIONS Despite the relatively high burden of HIV and TB in the Central African region, the amount of research activities on these topics is limited. A better understanding of the co-epidemics in this region is urgently needed. The occurrence of opportunistic infections, treatment complications and drug resistance in TB and HIV need to be better described; the failure of public health systems needs to be understood, and research infrastructure needs to be developed. Only then will it be possible to turn the tide against the HIV and TB epidemics in this region.
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Abstract
Acquired immunodeficiency syndrome (AIDS) of humans is caused by two lentiviruses, human immunodeficiency viruses types 1 and 2 (HIV-1 and HIV-2). Here, we describe the origins and evolution of these viruses, and the circumstances that led to the AIDS pandemic. Both HIVs are the result of multiple cross-species transmissions of simian immunodeficiency viruses (SIVs) naturally infecting African primates. Most of these transfers resulted in viruses that spread in humans to only a limited extent. However, one transmission event, involving SIVcpz from chimpanzees in southeastern Cameroon, gave rise to HIV-1 group M-the principal cause of the AIDS pandemic. We discuss how host restriction factors have shaped the emergence of new SIV zoonoses by imposing adaptive hurdles to cross-species transmission and/or secondary spread. We also show that AIDS has likely afflicted chimpanzees long before the emergence of HIV. Tracing the genetic changes that occurred as SIVs crossed from monkeys to apes and from apes to humans provides a new framework to examine the requirements of successful host switches and to gauge future zoonotic risk.
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Affiliation(s)
- Paul M Sharp
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
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6
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Designing of novel antigenic peptide cocktail for the detection of antibodies to HIV-1/2 by ELISA. J Immunol Methods 2013; 387:157-66. [DOI: 10.1016/j.jim.2012.10.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 10/12/2012] [Accepted: 10/16/2012] [Indexed: 11/23/2022]
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de Sousa JD, Alvarez C, Vandamme AM, Müller V. Enhanced heterosexual transmission hypothesis for the origin of pandemic HIV-1. Viruses 2012; 4:1950-83. [PMID: 23202448 PMCID: PMC3497036 DOI: 10.3390/v4101950] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 09/15/2012] [Accepted: 09/17/2012] [Indexed: 11/16/2022] Open
Abstract
HIV-1 M originated from SIVcpz endemic in chimpanzees from southeast Cameroon or neighboring areas, and it started to spread in the early 20th century. Here we examine the factors that may have contributed to simian-to-human transmission, local transmission between humans, and export to a city. The region had intense ape hunting, social disruption, commercial sex work, STDs, and traffic to/from Kinshasa in the period 1899-1923. Injection treatments increased sharply around 1930; however, their frequency among local patients was far lower than among modern groups experiencing parenteral HIV-1 outbreaks. Recent molecular datings of HIV-1 M fit better the period of maximal resource exploitation and trade links than the period of high injection intensity. We conclude that although local parenteral outbreaks might have occurred, these are unlikely to have caused massive transmission. World War I led to additional, and hitherto unrecognized, risks of HIV-1 emergence. We propose an Enhanced Heterosexual Transmission Hypothesis for the origin of HIV-1 M, featuring at the time and place of its origin a coincidence of favorable co-factors (ape hunting, social disruption, STDs, and mobility) for both cross-species transmission and heterosexual spread. Our hypothesis does not exclude a role for parenteral transmission in the initial viral adaptation.
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Affiliation(s)
- João Dinis de Sousa
- Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven B-3000, Belgium; (J.D.S.); (A.-M.V.)
| | - Carolina Alvarez
- Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven B-3000, Belgium; (J.D.S.); (A.-M.V.)
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima 31, Peru; (C.A.)
| | - Anne-Mieke Vandamme
- Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven B-3000, Belgium; (J.D.S.); (A.-M.V.)
- Centro de Malária e Outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa 1349-008, Portugal
| | - Viktor Müller
- Research Group of Theoretical Biology and Evolutionary Ecology, Eötvös Loránd University and the Hungarian Academy of Sciences, Budapest 1117, Hungary;
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Bibollet-Ruche F, Heigele A, Keele BF, Easlick JL, Decker JM, Takehisa J, Learn G, Sharp PM, Hahn BH, Kirchhoff F. Efficient SIVcpz replication in human lymphoid tissue requires viral matrix protein adaptation. J Clin Invest 2012; 122:1644-52. [PMID: 22505456 DOI: 10.1172/jci61429] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 03/05/2012] [Indexed: 12/20/2022] Open
Abstract
SIVs infecting wild-living apes in west central Africa have crossed the species barrier to humans on at least four different occasions, one of which spawned the AIDS pandemic. Although the chimpanzee precursor of pandemic HIV-1 strains must have been able to infect humans, the capacity of SIVcpz strains to replicate in human lymphoid tissues (HLTs) is not known. Here, we show that SIVcpz strains from two chimpanzee subspecies are capable of replicating in human tonsillary explant cultures, albeit only at low titers. However, SIVcpz replication in HLT was significantly improved after introduction of a previously identified human-specific adaptation at position 30 in the viral Gag matrix protein. An Arg or Lys at this position significantly increased SIVcpz replication in HLT, while the same mutation reduced viral replication in chimpanzee-derived CD4(+) T cells. Thus, naturally occurring SIVcpz strains are capable of infecting HLTs, the major site of HIV-1 replication in vivo. However, efficient replication requires the acquisition of a host-specific adaptation in the viral matrix protein. These results identify Gag matrix as a major determinant of SIVcpz replication fitness in humans and suggest a critical role in the emergence of HIV/AIDS.
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Affiliation(s)
- Frederic Bibollet-Ruche
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6060, USA
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Véras NMC, Santoro MM, Gray RR, Tatem AJ, Presti AL, Olearo F, Cappelli G, Colizzi V, Takou D, Torimiro J, Russo G, Callegaro A, Salpini R, D'Arrigo R, Perno CF, Goodenow MM, Ciccozzi M, Salemi M. Molecular epidemiology of HIV type 1 CRF02_AG in Cameroon and African patients living in Italy. AIDS Res Hum Retroviruses 2011; 27:1173-82. [PMID: 21453131 DOI: 10.1089/aid.2010.0333] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1 CRF02_AG accounts for >50% of infected individuals in Cameroon. CRF02_AG prevalence has been increasing both in Africa and Europe, particularly in Italy because of migrations from the sub-Saharan region. This study investigated the molecular epidemiology of CRF02_AG in Cameroon by employing Bayesian phylodynamics and analyzed the relationship between HIV-1 CRF02_AG isolates circulating in Italy and those prevalent in Africa to understand the link between the two epidemics. Among 291 Cameroonian reverse transcriptase sequences analyzed, about 70% clustered within three distinct clades, two of which shared a most recent common ancestor, all related to sequences from Western Africa. The major Cameroonian clades emerged during the mid-1970s and slowly spread during the next 30 years. Little or no geographic structure was detected within these clades. One of the major driving forces of the epidemic was likely the high accessibility between locations in Southern Cameroon contributing to the mobility of the population. The remaining Cameroonian sequences and the new strains isolated from Italian patients were interspersed mainly within West and Central African sequences in the tree, indicating a continuous exchange of CRF02_AG viral strains between Cameroon and other African countries, as well as multiple independent introductions in the Italian population. The evaluation of the spread of CRF02_AG may provide significant insight about the future dynamics of the Italian and European epidemic.
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Affiliation(s)
- Nazle Mendonca Collaço Véras
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida
- Pós-Graduação em Biologia Molecular, Instituto de Biologia, Universidade de Brasília, Brasília, Brazil
| | - Maria Mercedes Santoro
- Department of Experimental Medicine and Biochemical Sciences, University of Rome Tor Vergata, Rome, Italy
| | - Rebecca R. Gray
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
| | - Andrew J. Tatem
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
| | | | | | | | - Vittorio Colizzi
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- International Chantal Biya Reference Centre, Yaoundé, Cameroon
| | - Desiré Takou
- International Chantal Biya Reference Centre, Yaoundé, Cameroon
| | - Judith Torimiro
- International Chantal Biya Reference Centre, Yaoundé, Cameroon
| | - Gianluca Russo
- Department of Tropical and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | | | - Romina Salpini
- Department of Experimental Medicine and Biochemical Sciences, University of Rome Tor Vergata, Rome, Italy
| | - Roberta D'Arrigo
- Monitoring Unit of Antiretroviral Therapies, INMI, Lazzaro Spallanzani, Rome, Italy
| | - Carlo-Federico Perno
- Department of Experimental Medicine and Biochemical Sciences, University of Rome Tor Vergata, Rome, Italy
- Monitoring Unit of Antiretroviral Therapies, INMI, Lazzaro Spallanzani, Rome, Italy
| | - Maureen M. Goodenow
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida
| | | | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
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Separable determinants of subcellular localization and interaction account for the inability of group O HIV-1 Vpu to counteract tetherin. J Virol 2011; 85:9737-48. [PMID: 21775465 DOI: 10.1128/jvi.00479-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Tetherin (BST-2/CD317) is thought to restrict retroviral particle release by cross-linking nascent viral and cellular membranes. Unlike the Vpu proteins encoded by human immunodeficiency virus type 1 (HIV-1) group M strains (M-Vpu), those from the nonpandemic HIV-1 group O (O-Vpu) are not able to counteract tetherin activity. Here, we characterized the basis of this defect in O-Vpu. O-Vpu differs from M-Vpu in that it fails to interact with tetherin and downregulate it from the cell surface. Unlike M-Vpu, O-Vpu localizes to the endoplasmic reticulum (ER) rather than the trans-Golgi network (TGN). Interestingly M-Vpu bearing an ER retention signal at the C terminus localizes similarly to O-Vpu. While it still interacts with tetherin, it fails to promote virus release, suggesting that O-Vpu deficiency correlates with its cellular distribution in the endoplasmic reticulum as well as its failure to bind tetherin. O-Vpu-M-Vpu chimeras were designed to identify the minimal changes required to restore tetherin antagonism. While several chimeric proteins bearing residues of the M-Vpu transmembrane domain into the O-Vpu transmembrane domain recovered tetherin binding in coimmunoprecipitation studies, efficient antagonism required an additional glutamic acid-to-lysine change in the membrane-proximal hinge region of the O-Vpu cytoplasmic tail that was sufficient to abolish ER retention and permit TGN localization.
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Rouet F, Liégeois F, Mouinga-Ondémé A, Kania D, Viljoen J, Wambua S, Ngo-Giang-Huong N, Ménan H, Peeters M, Nerrienet E. Current challenges to viral load testing in the context of emerging genetic diversity of HIV-1. ACTA ACUST UNITED AC 2011; 5:183-202. [PMID: 23484497 DOI: 10.1517/17530059.2011.566860] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION One of the major characteristics of HIV-1 is its extreme genetic diversity. A key factor in assessing the sensitivity of a molecular-based assay measuring HIV-1 RNA viral load (VL) in plasma is its ability to detect/quantify all (or most of) relevant HIV-1 genetic subtype/recombinant forms accurately. AREAS COVERED This review provides an overview of the current commercially available quantitative real-time assays (the Abbott RealTime HIV-1, Roche TaqMan HIV-1 versions 1.0 and 2.0, BioMérieux Nuclisens EasyQ HIV-1, Siemens VERSANT HIV-1 RNA 1.0 kinetic PCR, and Biocentric Generic HIV Viral Load assays). For each assay, studies from 2005 to 2010 assessing the impact of HIV-1 genetic diversity on the reliability of HIV-1 RNA quantification are described. EXPERT OPINION In light of HIV-1 genetic diversity, a general recommendation to favor one test over the other cannot categorically be made. Larger field evaluations of HIV-1 RNA assays should be conducted in areas where HIV-1 genetic diversity is the highest. The large-scale implementation of HIV-1 VL testing is urgently required in the developing world to change HIV infection from a likely death sentence into a manageable chronic infection, as done in Northern countries.
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Affiliation(s)
- François Rouet
- Laboratoire de Rétrovirologie, Centre International de Recherches Médicales de Franceville (CIRMF) , BP 769, Franceville, Gabon , France +241 677 092/096 ; +241 677 295 ;
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12
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Abstract
Mammalian cells are equipped with so-called "restriction factors" that suppress virus replication and help to prevent virus transmission from one species to another. This Essay discusses the host restriction factor tetherin, which blocks the release of enveloped viruses like HIV-1, and the factors evolved by primate lentiviruses, such as Vpu and Nef, that antagonize tetherin's action.
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Affiliation(s)
- Daniel Sauter
- Institute of Molecular Virology, University Clinic Ulm, Meyerhofstrasse 1, 89081 Ulm, Germany
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13
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Rouet F, Chaix ML, Nerrienet E, Ngo-Giang-Huong N, Plantier JC, Burgard M, Peeters M, Damond F, Ekouevi DK, Msellati P, Ferradini L, Rukobo S, Maréchal V, Schvachsa N, Wakrim L, Rafalimanana C, Rakotoambinina B, Viard JP, Seigneurin JM, Rouzioux C. Impact of HIV-1 genetic diversity on plasma HIV-1 RNA Quantification: usefulness of the Agence Nationale de Recherches sur le SIDA second-generation long terminal repeat-based real-time reverse transcriptase polymerase chain reaction test. J Acquir Immune Defic Syndr 2007; 45:380-8. [PMID: 17468666 DOI: 10.1097/qai.0b013e3180640cf5] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The high genetic diversity of HIV-1 has a major impact on the quantification of plasma HIV-1 RNA, representing an increasingly difficult challenge. A total of 898 plasma specimens positive for HIV-1 RNA by commercial assays (Amplicor v1.5; Roche Diagnostic Systems, Alameda, CA or Versant v3.0; Bayer Diagnostics, Emeryville, CA) were tested using the Agence Nationale de Recherches sur le SIDA second-generation (G2) real-time reverse transcriptase polymerase chain reaction (RT-PCR) test: 518 samples containing HIV-1 of known subtype, including 88 from 2 subtype panels and 430 harboring B (n = 266) and non-B (n = 164) group M HIV-1 subtypes from patients followed up in 2002 through 2005 at Necker Hospital (Paris, France), and 380 samples from 10 different countries (Argentina, Cambodia, Cameroon, Central African Republic, France, Ivory Coast, Madagascar, Morocco, Thailand, and Zimbabwe). HIV-1 RNA values obtained by G2 real-time PCR were highly correlated with those obtained by the Amplicor v1.5 for B and non-B subtypes (R = 0.892 and 0.892, respectively) and for samples from diverse countries (R = 0.867 and 0.893 for real-time PCR vs. Amplicor v1.5 and real-time PCR vs. Versant v3.0, respectively). Approximately 30% of specimens harboring non-B subtypes were underquantified by at least -0.51 log10 in Amplicor v1.5 versus 5% underquantified in G2 real-time PCR. Discrepant results were also obtained with subtype B samples (14% underquantified by Amplicor v1.5 vs. 7% by G2 real-time PCR). Similar percentages were observed when comparing results obtained with the G2 real-time PCR assay with those obtained using the Versant assay. Addressing HIV-1 diversity, continual monitoring of HIV-1 RNA assays, together with molecular epidemiology studies, is required to improve the accuracy of all HIV RNA assays.
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Affiliation(s)
- François Rouet
- Laboratoire de Virologie, Centre Muraz, BP 390 Bobo-Dioulasso 01, Burkina Faso.
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14
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Abstract
OBJECTIVE To quantify the similarity (or lack of) between the phylogenetic substructure of HIV-1 groups O and M. METHODS Two phylogenetic tree statistics--the subtype diversity ratio (SDR) and the subtype diversity variance (SDV)--were used in conjunction with bootstrap replicates on gag, pol and env sequence alignments of group O and M strains. Randomly generated phylogenetic trees were used as a control. RESULTS We show that, as expected, the established global-group M subtypes have a high degree of phylogenetic symmetry in relation to each other in terms of inter- and intra-subtype diversification. They are significantly different from the substructure present amongst the random trees. To the contrary, the group O diversification does not display this highly symmetrical substructure and is not significantly different from the substructure present on randomly generated trees. Phylogenies comprised of group M strains from the epicentre of the HIV/AIDS pandemic, the Democratic Republic of Congo (DRC), exhibit a substructure more similar to group O than to global-group M. CONCLUSIONS The substructure present within groups O and M is quantifiably different. The well defined clades, the subtypes that characterize group M diversification, are not present in group O or amongst group M strains from the DRC. The group M subtypes are thus unique and a signature of pandemic HIV-1.
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Affiliation(s)
- John Archer
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, UK
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15
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Buonaguro L, Tornesello ML, Buonaguro FM. Human immunodeficiency virus type 1 subtype distribution in the worldwide epidemic: pathogenetic and therapeutic implications. J Virol 2007; 81:10209-19. [PMID: 17634242 PMCID: PMC2045484 DOI: 10.1128/jvi.00872-07] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- L Buonaguro
- Laboratory of Viral Oncogenesis and Immunotherapy & AIDS Reference Center, Ist. Naz. Tumori Fond. G. Pascale, Via Mariano Semmola, 1, 80131 Naples, Italy.
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Yamaguchi J, Coffey R, Vallari A, Ngansop C, Mbanya D, Ndembi N, Kaptué L, Gürtler LG, Bodelle P, Schochetman G, Devare SG, Brennan CA. Identification of HIV type 1 group N infections in a husband and wife in Cameroon: viral genome sequences provide evidence for horizontal transmission. AIDS Res Hum Retroviruses 2006; 22:83-92. [PMID: 16438650 DOI: 10.1089/aid.2006.22.83] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 is classified into three groups, M (major), N (non-M non-O), and O (outlier); each group arose from a separate transmission of SIVcpz into humans. HIV-1 group N was recently discovered and infections with this virus are rare with only eight documented cases. All group N infections have been found in Cameroon and there is no evidence of direct linkage between the infected patients. We report here the identification of HIV-1 group N infections in a husband and wife. The group N infection in the husband, 1131-03, was identified first based on seroreactivity in peptide EIAs and confirmed by PCR amplification of group N viral sequences. Subsequently the wife, 1015-04, was evaluated and confirmed to also be infected with a group N virus. Near full-length viral genomes were amplified and sequenced from each patient's specimen. The low level of diversity between the two viral sequences provides evidence of horizontal transmission of group N from one spouse to the other. Patient 1131-03 was receiving antiviral therapy consisting of reverse transcriptase inhibitors; the treatment appears effective for suppression of group N viral replication based on apparently low viral load in plasma specimens collected from the patient and the absence of drug resistance mutations in RT sequences amplified from 1131-03. This report brings to 10 the number of group N infections identified and to 5 the number of group N genomes sequenced. Although group N infections continue to be rare, group N is a pathogenic virus and its prevalence needs to be monitored.
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Gueudin M, Lemée V, Ferre V, Beby-Defaux A, Pathé JP, Guist'hau O, Braun J, Simon F, Plantier JC. Virologic diagnosis and follow-up of children born to mothers infected by HIV-1 group O. J Acquir Immune Defic Syndr 2005; 36:639-41. [PMID: 15097309 DOI: 10.1097/00126334-200405010-00014] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Parsyan AE. Protective correlates against HIVs may have evolved in human populations in the areas of historic occurrence of primate-to-man transmissions of SIVs ancestral to HIVs: studies in these populations may provide crucial insights for treatment and prevention of HIV infection. Med Hypotheses 2005; 64:433-7. [PMID: 15617844 DOI: 10.1016/j.mehy.2004.09.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2004] [Accepted: 09/27/2004] [Indexed: 10/26/2022]
Abstract
Recent findings suggest that Human Immunodeficiency Viruses, HIV-1 and 2, might have been transmitted to humans from particular primate species. It is thought that some Simian Immunodeficiency Viruses (SIVs), from which HIVs presumably originated, existed in their primate hosts for ages. Behavioral characteristics increasing the probability of contact between these primates and humans (such as keeping monkeys for pets, hunting monkeys for food, improper handling of the monkey meat, etc.) documented in some African countries could have facilitated cross-species transmissions (CSTs) of HIVs. As it has been shown, multiple CSTs took place for both HIVs (1 and 2) and then, in a globalizing world, these local events led to the pandemic. Here, it is brought forward that in the regions of epizooty of SIVs closely related to HIVs, some human populations might have had exposure history to these viruses dating back hundreds years. Lacking the important framework for further spread provided by nowadays globalization, these CSTs could have led to isolated local HIV outbreaks limited to particular tribes or groups. The infections could have extinguished some populations while on the other hand provided evolutionary pressure to select for mechanisms protective for HIV infection and/or disease. Thus, here it is hypothesized that in the areas of the habitat of primates infected with SIVs, from which HIVs are thought to be originated, there could be historically exposed populations which might possess biological correlates of protection from HIVs. Current knowledge on the distribution of primates hosting HIV-related SIVs suggests that epidemiological, primatological, anthropological and molecular biological studies in the areas of Cameroon, Gabon, both Congos and Equatorial Guinea (for HIV-1) and Guinea-Bissau, Senegal, Guinea, Ivory Cost, Sierra Leone and Liberia (for HIV-2) could lead to the discoveries of correlates of protection against HIVs. It is also hypothesized that virology studies in the same areas might reveal less virulent and/or infective viruses which could provide insights in the HIV pathogenesis and vaccinology.
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Affiliation(s)
- Armen E Parsyan
- Department of Epidemiology, School of Public Health, Boston University, 715 Albany Street, T3E, Boston, MA 02118-2526, USA.
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19
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Affiliation(s)
- Paul M Sharp
- Institute of Genetics, University of Nottingham, Queens Medical Centre, Nottingham, United Kingdom
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20
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Lemey P, Pybus OG, Rambaut A, Drummond AJ, Robertson DL, Roques P, Worobey M, Vandamme AM. The molecular population genetics of HIV-1 group O. Genetics 2005; 167:1059-68. [PMID: 15280223 PMCID: PMC1470933 DOI: 10.1534/genetics.104.026666] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
HIV-1 group O originated through cross-species transmission of SIV from chimpanzees to humans and has established a relatively low prevalence in Central Africa. Here, we infer the population genetics and epidemic history of HIV-1 group O from viral gene sequence data and evaluate the effect of variable evolutionary rates and recombination on our estimates. First, model selection tools were used to specify suitable evolutionary and coalescent models for HIV group O. Second, divergence times and population genetic parameters were estimated in a Bayesian framework using Markov chain Monte Carlo sampling, under both strict and relaxed molecular clock methods. Our results date the origin of the group O radiation to around 1920 (1890-1940), a time frame similar to that estimated for HIV-1 group M. However, group O infections, which remain almost wholly restricted to Cameroon, show a slower rate of exponential growth during the twentieth century, explaining their lower current prevalence. To explore the effect of recombination, the Bayesian framework is extended to incorporate multiple unlinked loci. Although recombination can bias estimates of the time to the most recent common ancestor, this effect does not appear to be important for HIV-1 group O. In addition, we show that evolutionary rate estimates for different HIV genes accurately reflect differential selective constraints along the HIV genome.
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Affiliation(s)
- Philippe Lemey
- Rega Institute for Medical Research, KULeuven, B-3000 Leuven, Belgium.
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21
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Plantier JC, Gueudin M, de Oliveira F, Damond F, Lemée V, Brun-Vézinet F, Simon F. Rapid discrimination between human immunodeficiency virus type 2 groups A and B by real-time PCR. J Clin Microbiol 2005; 42:5866-70. [PMID: 15583327 PMCID: PMC535281 DOI: 10.1128/jcm.42.12.5866-5870.2004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We studied the feasibility of genotyping human immunodeficiency virus (HIV) type 2 groups A and B by real-time PCR. Two group-specific PCRs were developed. Real-time genotyping of 22 samples of genotype A, 10 samples of genotype B, and the isolate of new group H were compared to genotyping by sequencing and phylogeny. The group-specific PCRs specifically identified 84.3% of group A or B samples; isolate H was not detected. This method allowed rapid and specific discrimination between HIV-2 groups A and B and could be a useful tool for molecular epidemiological studies.
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Affiliation(s)
- Jean-Christophe Plantier
- Unité de Virologie, laboratoire associé au Centre National de Référence du VIH, Equipe d'Accueil 2656, CHU Charles Nicolle, 1 rue de Germont, 76031 Rouen, France.
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22
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Tuaillon E, Gueudin M, Lemée V, Gueit I, Roques P, Corrigan GE, Plantier JC, Simon F, Braun J. Phenotypic Susceptibility to Nonnucleoside Inhibitors of Virion-Associated Reverse Transcriptase From Different HIV Types and Groups. J Acquir Immune Defic Syndr 2004; 37:1543-9. [PMID: 15577405 DOI: 10.1097/00126334-200412150-00001] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES To evaluate a phenotype assay based on plasma reverse transcriptase (RT) to assess HIV susceptibility to nonnucleoside RT inhibitors (NNRTIs). To compare RT-based phenotype with recombinant virus assay (RVA) phenotype- and genotype-based analysis. To assess group O and HIV-2 susceptibility to NNRTIs in correlation with genotype polymorphisms. METHODS RT activity was quantified and its susceptibility to efavirenz, nevirapine, and delavirdine measured as drug concentration resulting in 50% inhibition. RT phenotype was compared with genotype analysis. Eighteen plasma samples from 14 group M- and culture supernatants from 4 group M-, 9 group O-, and 7 HIV-2-infected patients were investigated. RT-based and RVA-based phenotypes were compared for identical plasma from 9 group M-infected patients. RESULTS RT-based and RVA-based phenotypes were in complete agreement. RT-based phenotype- and genotype-predicted susceptibility were concordant for all but 1 group M samples. One plasma showed susceptibility to 3 NNRTIs by phenotypes, despite the presence of 101E and 106I/V residues. The HIV-2 RTs were totally resistant to the NNRTIs tested. Among HIV-1 group O, 6 were totally resistant to NNRTIs independently of the presence of the 181C mutation and 3 were susceptible to some NNRTIs. CONCLUSION Plasma RT-based phenotype could be useful as a simple alternative for monitoring resistance to NNRTIs. This assay is suitable for highly divergent strains. It would be particularly useful for large epidemiologic survey of the natural HIV polymorphism and the potential impact in emergence of drug resistance, particularly to nevirapine, widely used to prevent mother-to-child transmission.
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Affiliation(s)
- Edouard Tuaillon
- Laboratoire de Virologie, Centre Hospitalier Charles Nicolle, Rouen, France
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23
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Aghokeng AF, Ewane L, Awazi B, Nanfack A, Delaporte E, Peeters M, Zekeng L. Evaluation of Four Simple/Rapid Assays and Two Fourth-Generation ELISAs for the Identification of HIV Infection on a Serum Panel Representing the HIV-1 Group M Genetic Diversity in Cameroon. J Acquir Immune Defic Syndr 2004; 37:1632-40. [PMID: 15577422 DOI: 10.1097/00126334-200412150-00018] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The performance of 4 rapid and simple assays: Camstix-HIV 1+2 (Camdiagnostix, Yaounde, Cameroon); Determine HIV 1+2+0 (Abbott Laboratories, Tokyo, Japan); Genie II HIV-1/HIV-2 (Bio-Rad, Marnes la Coquette, France); ImmunoComb II HIV 1 & 2 BiSpot (Orgenics, Yavne, Israel); and 2 fourth-generation ELISAs: Enzygnost HIV Integral (Dade Behring, Marburg, Germany) and Genscreen plus HIV Ag-Ab (Bio-Rad, Marnes la Coquette, France) currently used in Cameroon to detect HIV infections were evaluated on a local serum panel. A total of 503 samples were collected, using the Camstix-HIV 1+2 assay. Overall, 280 samples were confirmed HIV positive, 181 were negative, and 42 were indeterminate. All positive samples belonged to group M: CRF02_AG (73.5%), A1 (7.1%), A2 (1.2%), G (4.7%), F2 (5.1%), D (1.6%), CRF11 (1.6%), CRF06 (1.2%), and CRF01_AE (1.6%). Sensitivity, specificity, test efficiency, and positive and negative predictive values were calculated both including and excluding indeterminate samples. Except for Genie II and ImmunoComb II (98.9 and 99.3%, respectively), sensitivities were 100% for the remaining 4 tests. Specificities, efficiencies, and positive predictive values of all assays were negatively affected by the addition of HIV-indeterminate samples in the calculations. These data show the importance of prior test evaluations on local serum panels and in field conditions before a national policy for HIV screening is decided on and stress also the need to use tests and algorithms that can reduce the high number of HIV-indeterminate results in Africa.
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24
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Tebit DM, Zekeng L, Kaptué L, Gürtler L, Fackler OT, Keppler OT, Herchenröder O, Kräusslich HG. Construction and characterization of an HIV-1 group O infectious molecular clone and analysis of vpr- and nef-negative derivatives. Virology 2004; 326:329-39. [PMID: 15321704 DOI: 10.1016/j.virol.2004.05.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2004] [Accepted: 05/28/2004] [Indexed: 11/25/2022]
Abstract
In this report, we describe the construction and characterization of the first full-length infectious molecular clone from the Cameroonian HIV-1 group O primary isolate MVP8913. Virus obtained after transfection of the proviral clone pCMO2.3 replicated to levels comparable to its parental isolate in the human T-cell line PM-1, although replication was reduced by fivefold in peripheral blood mononuclear cells (PBMC) and was barely detectable in primary monocyte-derived macrophages (MDM). Phylogenetic analysis of the complete proviral sequence revealed a closer relationship to ANT70 than to MVP5180, the two prototypic group O primary isolates. All reading frames for structural and accessory genes were open except for vpr that contained an in-frame stop codon. In the nef gene, a mutation disrupting the functionally important myristoylation signal was observed. Repairing the defect in nef enhanced replication in PBMC and MDM, although repairing the vpr defect only affected replication in MDM, consistent with the known phenotypes of vpr and nef mutants in HIV-1 group M viruses. Repairing both vpr and nef showed an additive effect, but the resulting virus was still impaired compared to the parental isolate. This defect was overcome when the gag-pol coding region was exchanged for that from another O-type isolate giving rise to the proviral clone pCMO2.5. Virus obtained from pCMO2.5 replicated with similar kinetics as the parental O-type isolate in both PBMC and MDM, making this proviral clone a valuable tool for further studies on functional characteristics of HIV-1 group O viruses.
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Affiliation(s)
- Denis M Tebit
- Abteilung Virologie, Universitätsklinikum Heidelberg, D-69ab0, Germany
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25
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Pasquier C, Sandres-Sauné K, Mansuy JM, Puissant B, Viraben R, Spenato N, Miédougé M, Massip P, Blancher A, Izopet J. Virological exploration of individuals with discordant HIV screening tests. J Clin Virol 2004; 30:218-23. [PMID: 15135738 DOI: 10.1016/j.jcv.2003.09.018] [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] [Received: 07/28/2003] [Accepted: 09/22/2003] [Indexed: 10/26/2022]
Abstract
Screening for HIV infection can use many algorithms. When two different HIV antibody assays are used, discordant results may occur. To discriminate between HIV seroconversion, HIV variant infection and false positive reactivity, 30 consecutive subjects with two discordant HIV antibody-screening assays were extensively investigated for HIV infection. No subject had HIV seroconversion or reached HIV seropositivity criteria after a follow-up of 3 months. By contrast 36% became HIV negative by the use of both HIV screening assays. p24 Antigen, HIV-1 RNA, HIV-1 DNA, HIV-2 DNA assays and HIV isolation by sensitive culture were unable to identify HIV infection in the 30 subjects with discordant HIV screening assays. The data suggest that the use of two HIV screening assays increase false-positive HIV results without increasing clinical sensitivity. To compliment follow-up of HIV screening, early testing for HIV RNA could be useful to identify or eliminate a recent infection.
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Affiliation(s)
- C Pasquier
- Laboratoire de Virologie, variabilité virale, EA2046-IFR30, place du Dr. Baylac, Hôpital Purpan, TSA 40031, F-31 059 Toulouse Cedex, France.
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26
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Gueudin M, Plantier JC, Damond F, Roques P, Mauclère P, Simon F. Plasma viral RNA assay in HIV-1 group O infection by real-time PCR. J Virol Methods 2003; 113:43-9. [PMID: 14500126 DOI: 10.1016/s0166-0934(03)00223-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
HIV-1 group O infections remains essentially restricted to central Africa, and particularly Cameroon, although isolated cases have been reported in Western countries. Genomic differences explain why commercial tests used to quantify HIV-1 group M plasma load are unsuitable for HIV-1 group O. This lack of a quantitative tool hinders the clinical management of HIV-O-infected patients. We have therefore developed a real-time PCR assay, based on LightCycler technology, to quantify HIV-1 group O RNA in plasma. The primers were selected in the LTR 3' region. Forty-eight plasma samples containing strains belonging to the different HIV-1 type O clades (O:A, O:B and O:C) were tested. RNA was quantifiable in 40 of these samples. RNA was always detected in samples from untreated patients, except for one patient infected by a highly divergent strain. The kinetics of plasma viral load were also examined in seven patients for whom clinical and immunologic follow-up data were available. HIV-1 group O plasma load was high in the absence of treatment and correlated negatively with the CD4 cell count. Serial samples obtained during treatment allowed us to compare viral load changes with immunologic outcome. Despite the high initial cost of acquiring the required cycling device, the per-sample cost of this real-time quantitative PCR assay for HIV-1 group O is low, making it suitable for use in endemic zones.
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Affiliation(s)
- Marie Gueudin
- Laboratoire de Virologie, Hôpital Charles Nicolle, 1 rue de Germont, 76031 Rouen, France.
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27
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Plantier JC, Gueudin M, Damond F, Braun J, Mauclère P, Simon F. Plasma RNA quantification and HIV-1 divergent strains. J Acquir Immune Defic Syndr 2003; 33:1-7. [PMID: 12792348 DOI: 10.1097/00126334-200305010-00001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The diversity of HIV complicates viral load measurement for patient management and treatment monitoring. Numerous studies have shown that non-B group M variants can be underestimated and that group O strains are not detected by commercial tests. More recent versions of the kits used for previous studies have improved the quantification of non-B variants but are still unable to detect or correctly quantify group O strains. In this study, the authors evaluated the new Abbott LCx HIV RNA Quantitative viral load kit with a large collection of samples from Europe and central Africa. One hundred thirty-three group M samples, including 69 from patients infected with non-B variants, and 70 group O samples were tested. The LCx system was compared with the Cobas Amplicor HIV-1 Monitor v1.5 test and with a quantitative real-time polymerase chain reaction method based on LightCycler technology. The LCx and Cobas tests had similar quantification ranges for group M samples and a high degree of linearity (r2 = 0.9582). The LCx method quantified group O variants (31 of the 48 patients were quantifiable) and gave values within the range of those obtained with the LightCycler assay. The two assays were sensitive but showed only moderate linearity (r2 = 0.6195), probably because of higher diversity of group O strains and the use of primers and probes in different regions. In conclusion, the authors showed that the LCx kit allowed quantification of the large group M diversity and group O variants.
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28
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Vallejo A, Gurtler L, Zekeng L, Hewlett IK. Nucleotide sequence analysis of the accessory genes of HIV-1 group O isolates. Virus Res 2003; 91:189-93. [PMID: 12573497 DOI: 10.1016/s0168-1702(02)00270-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Human immunodeficiency virus type 1 group O strains have been described as highly divergent, compared with the majority of the viruses classified in group M. To study the diversity and genetic characteristics of group O, we have sequenced the accessory genes of 7 isolates. Analysis of the deduced amino acid sequences for Vif, Vpr, Tat, Vpu, and Rev indicate that most of the functional domains of these proteins, as described for group M viruses, are highly conserved and retained among all the group O strains we have characterized. The only difference concerns the Vif phosphorylation sites, which are absent in all of the group O isolated we have sequence with the exception of two isolates in which only one phosphorylation site was conserved. These sites, present in nearly all of the group M isolates, play a critical role in the regulation of viral replication and infectivity. As described for group M isolates, the vpu gene is the one with the highest diversity among group O viruses. Phylogenetic analysis of these sequences suggests that group O viruses could be differentiated into at least four different clusters.
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Affiliation(s)
- Alejandro Vallejo
- Laboratory of Molecular Virology, Food and Drug Administration, Bethesda, MD, USA.
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29
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Amendola A, Bordi L, Angeletti C, Visco-Comandini U, Abbate I, Cappiello G, Budabbus MA, Eljhawi OA, Mehabresh MI, Girardi E, Antinori A, Ippolito G, Capobianchi MR. Underevaluation of HIV-1 plasma viral load by a commercially available assay in a cluster of patients infected with HIV-1 A/G circulating recombinant form (CRF02). J Acquir Immune Defic Syndr 2002; 31:488-94. [PMID: 12473837 DOI: 10.1097/00126334-200212150-00006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The authors studied the correlation and agreement of commercially available assays in detection and quantification of the HIV-1 intersubtype A/G circulating recombinant form CRF02. The assays under comparison were Bayer Versant HIV-1 RNA, version 3.0; Roche Amplicor HIV-1 Monitor, version 1.5 (standard procedure); and Organon Teknika NucliSens HIV-1 RNA QT. Plasma samples from 114 patients infected with CRF02 were tested by the three assays under standard conditions. Although correlation among the assays was high and statistically significant for subtype B and CRF02, in the latter instance, NucliSens measured average viral load values (3.29 +/- 0.71 log(10) copies/mL) about 4 and >8 times lower than those obtained by Versant (3.90 +/- 0.90 log(10) copies/mL) and Amplicor (4.22 +/- 1.05 log(10) copies/mL), respectively. Furthermore, in a statistically significant percentage of CRF02-harboring samples, NucliSens produced viral load values undetectable or 1 log(10) lower than those obtained in Versant and Amplicor assays. Altogether, these data underline a low performance of NucliSens in detecting and quantifying viremia in plasma samples harboring the CRF02. These results are potentially important as global distribution of new HIV-1 subtypes is expanding, and recombinant strains, particularly CRF02, are emerging and becoming highly prevalent.
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Affiliation(s)
- Alessandra Amendola
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy
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30
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Roques P, Robertson DL, Souquière S, Damond F, Ayouba A, Farfara I, Depienne C, Nerrienet E, Dormont D, Brun-Vézinet F, Simon F, Mauclère P. Phylogenetic analysis of 49 newly derived HIV-1 group O strains: high viral diversity but no group M-like subtype structure. Virology 2002; 302:259-73. [PMID: 12441070 DOI: 10.1006/viro.2002.1430] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We assess the genetic relationships between 49 HIV-1 group O strains from 24 and 25 patients living in Cameroon and France, respectively. Strains were sequenced in four genomic regions: gag (p24) and three env regions (C2-V3, gp41, and for 22 C2-gp41). In each of the genomic regions analyzed, the genetic diversity among the group O strains was higher than that exhibited by group M. We characterize three major group O phylogenetic clusters (O:A, O:B, and O:C) that comprised the same virus strains in each of the genomic regions analyzed. The majority of strains cluster in O:A, a cluster previously identified by analysis of pol and env sequences. Group O recombinants were also identified. Importantly, the distinction between these three major group O clades was weak compared to the strong clustering apparent in the global group M phylogenetic tree that led to the identification of subtypes. Thus, these clusters of group O viruses should not be considered as equivalent to the group M subtypes. This difference between the pattern of group O and the global group M diversity, both taking into account the pandemic status of the group M subtypes and the comparatively small number of group O-infected individuals (the majority being from Cameroon), indicates that the group O phylogeny primarily represents viral divergence in the Cameroon region, analogous to group M viral diversity present in the Democratic Republic of Congo.
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Affiliation(s)
- P Roques
- Service de Neurovirologie, CEA, Fontenay-aux-Roses, France.
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31
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Luk KC, Kaptué L, Zekeng L, Soriano V, Gürtler L, Devare SG, Schochetman G, Hackett J. Naturally occurring sequence polymorphisms within HIV type 1 group O protease. AIDS Res Hum Retroviruses 2001; 17:1555-61. [PMID: 11709100 DOI: 10.1089/08892220152644269] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mutations within the protease gene associated with reduced susceptibility to protease inhibitors have been well documented for HIV-1 group M subtype B strains. In contrast, limited genotypic and phenotypic information is available for the genetically diverse HIV-1 group O strains. Preexisting resistance-associated polymorphisms have the potential to contribute to a poor virological response to antiviral drug treatment in group O-infected patients. In the present study, the protease genes of 28 protease inhibitor-naive HIV-1 group O-infected patients were analyzed to identify any naturally occurring amino acid polymorphisms associated with drug resistance. Comparison of the consensus group O protease sequence with subtype B of group M indicated that both groups have almost identical sequences in the protease active site, the flap and the substrate-binding site. Analysis of the 28 individual protease sequences revealed polymorphisms at 34% of the positions within the protease gene, but no primary mutations associated with protease inhibitor resistance. In contrast, each of the strains harbored multiple secondary or accessory mutations associated with resistance to protease inhibitors in group M viruses. Residues 10I, 15V, 36I, 41K, 62V, 63T/A/K/I, 64V, 71V, and 93L were identified in most strains. The presence of multiple natural sequence polymorphisms associated with drug resistance in the protease gene of group O viruses may contribute to a more rapid emergence of drug resistance phenotype and treatment failure in group O-infected patients.
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Affiliation(s)
- K C Luk
- AIDS Research and Retrovirus Discovery, Abbott Laboratories, Abbott Park, Illinois 60064, USA
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32
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Plantier JC, Damond F, Souquières S, Brun-Vézinet F, Simon F, Barin F. V3 serological subtyping of human immunodeficiency virus type 2 infection is not relevant. J Clin Microbiol 2001; 39:3803-7. [PMID: 11574625 PMCID: PMC88441 DOI: 10.1128/jcm.39.10.3803-3807.2001] [Citation(s) in RCA: 5] [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
V3 enzyme immunoassays have been shown to discriminate effectively between human immunodeficiency virus type 1 (HIV-1) subtypes. The aim of this study was to investigate the feasibility of V3 serotyping for HIV-2 infection. We serotyped 29 sera with three peptides, corresponding to the V3 loop of subtypes A, B, and D of HIV-2. Sera were collected from HIV-2-infected patients, whose infecting strains were sequenced and subjected to phylogenetic analysis. Our results indicate that HIV-2 serotyping using V3 peptides is not relevant. V3 serotyping data were not consistent with genotyping results. The V3-A and V3-D peptides displayed poor discrimination, and the V3-B peptide was not representative of circulating viruses. Comparison of amino acid sequences and serotype reactivities demonstrated the importance of positions 309 and 314, located on either side of the tip of the V3 loop, in antibody binding.
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Affiliation(s)
- J C Plantier
- Laboratoire de Virologie, Equipe Associée 2639, Université François Rabelais, Tours, France
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33
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Souquière S, Bibollet-Ruche F, Robertson DL, Makuwa M, Apetrei C, Onanga R, Kornfeld C, Plantier JC, Gao F, Abernethy K, White LJ, Karesh W, Telfer P, Wickings EJ, Mauclère P, Marx PA, Barré-Sinoussi F, Hahn BH, Müller-Trutwin MC, Simon F. Wild Mandrillus sphinx are carriers of two types of lentivirus. J Virol 2001; 75:7086-96. [PMID: 11435589 PMCID: PMC114437 DOI: 10.1128/jvi.75.15.7086-7096.2001] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mandrillus sphinx, a large primate living in Cameroon and Gabon and belonging to the Papionini tribe, was reported to be infected by a simian immunodeficiency virus (SIV) (SIVmndGB1) as early as 1988. Here, we have identified a second, highly divergent SIVmnd (designated SIVmnd-2). Genomic organization differs between the two viral types; SIVmnd-2 has the additional vpx gene, like other SIVs naturally infecting the Papionini tribe (SIVsm and SIVrcm) and in contrast to the other SIVmnd type (here designated SIVmnd-1), which is more closely related to SIVs infecting l'hoest (Cercopithecus lhoesti lhoesti) and sun-tailed (Cercopithecus lhoesti solatus) monkeys. Importantly, our epidemiological studies indicate a high prevalence of both types of SIVmnd; all 10 sexually mature wild-living monkeys and 3 out of 17 wild-born juveniles tested were infected. The geographic distribution of SIVmnd seems to be distinct for the two types: SIVmnd-1 viruses were exclusively identified in mandrills from central and southern Gabon, whereas SIVmnd-2 viruses were identified in monkeys from northern and western Gabon, as well as in Cameroon. SIVmnd-2 full-length sequence analysis, together with analysis of partial sequences from SIVmnd-1 and SIVmnd-2 from wild-born or wild-living mandrills, shows that the gag and pol regions of SIVmnd-2 are closest to those of SIVrcm, isolated from red-capped mangabeys (Cercocebus torquatus), while the env gene is closest to that of SIVmnd-1. pol and env sequence analyses of SIV from a related Papionini species, the drill (Mandrillus leucophaeus), shows a closer relationship of SIVdrl to SIVmnd-2 than to SIVmnd-1. Epidemiological surveys of human immunodeficiency virus revealed a case in Cameroon of a human infected by a virus serologically related to SIVmnd, raising the possibility that mandrills represent a viral reservoir for humans similar to sooty mangabeys in Western Africa and chimpanzees in Central Africa.
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Affiliation(s)
- S Souquière
- Laboratoire de Virologie, UGENET, SEGC, Réserve de la Lopé, Centre International de Recherches Médicales, Franceville, Gabon
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34
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Simon F, Souquière S, Damond F, Kfutwah A, Makuwa M, Leroy E, Rouquet P, Berthier JL, Rigoulet J, Lecu A, Telfer PT, Pandrea I, Plantier JC, Barré-Sinoussi F, Roques P, Müller-Trutwin MC, Apetrei C. Synthetic peptide strategy for the detection of and discrimination among highly divergent primate lentiviruses. AIDS Res Hum Retroviruses 2001; 17:937-52. [PMID: 11461679 DOI: 10.1089/088922201750290050] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We developed a simple, rapid, inexpensive, and highly sensitive and specific strategy for the detection and lineage differentiation of primate lentiviruses (PIV-ELISA). It is based on the use of two indirect ELISA methods using synthetic peptides mapping the gp41/36 region (detection component) and the V3 region (differentiation component) of four lentivirus lineages, namely SIVcpz/HIV-1 (groups M, O, N, and SIVcpz-gab), SIVmnd, SIVagm, and SIVsm/SIVmac/HIV-2. This strategy was evaluated with panels of sera originating from both humans and nonhuman primates. The human reference panel consisted of 144 HIV Western blot (WB)-positive sera in which the corresponding virus had been genotyped (HIV-1: 72 group M, 28 group O, and 6 group N; HIV-2: 21 subtype A and 10 subtype B; and 7 HIV-1+2) and 105 HIV WB-negative samples. The nonhuman primate reference panel consisted of 24 sera from monkeys infected by viruses belonging to the four lineages included in the PIV-ELISA strategy (5 chimpanzees, 5 macaques, 8 mandrills, and 6 vervets) and 42 samples from seronegative animals. Additional field evaluation panels consisted of 815 human sera from Gabon, Cameroon, and France and 537 samples from 25 nonhuman primate species. All the samples from the two reference panels were correctly detected and discriminated by PIV-ELISA. In the human field evaluation panel, the gp41/36 component correctly identified all the test samples, with 98% specificity. The V3 component discriminated 206 HIV-1 group M, 98 group O, 12 group M+O, and 128 HIV-2 sera. In the primate field evaluation panel, both gp41/36 and V3 detected and discriminated all the WB-positive samples originating from monkeys infected with SIVcpz, SIVagm-ver, SIVmnd-1, SIVmnd-2, SIVdrl, or SIVsun. These results were confirmed by genotyping in every case. Four SIV-infected red-capped mangabeys (confirmed by PCR) were correctly identified by gp41/36, but only two reacted with the V3 peptides in the absence of a specific SIVrcm V3 peptide. Addition of a V3 SIVrcm peptide discriminated all the SIVrcm-positive samples. Fourteen Papio papio samples were positive for SIVsm gp 36 and by WB, but negative by PCR, whereas three Papio cynocephalus samples were positive by gp41/36 but indeterminate by WB and negative by PCR. This combined ELISA system is thus highly sensitive and specific for antibodies directed against HIV and SIV. In addition, the V3-based serotyping results always agreed with genotyping results. This method should prove useful for studies of lentivirus prevalence and diversity in human and nonhuman primates, and may also have the potential to detect previously undescribed SIVs.
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Affiliation(s)
- F Simon
- Laboratoire de Virologie and Centre de Primatologie, Centre International de Recherches Médicales, Franceville, Gabon
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35
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Baldrich-Rubio E, Anagonou S, Stirrups K, Lafia E, Candotti D, Lee H, Allain JP. A complex human immunodeficiency virus type 1 A/G/J recombinant virus isolated from a seronegative patient with AIDS from Benin, West Africa. J Gen Virol 2001; 82:1095-1106. [PMID: 11297684 DOI: 10.1099/0022-1317-82-5-1095] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A human immunodeficiency virus type 1 (HIV-1(B76)) originating from Benin (West Africa) was isolated and characterized. The patient had severe clinical AIDS and presented an unusual serological profile. Only one out of five different detection assays was able to demonstrate the presence of antibodies to HIV, whereas confirmatory assays remained indeterminate. In contrast, both plasma viral load and p24 antigen level were unusually high. HIV-1 infection was proved by viral RNA and proviral DNA amplification. HIV-1(B76) partially purified lysate reacted strongly with all anti-HIV-1-positive sera from the region but B76 plasma did not react with subtype A control viral antigen. This patient is likely to have had severe acquired immune dysfunction explaining her lack of immunological reactivity. Phylogenetic analysis of the genome identified a complex HIV-1 A/G/J recombinant. The gag and pol genes, and the majority of nef,are characteristic of subtype A; the gag/pol junction, the 3' end of pol, vpu and env genes were characteristic of subtype G; vif, vpr and the 5' end of nef were subtype J. In addition, part of the HIV-1(B76) genome had considerable sequence similarity with the previously described CRF06 cpx (BFP90) isolate. HIV-1(B76) did not exhibit any remarkable replication properties or cell tropism in vitro.
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Affiliation(s)
- E Baldrich-Rubio
- Department of Haematology, University of Cambridge, East Anglia Blood Centre, Long Road, Cambridge CB2 2PT, UK1
| | - S Anagonou
- Department of Microbiology, Centre National Hôpitalier Universitaire and Programme National de Lutte contre le SIDA, Cotonou, Benin2
| | - K Stirrups
- Department of Haematology, University of Cambridge, East Anglia Blood Centre, Long Road, Cambridge CB2 2PT, UK1
| | - E Lafia
- Department of Microbiology, Centre National Hôpitalier Universitaire and Programme National de Lutte contre le SIDA, Cotonou, Benin2
| | | | - H Lee
- Department of Haematology, University of Cambridge, East Anglia Blood Centre, Long Road, Cambridge CB2 2PT, UK1
| | - J P Allain
- Division of Transfusion Medicine, Department of Haematology, University of Cambridge, UK4
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36
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Korber B, Gaschen B, Yusim K, Thakallapally R, Kesmir C, Detours V. Evolutionary and immunological implications of contemporary HIV-1 variation. Br Med Bull 2001; 58:19-42. [PMID: 11714622 DOI: 10.1093/bmb/58.1.19] [Citation(s) in RCA: 364] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Evolutionary modelling studies indicate less than a century has passed since the most recent common ancestor of the HIV-1 pandemic strains and, in that time frame, an extraordinarily diverse viral population has developed. HIV-1 employs a multitude of schemes to generate variants: accumulation of base substitutions, insertions and deletions, addition and loss of glycosylation sites in the envelope protein, and recombination. A comparison between HIV and influenza virus illustrates the extraordinary scale of HIV variation, and underscores the importance of exploring innovative HIV vaccine strategies. Deeper understanding of the implications of variation for both antibody and T-cell responses may help in the effort to rationally design vaccines that stimulate broad cross-reactivity. The impact of HIV-1 variation on host immune response is reviewed in this context.
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Affiliation(s)
- B Korber
- Division of Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 98545, USA
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37
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Allain JP. Will genome detection replace serology in blood screening for microbial agents? Best Pract Res Clin Haematol 2000; 13:615-29. [PMID: 11102280 DOI: 10.1053/beha.2000.0103] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The residual risk of transfusion-transmitted viral infection in developed countries is considered minimal or negligible. However, zero risk remains a strong political objective. Genomic screening for HCV, HIV and HBV represents a major advance, eliminating infectious blood donations collected during the pre-seroconversion window period, rare cases of immunosilent infections and, possibly, a large spectrum of viral variants. In Western countries, HCV RNA genomic screening started on pools of 16-400 plasma samples from individual donations. Pooling may produce false-positive and false-negative results. Individual donation testing is more suitable to blood screening but requires multiplexing, automation, and affordable cost. Because donations from individuals who are HBV DNA-negative/serologically positive, or those apparently recovered from HCV infection, may remain infectious, it is unlikely that HBsAg, anti-HCV, and anti-HIV will be discontinued when genomic screening is extended to all three viruses. HIV-1 p24 antigen may prove redundant with HIV RNA screening. Anti-HTLV-I and HTLV-II will remain more effective than genomic testing.
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Affiliation(s)
- J P Allain
- Division of Transfusion Medicine, University of Cambridge, Cambridge, UK
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38
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Ayouba A, Souquières S, Njinku B, Martin PM, Müller-Trutwin MC, Roques P, Barré-Sinoussi F, Mauclère P, Simon F, Nerrienet E. HIV-1 group N among HIV-1-seropositive individuals in Cameroon. AIDS 2000; 14:2623-5. [PMID: 11101082 DOI: 10.1097/00002030-200011100-00033] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- A Ayouba
- Centre Pasteur du Cameroun, Laboratoire National de Santé Publique et de Reference, Yaoundé
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39
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Candotti D, Adu-Sarkodie Y, Davies F, Baldrich-Rubio E, Stirrups K, Lee H, Allain JP. AIDS in an HIV-seronegative Ghanaian woman with intersubtype A/G recombinant HIV-1 infection. J Med Virol 2000; 62:1-8. [PMID: 10935981 DOI: 10.1002/1096-9071(200009)62:1<1::aid-jmv1>3.0.co;2-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A 29-year-old Ghanaian woman who developed AIDS while being HIV-antibody seronegative was investigated during a collaborative study aimed at the identification of viral causes of a HIV-seronegative AIDS syndrome in West Africa. Plasma was screened with a panel of EIA tests for antibodies to HIV and HIV-1 p24 antigen. Retroviral infection was investigated by detection of reverse transcriptase (RT) activity in plasma, viral RNA amplification and quantification, and virus isolation. Positive amplification products were sequenced and phylogenetic analyses were carried out. Most EIA tests were unable to demonstrate the presence of anti-HIV anti-bodies, whereas confirmatory assays yielded inconclusive results. Retroviral infection was documented by detection of RT activity, HIV-1-specific genomic amplification and virus isolation. This virus was HIV-1 subtype A with an unusual six amino acid insertion in the gp120 V4 loop and with the nef gene of subtype G. The patient's plasma did not react with either autologous or heterologous viral lysates or HIV-1 peptides, whereas antibodies to other viral antigens were present. In conclusion, the Ghanaian patient exhibited a rare subtype A/G recombinant HIV-1 infection with a near absence of a HIV-specific humoral response. The lack of detectable antibody response might be due to either a highly pathogenic, rapidly fatal, HIV-1 infection preventing the development of the typical humoral immune response or to a host-related dysfunction of the immune system. Direct antigenemia or genomic detection of the virus should be undertaken when clinical or biological data suggests an HIV infection in the absence of serological evidence.
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Affiliation(s)
- D Candotti
- Department of Haematology, University of Cambridge, United Kingdom
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40
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Makuwa M, Souquière S, Apetrei C, Tevi-Benissan C, Bedjabaga I, Simon F. HIV prevalence and strain diversity in Gabon: the end of a paradox. AIDS 2000; 14:1275-6. [PMID: 10894293 DOI: 10.1097/00002030-200006160-00026] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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41
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Montavon C, Toure-Kane C, Liegeois F, Mpoudi E, Bourgeois A, Vergne L, Perret JL, Boumah A, Saman E, Mboup S, Delaporte E, Peeters M. Most env and gag subtype A HIV-1 viruses circulating in West and West Central Africa are similar to the prototype AG recombinant virus IBNG. J Acquir Immune Defic Syndr 2000; 23:363-74. [PMID: 10866228 DOI: 10.1097/00126334-200004150-00001] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The genetic subtype was identified in gag and env of 219 HIV-1-positive samples collected in different African countries, 44 from Senegal, 55 from Cameroon, 82 from Gabon, and 38 from Djibouti. In total, 20 (9.1%) samples had discordant subtypes between gag and env, 6 of 44 (13.9%) in Senegal, 4 of 55 (7.2%) in Cameroon, 1 of 38 (2.6%) in Djibouti, and 10 of 82 (12.1%) in Gabon. Subtypes A and G were predominantly involved in the recombination events. Phylogenetic tree analysis of gag showed that an important number of the A sequences form a distinct subcluster with the AG-IBNG prototype strain (a complex A/G mosaic virus): 27 of 32 (84.3%) in Senegal, 12 of 17 (70.6%) in Nigeria, 24 of 39 (61.5%) in Cameroon, and 38 of 70 (54.3%) in Gabon. Full-length genome analysis of 3 and additional sequences in pol for 10 such strains confirmed that they have a similar complex A/G mosaic genomic structure. These data suggest that in West Africa, most probably between 60% and 84% of the subtype A viruses are recombinant AG-IBNG viruses. This finding has potential implications on future vaccine, diagnostic, and treatment strategies. The actual and future role of these viruses in the global pandemic must be monitored in all new molecular epidemiologic studies, a discrimination between subtype A and AG-IBNG-like viruses is necessary.
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Affiliation(s)
- C Montavon
- Laboratoire Retrovirus, Institut pour la Recherche en Developement, Montpellier, France
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42
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Montavon C, Toure-Kane C, Liegeois F, Mpoudi E, Bourgeois A, Vergne L, Perret JL, Boumah A, Saman E, Mboup S, Delaporte E, Peeters M. Most env and gag Subtype A HIV-1 Viruses Circulating in West and West Central Africa Are Similar to the Prototype AG Recombinant Virus IBNG. J Acquir Immune Defic Syndr 2000. [DOI: 10.1097/00042560-200004150-00001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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43
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Abstract
Evidence of simian immunodeficiency virus (SIV) infection has been reported for 26 different species of African nonhuman primates. Two of these viruses, SIVcpz from chimpanzees and SIVsm from sooty mangabeys, are the cause of acquired immunodeficiency syndrome (AIDS) in humans. Together, they have been transmitted to humans on at least seven occasions. The implications of human infection by a diverse set of SIVs and of exposure to a plethora of additional human immunodeficiency virus-related viruses are discussed.
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Affiliation(s)
- B H Hahn
- Department of Medicine, Howard Hughes Medical Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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44
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Corbet S, Müller-Trutwin MC, Versmisse P, Delarue S, Ayouba A, Lewis J, Brunak S, Martin P, Brun-Vezinet F, Simon F, Barre-Sinoussi F, Mauclere P. env sequences of simian immunodeficiency viruses from chimpanzees in Cameroon are strongly related to those of human immunodeficiency virus group N from the same geographic area. J Virol 2000; 74:529-34. [PMID: 10590144 PMCID: PMC111566 DOI: 10.1128/jvi.74.1.529-534.2000] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.6] [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) group N from Cameroon is phylogenetically close, in env, to the simian immunodeficiency virus (SIV) cpz-gab from Gabon and SIVcpz-US of unknown geographic origin. We screened 29 wild-born Cameroonian chimpanzees and found that three (Cam3, Cam4, and Cam5) were positive for HIV-1 by Western blotting. Mitochondrial DNA sequence analysis demonstrated that Cam3 and Cam5 belonged to Pan troglodytes troglodytes and that Cam4 belonged to P. t. vellerosus. Genetic analyses of the viruses together with serological data demonstrated that at least one of the two P. t. troglodytes chimpanzees (Cam5) was infected in the wild, and revealed a horizontal transmission between Cam3 and Cam4. These data confirm that P. t. troglodytes is a natural host for HIV-1-related viruses. Furthermore, they show that SIVcpz can be transmitted in captivity, from one chimpanzee subspecies to another. All three SIVcpz-cam viruses clustered with HIV-1 N in env. The full Cam3 SIVcpz genome sequence showed a very close phylogenetic relationship with SIVcpz-US, a virus identified in a P. t. troglodytes chimpanzee captured nearly 40 years earlier. Like SIVcpz-US, SIVcpz-cam3 was closely related to HIV-1 N in env, but not in pol, supporting the hypothesis that HIV-1 N results from a recombination event. SIVcpz from chimpanzees born in the wild in Cameroon are thus strongly related in env to HIV-1 N from Cameroon, demonstrating the geographic coincidence of these human and simian viruses and providing a further strong argument in favor of the origin of HIV-1 being in chimpanzees.
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Affiliation(s)
- S Corbet
- Unité de Biologie des Rétrovirus, Institut Pasteur, Paris, France
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45
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Bilodeau PS, Domsic JK, Stoltzfus CM. Splicing regulatory elements within tat exon 2 of human immunodeficiency virus type 1 (HIV-1) are characteristic of group M but not group O HIV-1 strains. J Virol 1999; 73:9764-72. [PMID: 10559286 PMCID: PMC113023 DOI: 10.1128/jvi.73.12.9764-9772.1999] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the NL4-3 strain of human immunodeficiency virus type 1 (HIV-1), regulatory elements responsible for the relative efficiencies of alternative splicing at the tat, rev, and the env/nef 3' splice sites (A3 through A5) are contained within the region of tat exon 2 and its flanking sequences. Two elements affecting splicing of tat, rev, and env/nef mRNAs have been localized to this region. First, an exon splicing silencer (ESS2) in NL4-3, located approximately 70 nucleotides downstream from the 3' splice site used to generate tat mRNA, acts specifically to inhibit splicing at this splice site. Second, the A4b 3' splice site, which is the most downstream of the three rev 3' splice sites, also serves as an element inhibiting splicing at the env/nef 3' splice site A5. These elements are conserved in some but not all HIV-1 strains, and the effects of these sequence changes on splicing have been investigated in cell transfection and in vitro splicing assays. SF2, another clade B virus and member of the major (group M) viruses, has several sequence changes within ESS2 and uses a different rev 3' splice site. However, splicing is inhibited by the two elements similarly to NL4-3. As with the NL4-3 strain, the SF2 A4b AG dinucleotide overlaps an A5 branchpoint, and thus the inhibitory effect may result from competition of the same site for two different splicing factors. The sequence changes in ANT70C, a member of the highly divergent outlier (group O) viruses, are more extensive, and ESS2 activity in tat exon 2 is not present. Group O viruses also lack the rev 3' splice site A4b, which is conserved in all group M viruses. Mutagenesis of the most downstream rev 3' splice site of ANT70C does not increase splicing at A5, and all of the branchpoints are upstream of the two rev 3' splice sites. Thus, splicing regulatory elements in tat exon 2 which are characteristic of most group M HIV-1 strains are not present in group O HIV-1 strains.
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Affiliation(s)
- P S Bilodeau
- Department of Microbiology, Program in Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA
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46
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Peeters M, Liegeois F, Torimiro N, Bourgeois A, Mpoudi E, Vergne L, Saman E, Delaporte E, Saragosti S. Characterization of a highly replicative intergroup M/O human immunodeficiency virus type 1 recombinant isolated from a Cameroonian patient. J Virol 1999; 73:7368-75. [PMID: 10438826 PMCID: PMC104263 DOI: 10.1128/jvi.73.9.7368-7375.1999] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/1999] [Accepted: 05/24/1999] [Indexed: 11/20/2022] Open
Abstract
A Cameroonian patient with antibodies reacting simultaneously to human immunodeficiency virus type 1 (HIV-1) group O- and group M-specific V3-loop peptides was identified. In order to confirm that this patient was coinfected with both viruses, PCRs with O- and M-specific discriminating primers corresponding to different regions of the genome were carried out with both primary lymphocyte DNA and the corresponding viral strains isolated from three consecutive patient samples. The PCR data suggested that this patient is coinfected with a group M virus and a recombinant M/O virus. Indeed, only type M gag sequences could be amplified, while for the env region, both type M and O sequences were amplified, from plasma or from DNA extracted from primary lymphocytes. Sequence analysis of a complete recombinant genome isolated from the second sample (97CA-MP645 virus isolate) revealed two intergroup breakpoints, one in the vpr gene and the second in the long terminal repeat region around the TATA box. Comparison of the type M sequences shared by the group M and the recombinant M/O viruses showed that these sequences were closely related, with only 3% genetic distance, suggesting that the M virus was one of the parental viruses. In this report we describe for the first time a recombination event in vivo between viruses belonging to two different groups, leading to a replicative virus. Recombination between strains with such distant lineages (65% overall homology) may contribute substantially to the emergence of new HIV-1 variants. We documented that this virus replicates well and became predominant in vitro. At this time, group O viruses represent a minority of the strains responsible for the HIV-1 pandemic. If such recombinant intergroup viruses gained better fitness, inducing changes in their biological properties compared to the parental group O virus, the prevalences of group O sequences could increase rapidly. This will have important implications for diagnosis of HIV-1 infections by serological and molecular tests, as well as for antiviral treatment.
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Affiliation(s)
- M Peeters
- Institut de Recherche pour le Developpement, Montpellier, France.
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47
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Takehisa J, Zekeng L, Ido E, Yamaguchi-Kabata Y, Mboudjeka I, Harada Y, Miura T, Kaptu L, Hayami M. Human immunodeficiency virus type 1 intergroup (M/O) recombination in cameroon. J Virol 1999; 73:6810-20. [PMID: 10400779 PMCID: PMC112766 DOI: 10.1128/jvi.73.8.6810-6820.1999] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here we describe, for the first time, recombinants between two highly divergent major groups of human immunodeficiency virus type 1 (HIV-1), M and O, within a Cameroonian woman infected with three different HIV-1 strains, a group O virus, a subtype D virus, and a recently reported IBNG (A/G)-like recombinant virus. Using nested extra-long PCR amplification, we sequenced from the pol region to the env region including accessory genes of the viral genome obtained from the patient's uncultured peripheral blood mononuclear cells and examined the phylogenetic position of each gene. Compared with sequential blood samples obtained in 1995 and 1996, there were multiple segmental exchanges between three HIV-1 strains (O, D, and IBNG) and all the recombinants appeared to be derived from a common M/O ancestor. Importantly, recombination between groups M and O occurred, even though the homology between these two groups is 69, 76, 68, and 55% in the gag, pol, vif-vpr, and env regions, respectively. Recombination between strains with such distant lineages may contribute substantially to generating new HIV-1 variants.
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Affiliation(s)
- J Takehisa
- Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
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48
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Yang C, Pieniazek D, Owen SM, Fridlund C, Nkengasong J, Mastro TD, Rayfield MA, Downing R, Biryawaho B, Tanuri A, Zekeng L, van der Groen G, Gao F, Lal RB. Detection of phylogenetically diverse human immunodeficiency virus type 1 groups M and O from plasma by using highly sensitive and specific generic primers. J Clin Microbiol 1999; 37:2581-6. [PMID: 10405405 PMCID: PMC85288 DOI: 10.1128/jcm.37.8.2581-2586.1999] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The high degree of genetic diversity within human immunodeficiency virus type 1 (HIV-1), which includes two major groups, M (major) and O (outlier), and various env subtypes within group M (subtypes A to J), has made designing assays that will detect all known HIV-1 strains difficult. We have developed a generic primer set based on the conserved immunodominant region of transmembrane protein gp41 that can reliably amplify as few as 10 copies/PCR of viral DNA from near-full-length clones representing group M subtypes A to H (subtypes I and J were not available). The assay is highly sensitive in detecting plasma viral RNA from HIV-1 strains of diverse geographic origins representing different subtypes of HIV-1 group M as well as HIV-1 group O. Of the 253 group M plasma specimens (subtypes A, 68 specimens; B, 71; C, 19; D, 27; E, 23; F, 33; and G, 12), 250 (98.8%) were amplified by using the gp41 M/O primer set. More importantly, all 32 (100%) group O plasma samples were also amplified with these primers. In vitro spiking experiments further revealed that the assay could reliably detect as few as 25 copies/ml of viral RNA and gave positive signals in HIV-1-seropositive specimens with plasma copy numbers below the limits of detection by all commercially available viral load assays. In addition, analysis of five seroconversion panels indicated that the assay is highly sensitive for early detection of plasma viremia during the "window period." Thus, the highly sensitive assay will be useful for early detection of HIV-1 in clinical specimens from all known HIV-1 infections, regardless of their genotypes and geographic origins.
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Affiliation(s)
- C Yang
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
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Mas A, Quiñones-Mateu ME, Domingo E, Soriano V. Phylogeny of HIV type 1 group O isolates based on env gene sequences. AIDS Res Hum Retroviruses 1999; 15:769-73. [PMID: 10357472 DOI: 10.1089/088922299310854] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- A Mas
- Centro de Biología Molecular Severo Ochoa, UAM, Cantoblanco, Madrid, Spain
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50
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Candotti D, Tareau C, Barin F, Joberty C, Rosenheim M, M'Pele P, Huraux JM, Agut H. Genetic subtyping and V3 serotyping of HIV type 1 isolates in Congo. AIDS Res Hum Retroviruses 1999; 15:309-14. [PMID: 10052763 DOI: 10.1089/088922299311501] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- D Candotti
- Laboratoire de Virologie EA 2387, CERVI, Hôpital Pitié-Salpêtière, Paris, France
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