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Kim MJ, Yu KL, Han R, Lee Y, Oh K, You JC. Identification of a Non-Nucleoside Reverse Transcriptase Inhibitor against Human Immunodeficiency Virus-1. ACS Infect Dis 2023; 9:1582-1592. [PMID: 37415514 DOI: 10.1021/acsinfecdis.3c00166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
The HIV-1 infection epidemic remains a global health problem. Current antiretroviral treatments are effective in controlling the progression of a severe infection. However, the emergence of drug resistance requires an urgent identification of new treatment regimes. HIV-1 reverse transcriptase (RTs) has been a successful therapeutic target owing to its high specificity and potent antiviral properties; therefore, it has become an essential component of current HIV-1 standard treatments. This study identified a new HIV-1 RTs inhibitor (Compound #8) that is structurally unique and greatly effective against HIV-1 through chemical library screening and a medicinal chemistry program by analyzing the structure-activity relationship (SAR). Further analysis of molecular docking and mechanisms of action demonstrated that Compound #8 is a novel type of HIV-1 non-nucleoside reverse transcriptase inhibitor (NNRTI) with a flexible binding mode. Therefore, it exhibits great therapeutic potential when combined with other existing HIV-1 drugs. Our current studies suggest that Compound #8 is a promising novel scaffold for the development of new HIV-1 treatments.
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Affiliation(s)
- Min-Jung Kim
- Avixgen Inc., 2477 Nambusunhwan-ro, Seocho, Seoul 06725, Republic of Korea
| | - Kyung Lee Yu
- National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho, Seoul 06591, Republic of Korea
| | - Ri Han
- College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak, Seoul 06974, Republic of Korea
| | - Yoonji Lee
- College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak, Seoul 06974, Republic of Korea
| | - Kyungsoo Oh
- College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak, Seoul 06974, Republic of Korea
- Center for Metareceptome Research, Graduate School of Pharmaceutical Sciences, Chung-Ang University, 84 Heukseok-ro, Dongjak, Seoul 06974, Republic of Korea
| | - Ji Chang You
- Avixgen Inc., 2477 Nambusunhwan-ro, Seocho, Seoul 06725, Republic of Korea
- National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho, Seoul 06591, Republic of Korea
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Mulinge MM, Oluoch JO, Abisi HK, Otieno LE, Anzala O, Wamalwa DC, Nduati RW, Kimani J, Herbeck J, McKinnon L. Age and CD4+ T cell counts are inversely associated with HIV drug resistance mutations in treatment naive female sex workers. Medicine (Baltimore) 2023; 102:e34060. [PMID: 37327289 PMCID: PMC10270489 DOI: 10.1097/md.0000000000034060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/31/2023] [Indexed: 06/18/2023] Open
Abstract
The increasing prevalence of human immunodeficiency virus (HIV) drug resistance mutations (HIVDRM) in untreated seropositive persons has consequences for future treatment options. This is extremely important in key populations such as female sex workers (FSWs), where the prevalence of pretreatment drug resistance (PDR) and associated risk factors are unknown. In this study, we analyzed PDR and associated risk factors in recently diagnosed and treatment-naive FSWs in Nairobi, Kenya. In this cross-sectional study, we used 64 HIV-seropositive plasma samples collected from FSWs between November 2020 and April 2021. To identify HIVDRM, the pol gene was amplified and genotyped using sanger sequencing. The effects of age, tropism, CD4+ T cell count, subtype, and location on HIVDRM counts were examined using Poisson regression. Overall, the prevalence of PDR was 35.9% (95% CI: 24.3-48.9), which was strongly influenced by K103N and M184V mutations, which confer resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) and nucleoside reverse transcriptase inhibitors (NRTI), respectively. Subtype A1 was predominant followed by subtype D with a notable increase in inter-subtype recombinants. We found statistically significant evidence that age was inversely related to HIVDRM. A FSW who is 1 year older had 12% less HIVDRM (incidence rate ratios [IRR]: 0.88; 95% CI: 0.82-0.95; P < .001), after adjusting for CD4+ T cell count, subtype, location, and tropism. Similarly, an increase in CD4+ T cell count by 1 unit, was associated with 0.4% fewer HIVDRM (IRR: 0.996; 95% CI: 0.994-0.998; P = .001), while controlling for the other variables. HIV-1 tropism was not associated with HIVDRM counts. In conclusion, our findings show a high prevalence of NNRTIs. Lower CD4+ T cell counts and younger age were significant risk factors that influenced HIVDRM loads. This finding underscores the relevance of targeted interventions and the importance of continuing to focus on FSWs as a way of addressing the HIV epidemic.
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Affiliation(s)
- Martin M. Mulinge
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
- Kenya AIDS Vaccine Initiative - Institute of Clinical Research (KAVI-ICR), University of Nairobi, Nairobi, Kenya
| | - Jeff O. Oluoch
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Hellen K. Abisi
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
| | - Leon E. Otieno
- Molecular Medicine and Infectious Diseases Laboratory, University of Nairobi, Kenya
| | - Omu Anzala
- Kenya AIDS Vaccine Initiative - Institute of Clinical Research (KAVI-ICR), University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Dalton C. Wamalwa
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Ruth W. Nduati
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Joshua Kimani
- Partners for Health and Development in Africa (PHDA), Nairobi, Kenya
| | - Joshua Herbeck
- Department of Global Health, University of Washington, Seattle, WA
| | - Lyle McKinnon
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
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Singsumran K, Sungkanuparph S. Long-term virological and immunological outcomes between HIV-positive individuals with and without pretreatment HIV drug resistance. Int J STD AIDS 2023; 34:322-327. [PMID: 36626357 DOI: 10.1177/09564624221149775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND Pretreatment HIV drug resistance (PHDR) has emerged after scaling-up access to antiretroviral therapy (ART). This study aimed to compare long-term virological and immunological outcomes between HIV-positive individuals with and without PHDR. METHODS An observational cohort study was conducted in HIV-positive individuals who had a genotypic resistance test performed prior to ART initiation. RESULTS Of 335 participants, 39 were in the PHDR group and 296 were in the control group. ART regimen in PHDR group was adjusted at 6-10 weeks after ART initiation when results of baseline genotypic resistance test were available. Proportions of participants with undetectable viral load were significantly lower in PHDR group at 6 and 12 months (46.2% vs 79.4% (p < .001) and 74.4% vs 90.5% (p = .003), respectively). These virological responses became similar between two groups (p > .05) from 18 through 60 months. Mean change of CD4 counts of PHDR group was significantly lower only at 6 months (+59 vs + 81 cells/mm3 (p = .012); these immunological responses were similar between two groups from 12 through 60 months. CONCLUSION Early virological response was lower in HIV-positive participants with PHDR compared to participants without PHDR. Subsequent adjustment of ART according to pretreatment genotypic resistance has contributed to the long-term virological and immunological success that is similar to participants without PHDR.
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Affiliation(s)
- Kanokwan Singsumran
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Somnuek Sungkanuparph
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, 26685Mahidol University, Samut Prakan, Thailand
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Mótyán JA, Mahdi M, Hoffka G, Tőzsér J. Potential Resistance of SARS-CoV-2 Main Protease (Mpro) against Protease Inhibitors: Lessons Learned from HIV-1 Protease. Int J Mol Sci 2022; 23:3507. [PMID: 35408866 PMCID: PMC8998604 DOI: 10.3390/ijms23073507] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/16/2022] [Accepted: 03/22/2022] [Indexed: 02/06/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome 2 (SARS-CoV-2), has been one of the most devastating pandemics of recent times. The lack of potent novel antivirals had led to global health crises; however, emergence and approval of potent inhibitors of the viral main protease (Mpro), such as Pfizer's newly approved nirmatrelvir, offers hope not only in the therapeutic front but also in the context of prophylaxis against the infection. By their nature, RNA viruses including human immunodeficiency virus (HIV) have inherently high mutation rates, and lessons learnt from previous and currently ongoing pandemics have taught us that these viruses can easily escape selection pressure through mutation of vital target amino acid residues in monotherapeutic settings. In this paper, we review nirmatrelvir and its binding to SARS-CoV-2 Mpro and draw a comparison to inhibitors of HIV protease that were rendered obsolete by emergence of resistance mutations, emphasizing potential pitfalls in the design of inhibitors that may be of important relevance to the long-term use of novel inhibitors against SARS-CoV-2.
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Affiliation(s)
- János András Mótyán
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (J.A.M.); (M.M.); (G.H.)
| | - Mohamed Mahdi
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (J.A.M.); (M.M.); (G.H.)
| | - Gyula Hoffka
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (J.A.M.); (M.M.); (G.H.)
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (J.A.M.); (M.M.); (G.H.)
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Mechanochemical synthesis and characterization of Zidovudine-lamivudine solid dispersion (binary eutectic mixture). J Drug Deliv Sci Technol 2021. [DOI: 10.1016/j.jddst.2021.102639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Baxter JD, Dunn D, Tostevin A, Marvig RL, Bennedbaek M, Cozzi-Lepri A, Sharma S, Kozal MJ, Gompels M, Pinto AN, Lundgren J. Transmitted HIV-1 drug resistance in a large international cohort using next-generation sequencing: results from the Strategic Timing of Antiretroviral Treatment (START) study. HIV Med 2021; 22:360-371. [PMID: 33369017 PMCID: PMC8049964 DOI: 10.1111/hiv.13038] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/11/2020] [Accepted: 11/10/2020] [Indexed: 01/13/2023]
Abstract
OBJECTIVES The aim of this analysis was to characterize transmitted drug resistance (TDR) in Strategic Timing of Antiretroviral Treatment (START) study participants by next-generation sequencing (NGS), a sensitive assay capable of detecting low-frequency variants. METHODS Stored plasma from participants with entry HIV RNA > 1000 copies/mL were analysed by NGS (Illumina MiSeq). TDR was based on the WHO 2009 surveillance definition with the addition of reverse transcriptase (RT) mutations T215N and E138K, and integrase strand transfer inhibitor (INSTI) surveillance mutations (Stanford HIVdb). Drug resistance mutations (DRMs) detected at three thresholds are reported: > 2%, 5% and 20% of the viral population. RESULTS Between 2009 and 2013, START enrolled 4684 antiretroviral therapy (ART)-naïve individuals in 35 countries. Baseline NGS data at study entry were available for 2902 participants. Overall prevalence rates of TDR using a detection threshold of 2%/5%/20% were 9.2%/5.6%/3.2% for nucleoside reverse transcriptase inhibitors (NRTIs), 9.2%/6.6%/4.9% for non-NRTIs, 11.4%/5.5%/2.4% for protease inhibitors (PIs) and 3.5%/1.6%/0.1% for INSTI DRMs and varied by geographic region. Using the 2% detection threshold, individual DRMs with the highest prevalence were: PI M46IL (5.5%), RT K103NS (3.5%), RT G190ASE (3.1%), T215ISCDVEN (2.5%), RT M41L (2.2%), RT K219QENR (1.7%) and PI D30N (1.6%). INSTI DRMs were detected almost exclusively below the 20% detection threshold, most commonly Y143H (0.4%), Q148R (0.4%) and T66I (0.4%). CONCLUSIONS Use of NGS in this study population resulted in the detection of a large proportion of low-level variants which would not have been detected by traditional Sanger sequencing. Global surveillance studies utilizing NGS should provide a more comprehensive assessment of TDR prevalence in different regions of the world.
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Affiliation(s)
- J D Baxter
- Cooper University Hospital/Cooper Medical School of Rowan University, Camden, NJ, USA
| | - D Dunn
- Institute for Global Health, UCL, London, UK
| | - A Tostevin
- Institute for Global Health, UCL, London, UK
| | - R L Marvig
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - M Bennedbaek
- Copenhagen HIV Programme, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - S Sharma
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - M J Kozal
- Yale University School of Medicine, New Haven, CT, USA
| | - M Gompels
- North Bristol NHS Trust, Westbury on Trym, UK
| | - A N Pinto
- The Kirby Institute, University of New South Wales, Sydney, Australia
| | - J Lundgren
- Copenhagen HIV Programme, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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Khairunisa SQ, Megasari NLA, Rahayu RP, Witaningrum AM, Ueda S, Yunifiar M MQ, Indriati DW, Kotaki T, Rusli A, Nasronudin, Kameoka M. Detection of human immunodeficiency virus type 1 transmitted drug resistance among treatment-naive individuals residing in Jakarta, Indonesia. Infect Dis Rep 2020; 12:8740. [PMID: 32874468 PMCID: PMC7447941 DOI: 10.4081/idr.2020.8740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/01/2020] [Indexed: 12/02/2022] Open
Abstract
The presence of transmitted drug resistance (TDR) in human immunodeficiency virus type 1 (HIV-1) infected individuals naive to antiretroviral therapy, may affect the effectiveness of treatment. Jakarta, the capital city of Indonesia, recorded the highest number of cumulative HIV infection cases in the country. This study aimed to identify on the appearance of TDR, as well as to identify HIV-1 subtypes circulating among treatment-naive individuals in Jakarta. Whole blood samples collected from 43 HIV-1 infected, treatment-naive individuals. Viral subtyping and drug resistance testing were performed on HIV-1 pol genes amplified using nested polymerase chain reaction. CRF01_AE was detected most frequently in Jakarta (73.08%). Drug resistance-related major mutation was not detected in protease fragments of pol gene, but two major mutations, K103N (6.67%) and Y181C (6.67%), were detected in reverse transcriptase fragments of pol gene. Our results suggest that TDR was emerged in Jakarta at a certain extent, thus further surveillance study to monitor the TDR prevalence and circulating HIV-1 subtypes in this region is considered to be necessary.
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Affiliation(s)
- Siti Qamariyah Khairunisa
- Doctoral Program,Faculty of Medicine, Universitas Airlangga, Surabaya
- Indonesia-Japan Collaborative Research Centre for Emerging and Reemerging Infectious Diseases (CRCERI), Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Ni Luh Ayu Megasari
- Indonesia-Japan Collaborative Research Centre for Emerging and Reemerging Infectious Diseases (CRCERI), Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Retno Pudji Rahayu
- Indonesia-Japan Collaborative Research Centre for Emerging and Reemerging Infectious Diseases (CRCERI), Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Adiana Mutamsari Witaningrum
- Indonesia-Japan Collaborative Research Centre for Emerging and Reemerging Infectious Diseases (CRCERI), Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Shuhei Ueda
- Indonesia-Japan Collaborative Research Centre for Emerging and Reemerging Infectious Diseases (CRCERI), Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Department of Public Health
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Muhammad Qushai Yunifiar M
- Indonesia-Japan Collaborative Research Centre for Emerging and Reemerging Infectious Diseases (CRCERI), Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Dwi Wahyu Indriati
- Indonesia-Japan Collaborative Research Centre for Emerging and Reemerging Infectious Diseases (CRCERI), Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Department of Health, Vocational Faculty
| | | | - Adria Rusli
- Sulianti Saroso Hospital, Jakarta, Indonesia
| | - Nasronudin
- Indonesia-Japan Collaborative Research Centre for Emerging and Reemerging Infectious Diseases (CRCERI), Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Airlangga Hospital, Universitas Airlangga, Surabaya, Indonesia
| | - Masanori Kameoka
- Indonesia-Japan Collaborative Research Centre for Emerging and Reemerging Infectious Diseases (CRCERI), Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Department of Public Health
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan
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The effect of primary drug resistance on CD4+ cell decline and the viral load set-point in HIV-positive individuals before the start of antiretroviral therapy. AIDS 2019; 33:315-326. [PMID: 30325769 DOI: 10.1097/qad.0000000000002046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To evaluate the effect of primary resistance and selected polymorphic amino-acid substitutions in HIV reverse transcriptase and protease on the CD4 cell count and viral load set point before the start of antiretroviral treatment. DESIGN Prospective cohort study. METHODS A total of 6180 individuals with a resistance test prior to starting antiretroviral treatment accessing care in HIV clinics across Europe who had at least one viral load and one CD4+ test available were included in the analysis. The impact of amino-acid substitutions variants on viral load and CD4+ trends was investigated using linear mixed models. Clusters of mutations were studied using principal component analysis. RESULTS Overall, the detection of any primary resistance was not associated with either the speed of CD4+ cell decline or the viral load set point. However, transmitted nucleoside reverse transcriptase inhibitor and protease inhibitor resistance appeared to be weakly associated with lower viral load set points, as were the polymorphic G16E or Q92K protease mutations. There was some evidence suggesting that these effects varied according to HIV subtype, with the effects of transmitted nucleoside reverse transcriptase inhibitor and protease resistance being particularly marked among individuals with a subtype B virus. A cluster of five polymorphic protease substitutions at position 20, 13, 36, 69 and 89 was associated with less steep CD4+ cell declines and lower viral load set points. CONCLUSION Although we found little evidence for an association between primary resistance and CD4+ speed of decline and viral load set point, the potential role of polymorphic protease (alone or in clusters) and their interplay with HIV subtype needs to be further evaluated.
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Abstract
A molecular epidemiology study of HIV-1 infection was conducted in one hundred diagnosed and untreated HIV-1-infected patients in Cyprus between 2010 and 2012, representing 65.4% of all the reported HIV-1 infections in Cyprus in this three-year period, using a previously defined enrolment strategy. Eighty-two patients were newly diagnosed (genotypic drug resistance testing within six months from diagnosis), and eighteen patients were HIV-1 diagnosed for a longer period or the diagnosis date was unknown. Phylogenetic trees of the pol sequences obtained in this study with reference sequences indicated that subtypes B and A1 were the most common subtypes present and accounted for 41.0 and 19.0% respectively, followed by subtype C (7.0%), F1 (8.0%), CRF02_AG (4.0%), A2 (2.0%), other circulating recombinant forms (CRFs) (7.0%) and unknown recombinant forms (URFs) (12%). Most of the newly-diagnosed study subjects were Cypriots (63%), males (78%) with median age 39 (Interquartile Range, IQR 33–48) reporting having sex with other men (MSM) (51%). A high rate of clustered transmission of subtype B drug-sensitive strains to reverse transcriptase and protease inhibitors was observed among MSM, twenty-eight out of forty-one MSM study subjects (68.0%) infected were implicated in five transmission clusters, two of which are sub-subtype A1 and three of which are subtype B strains. The two largest MSM subtype B clusters included nine and eight Cypriot men, respectively, living in all major cities in Cyprus. There were only three newly diagnosed patients with transmitted drug resistant HIV-1 strains, one study subject from the United Kingdom infected with subtype B strain and one from Romania with sub-subtype A2 strain, both with PI drug resistance mutation M46L and one from Greece with sub-subtype A1 with non-nucleoside reverse transcriptase inhibitors (NNRTI) drug resistance mutation K103N.
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Ghosh AK, Sarkar A. An enantioselective enzymatic desymmetrization route to hexahydro-4 H-furopyranol, a high-affinity ligand for HIV-1 protease inhibitors. Tetrahedron Lett 2017; 58:3230-3233. [PMID: 29200514 DOI: 10.1016/j.tetlet.2017.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
An enantioselective synthesis of (3aS,4S,7aR)-hexahydro-4H-furo[2,3-b]pyran-4-ol, a high-affinity nonpeptide ligand for a variety of potent HIV-1 protease inhibitors is described. The key steps involved a highly enantioselective enzymatic desymmetrization of meso-diacetate, an efficient transacetalization, and a highly diastereoselective reduction of a ketone. This route is amenable to large-scale synthesis using readily available starting materials.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 479 07, United States
| | - Anindya Sarkar
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 479 07, United States
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Transmitted drug resistance in patients with acute/recent HIV infection in Brazil. Braz J Infect Dis 2017; 21:396-401. [PMID: 28539254 PMCID: PMC9427834 DOI: 10.1016/j.bjid.2017.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 03/27/2017] [Accepted: 03/28/2017] [Indexed: 11/20/2022] Open
Abstract
Introduction The widespread use of antiretroviral therapy increased the transmission of antiretroviral resistant HIV strains. Antiretroviral therapy initiation during acute/recent HIV infection limits HIV reservoirs and improves immune response in HIV infected individuals. Transmitted drug resistance may jeopardize the early goals of early antiretroviral treatment among acute/recent HIV infected patients. Methods Patients with acute/recent HIV infection who underwent resistance test before antiretroviral treatment initiation were included in this analysis. HIV-1 sequences were obtained using an in house protease/reverse transcriptase genotyping assay. Transmitted drug resistance was identified according to the Stanford HIV Database for Transmitted Drug Resistance Mutations, based on WHO 2009 surveillance list, and HIV-1 subtyping according to Rega HIV-1 subtyping tool. Comparison between patients with and without transmitted drug resistance was made using Kruskal–Wallis and Chi-square tests. Results Forty-three patients were included, 13 with acute HIV infection and 30 with recent HIV infection. The overall transmitted drug resistance prevalence was 16.3% (95% confidence interval [CI]: 8.1–30.0%). The highest prevalence of resistance (11.6%, 95% CI: 8.1–24.5) was against non-nucleoside reverse transcriptase inhibitors, and K103N was the most frequently identified mutation. Conclusions The high prevalence of nonnucleoside reverse transcriptase inhibitors resistance indicates that efavirenz-based regimen without prior resistance testing is not ideal for acutely/recently HIV-infected individuals in our setting. In this context, the recent proposal of including integrase inhibitors as a first line regimen in Brazil could be an advantage for the treatment of newly HIV infected individuals. However, it also poses a new challenge, since integrase resistance test is not routinely performed for antiretroviral naive individuals. Further studies on transmitted drug resistance among acutely/recently HIV-infected are needed to inform the predictors of transmitted resistance and the antiretroviral therapy outcomes among these population.
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Barral MF, Sousa AK, Santos AF, Abreu CM, Tanuri A, Soares MA, for the Brazilian Consortium for th. Identification of Novel Resistance-Related Polymorphisms in HIV-1 Subtype C RT Connection and RNase H Domains from Patients Under Virological Failure in Brazil. AIDS Res Hum Retroviruses 2017; 33:465-471. [PMID: 27875905 DOI: 10.1089/aid.2015.0376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Mutations in the connection and RNase H C-terminal reverse transcriptase (RT) domains of HIV-1 have been shown to impact drug resistance to RT inhibitors. However, their impact in the context of non-B subtypes has been poorly assessed. This study aimed to characterize resistance-related mutations in the C-terminal portions of RT in treatment-failing patients from southern Brazil, a region with endemic HIV-1 subtype C (HIV-1C). Viral RNA was isolated and reverse transcribed from 280 infected subjects, and genomic regions were analyzed by polymerase chain reaction, DNA sequencing, and phylogenetic analysis. Two novel mutations, M357R and E529D, were evidenced in Brazilian HIV-1C strains from treatment-failing patients. In global viral isolates of subjects on treatment, M357R was selected in HIV-1C and CRF01_AE and E529D was selected in HIV-1 subtype B (HIV-1B). While most C-terminal RT mutations described for HIV-1B also occur in HIV-1C, this work pinpointed novel mutations that display subtype-specific predominance or occurrence.
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Affiliation(s)
- Maria F.M. Barral
- Departamento de Medicina, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Arielly K.P. Sousa
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - André F. Santos
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Celina M. Abreu
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amilcar Tanuri
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo A. Soares
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
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Onywera H, Maman D, Inzaule S, Auma E, Were K, Fredrick H, Owiti P, Opollo V, Etard JF, Mukui I, Kim AA, Zeh C. Surveillance of HIV-1 pol transmitted drug resistance in acutely and recently infected antiretroviral drug-naïve persons in rural western Kenya. PLoS One 2017; 12:e0171124. [PMID: 28178281 PMCID: PMC5298248 DOI: 10.1371/journal.pone.0171124] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/16/2017] [Indexed: 11/21/2022] Open
Abstract
HIV-1 transmitted drug resistance (TDR) is of increasing public health concern in sub-Saharan Africa with the rollout of antiretroviral (ARV) therapy. Such data are, however, limited in Kenya, where HIV-1 drug resistance testing is not routinely performed. From a population-based household survey conducted between September and November 2012 in rural western Kenya, we retrospectively assessed HIV-1 TDR baseline rates, its determinants, and genetic diversity among drug-naïve persons aged 15–59 years with acute HIV-1 infections (AHI) and recent HIV-1 infections (RHI) as determined by nucleic acid amplification test and both Limiting Antigen and BioRad avidity immunoassays, respectively. HIV-1 pol sequences were scored for drug resistance mutations using Stanford HIVdb and WHO 2009 mutation guidelines. HIV-1 subtyping was computed in MEGA6. Eighty seven (93.5%) of the eligible samples were successfully sequenced. Of these, 8 had at least one TDR mutation, resulting in a TDR prevalence of 9.2% (95% CI 4.7–17.1). No TDR was observed among persons with AHI (n = 7). TDR prevalence was 4.6% (95% CI 1.8–11.2) for nucleoside reverse transcriptase inhibitors (NRTIs), 6.9% (95% CI 3.2–14.2) for non- nucleoside reverse transcriptase inhibitors (NNRTIs), and 1.2% (95% CI 0.2–6.2) for protease inhibitors. Three (3.4% 95% CI 0.8–10.1) persons had dual-class NRTI/NNRTI resistance. Predominant TDR mutations in the reverse transcriptase included K103N/S (4.6%) and M184V (2.3%); only M46I/L (1.1%) occurred in the protease. All the eight persons were predicted to have different grades of resistance to the ARV regimens, ranging from potential low-level to high-level resistance. HIV-1 subtype distribution was heterogeneous: A (57.5%), C (6.9%), D (21.8%), G (2.3%), and circulating recombinant forms (11.5%). Only low CD4 count was associated with TDR (p = 0.0145). Our findings warrant the need for enhanced HIV-1 TDR monitoring in order to inform on population-based therapeutic guidelines and public health interventions.
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Affiliation(s)
- Harris Onywera
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
- * E-mail: (CZ); (HO)
| | - David Maman
- Epicentre, Médecins Sans Frontières (MSF), Paris, France
| | - Seth Inzaule
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Erick Auma
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Kennedy Were
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Harrison Fredrick
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Prestone Owiti
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Valarie Opollo
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Jean-François Etard
- TransVIHMI IRD UMI 233 –INSERM U 1175 –Université de Montpellier, Montpellier, France
| | - Irene Mukui
- National AIDS and STI Control Programme (NASCOP), Ministry of Health, Nairobi, Kenya
| | - Andrea A. Kim
- US Centers for Disease Control and Prevention (CDC), Nairobi, Kenya
| | - Clement Zeh
- US Centers for Disease Control and Prevention (CDC), Kisumu, Kenya
- * E-mail: (CZ); (HO)
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Gonzalez-Serna A, Glas AC, Brumme CJ, Poon AFY, Nohpal De La Rosa A, Mudrikova T, Dias Lima V, Wensing AMJ, Harrigan R. Genotypic susceptibility score (GSS) and CD4+ T cell recovery in HIV-1 patients with suppressed viral load. J Antimicrob Chemother 2016; 72:496-503. [PMID: 27999069 DOI: 10.1093/jac/dkw455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/23/2016] [Accepted: 09/23/2016] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES HIV drug resistance, measured by the genotypic susceptibility score (GSS), has a deleterious effect on the virological outcome of HIV-1-infected patients. However, it is not known if GSS retains any predictive value for CD4 recovery in patients with suppressed viral load. METHODS Four hundred and six patients on virological failure (>500 copies/mL) with GSS : <6 months prior to switch therapy who achieved undetectable plasma viral load (<50 copies/mL) within 1 year, remained undetectable >1 year on an unchanged regimen and had CD4 data available during entire follow-up were included. Adjusted and unadjusted analyses of all characteristics at switch related to CD4 recovery were made for three time frames: (i) 'switch-suppression'; (ii) 'suppression-1 year'; and (iii) 'switch-1 year'. RESULTS Higher GSS was associated with a greater CD4 recovery between 'switch' and '1 year' in the unadjusted analysis (P = 0.010); however, the effect of GSS was no longer statistically significant after adjusting for pre-switch clinical (CD4 count and plasma viral load) and demographic variables. Furthermore, only a lower pre-switch CD4 count was associated with increased CD4 recovery in the 'suppression-1 year' period in both unadjusted and adjusted models. The main CD4 recovery occurred in 'switch-suppression' and the variables associated, both unadjusted and adjusted, were CD4 and plasma viral load at switch, maintaining a trend for GSS (P = 0.06). CONCLUSIONS In individuals who re-suppressed HIV viraemia after switching therapy, regimens having a higher GSS were associated with improved CD4 recovery only during the period from switch to virological suppression, but, once viral load is re-suppressed, the GSS of the new regimen has no further effect on subsequent CD4 recovery.
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Affiliation(s)
- Alejandro Gonzalez-Serna
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada .,Laboratory of Molecular Immunobiology, Hospital General Universitario Gregorio Maranon, Madrid, Spain
| | - Arie C Glas
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - C J Brumme
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Art F Y Poon
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | | | - Tania Mudrikova
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Annemarie M J Wensing
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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15
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Witaningrum AM, Kotaki T, Khairunisa SQ, Yunifiar M MQ, Indriati DW, Bramanthi R, Nasronudin, Kameoka M. Genotypic Characterization of Human Immunodeficiency Virus Type 1 Derived from Antiretroviral Therapy-Naive Individuals Residing in Sorong, West Papua. AIDS Res Hum Retroviruses 2016; 32:812-7. [PMID: 27009513 DOI: 10.1089/aid.2016.0054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Papua and West Papua provinces have the highest prevalence rate of human immunodeficiency virus type 1 (HIV-1) infection in Indonesia; however, data on the molecular epidemiology of HIV-1 are limited. We conducted a genotypic study on HIV-1 genes derived from antiretroviral therapy-naive individuals residing in Sorong, West Papua. HIV-1 genomic fragments were amplified from 43 peripheral blood samples, and sequencing analysis of the genes was carried out. Of the 43 samples, 41 protease (PR), 31 reverse transcriptase (RT), 26 gag, and 25 env genes were sequenced. HIV-1 subtyping revealed that CRF01_AE (48.8%, 21/43) and subtype B (41.9%, 18/43) were the major subtypes prevalent in the region, whereas other recombinant forms were also detected. Major drug resistance-associated mutations for PR inhibitors were not detected; however, mutations for the RT inhibitors, A62V and E138A, appeared in a few samples, indicating the possible emergence of transmitted HIV-1 drug resistance in Sorong, West Papua.
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Affiliation(s)
- Adiana Mutamsari Witaningrum
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Tomohiro Kotaki
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
- Department of International Health, Kobe University Graduate School of Health Sciences, Hyogo, Japan
| | - Siti Qamariyah Khairunisa
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Muhammad Qushai Yunifiar M
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Dwi Wahyu Indriati
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | | | - Nasronudin
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
- Faculty of Medicine, Airlangga University, Surabaya, Indonesia
| | - Masanori Kameoka
- Department of International Health, Kobe University Graduate School of Health Sciences, Hyogo, Japan
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan
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Doravirine Suppresses Common Nonnucleoside Reverse Transcriptase Inhibitor-Associated Mutants at Clinically Relevant Concentrations. Antimicrob Agents Chemother 2016; 60:2241-7. [PMID: 26833152 DOI: 10.1128/aac.02650-15] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/17/2016] [Indexed: 12/31/2022] Open
Abstract
Doravirine (DOR), which is currently in a phase 3 clinical trial, is a novel human immunodeficiency type 1 virus (HIV-1) nonnucleoside reverse transcriptase inhibitor (NNRTI). DOR exhibits potent antiviral activity against wild-type virus and K103N, Y181C, and K103N/Y181C mutant viruses, with 50% inhibitory concentrations (IC50s) of 12, 21, 31, and 33 nM, respectively, when measured in 100% normal human serum (NHS). To assess the potential for DOR to suppress NNRTI-associated and rilpivirine (RPV)-specific mutants at concentrations achieved in the clinic setting, inhibitory quotients (IQs) were calculated by determining the ratio of the clinical trough concentration over the antiviral IC50for each virus with DOR and RPV and efavirenz (EFV). DOR displayed IQs of 39, 27, and 25 against the K103N, Y181C, and K103N/Y181C mutants, respectively. In contrast, RPV exhibited IQs of 4.6, 1.4, and 0.8, and EFV showed IQs of 2.5, 60, and 1.9 against these viruses, respectively. DOR also displayed higher IQs than those of RPV and EFV against other prevalent NNRTI-associated mutants, with the exception of Y188L. Both DOR and EFV exhibited higher IQs than RPV when analyzed with RPV-associated mutants. Resistance selections were conducted with K103N, Y181C, G190A, and K103N/Y181C mutants at clinically relevant concentrations of DOR, RPV, and EFV. No viral breakthrough was observed with DOR, whereas breakthrough viruses were readily detected with RPV and EFV against Y181C and K103N viruses, respectively. These data suggest that DOR should impose a higher barrier to the development of resistance than RPV and EFV at the concentrations achieved in the clinic setting.
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Baxter JD, Dunn D, White E, Sharma S, Geretti AM, Kozal MJ, Johnson MA, Jacoby S, Llibre JM, Lundgren J. Global HIV-1 transmitted drug resistance in the INSIGHT Strategic Timing of AntiRetroviral Treatment (START) trial. HIV Med 2015; 16 Suppl 1:77-87. [PMID: 25711326 DOI: 10.1111/hiv.12236] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2014] [Indexed: 01/21/2023]
Abstract
OBJECTIVES HIV-1 transmitted drug resistance (TDR) in treatment-naïve individuals is a well-described phenomenon. Baseline genotypic resistance testing is considered standard of care in most developed areas of the world. The aim of this analysis was to characterize HIV-1 TDR and the use of resistance testing in START trial participants. METHODS In the Strategic Timing of AntiRetroviral Treatment (START) trial, baseline genotypic resistance testing results were collected at study entry and analysed centrally to determine the prevalence of TDR in the study population. Resistance was based on a modified 2009 World Health Organization definition to reflect newer resistance mutations. RESULTS Baseline resistance testing was available in 1946 study participants. Higher rates of testing occurred in Europe (86.7%), the USA (81.3%) and Australia (89.9%) as compared with Asia (22.2%), South America (1.8%) and Africa (0.1%). The overall prevalence of TDR was 10.1%, more commonly to nonnucleoside reverse transcriptase inhibitors (4.5%) and nucleoside reverse transcriptase inhibitors (4%) compared with protease inhibitors (2.8%). The most frequent TDR mutations observed were M41L, D67N/G/E, T215F/Y/I/S/C/D/E/V/N, 219Q/E/N/R, K103N/S, and G190A/S/E in reverse transcriptase, and M46I/L and L90M in protease. By country, the prevalence of TDR was highest in Australia (17.5%), France (16.7%), the USA (12.6%) and Spain (12.6%). No participant characteristics were identified as predictors of the presence of TDR. CONCLUSIONS START participants enrolled in resource-rich areas of the world were more likely to have baseline resistance testing. In Europe, the USA and Australia, TDR prevalence rates varied by country.
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Affiliation(s)
- J D Baxter
- Cooper University Hospital/Cooper Medical School of Rowan University, Camden, NJ, USA
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Viciana I, González-Domenech CM, Palacios R, Delgado M, Del Arco A, Tellez F, Jarilla F, Fernández S, Clavijo E, Santos J. Clinical, virological and phylogenetic characterization of a multiresistant HIV-1 strain outbreak in naive patients in southern Spain. J Antimicrob Chemother 2015; 71:357-61. [PMID: 26483513 DOI: 10.1093/jac/dkv332] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 09/15/2015] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND We describe the characteristics of an HIV-1 strain with six viral reverse transcriptase mutations (D67N, T69N/D, V118I, V179D, T215S and K219Q), which we have called the Malaga strain. This strain was detected in treatment-naive patients from southern Spain. METHODS The study was undertaken at the Virgen de la Victoria Hospital, Malaga, a reference centre for the study of HIV-1 genotype resistance in Andalusia (the 'Costa del Sol'), Spain. Genotypic resistance testing was done in an automated sequencer. Phylogenetic analysis was performed using a 630 bp region of the reverse transcriptase with the mutations mentioned. RESULTS Between 2007 and 2014, we detected the Malaga strain in 30 treatment-naive patients. All were MSM, seen at five hospitals on the Costa del Sol. In all cases, the HIV-1 was subtype B with viral tropism R5. Phylogenetic analysis based on the reverse transcriptase sequence showed consistent grouping (with a bootstrap value of the common node of 100%) of the isolates that shared the mutation pattern mentioned. This strain has not been detected elsewhere or in previously treated patients. All of the patients treated with first-line combination ART responded. CONCLUSIONS We report a cluster of an HIV-1 strain with multiple resistance mutations that was transmitted over a period of >8 years, affecting 30 naive patients from the same geographical area. The strain was susceptible to first-line combination ART.
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Affiliation(s)
- I Viciana
- UGCI de Enfermedades Infecciosas y Microbiología Clínica, Hospital Virgen de la Victoria, Málaga, Spain Instituto de Investigación de Biomedicina de Málaga (IBIMA), Malaga, Spain
| | | | - R Palacios
- UGCI de Enfermedades Infecciosas y Microbiología Clínica, Hospital Virgen de la Victoria, Málaga, Spain Instituto de Investigación de Biomedicina de Málaga (IBIMA), Malaga, Spain
| | - M Delgado
- UGCI de Enfermedades Infecciosas y Microbiología Clínica, Hospital Regional Carlos Haya, Málaga, Spain
| | - A Del Arco
- UGC de Enfermedades Infecciosas, Hospital Costa del Sol, Marbella, Spain
| | - F Tellez
- UGC de Enfermedades Infecciosas y Microbiología Clínica, Hospital La Línea, AGS Campo de Gibraltar, Cádiz, Spain
| | - F Jarilla
- Servicio de Medicina Interna, Hospital Comarcal de Antequera, Malaga, Spain
| | - S Fernández
- Servicio de Medicina Interna, Hospital Comarcal de la Axarquía, Vélez-Málaga, Spain
| | - E Clavijo
- UGCI de Enfermedades Infecciosas y Microbiología Clínica, Hospital Virgen de la Victoria, Málaga, Spain
| | - J Santos
- UGCI de Enfermedades Infecciosas y Microbiología Clínica, Hospital Virgen de la Victoria, Málaga, Spain Instituto de Investigación de Biomedicina de Málaga (IBIMA), Malaga, Spain
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Matthew JS, Virginia LK, David MP. Human immunodeficiency virus (HIV) in Washington, D.C.: Prevalence of antiretroviral resistance in treatment nave patients from 2007 to 2010. ACTA ACUST UNITED AC 2015. [DOI: 10.5897/jahr2015.0327] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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20
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Kotaki T, Khairunisa SQ, Witaningrum AM, M MQY, Sukartiningrum SD, Diansyah MN, Rahayu RP, Nasronudin, Kameoka M. HIV-1 transmitted drug resistance mutations among antiretroviral therapy-Naïve individuals in Surabaya, Indonesia. AIDS Res Ther 2015; 12:5. [PMID: 28561075 PMCID: PMC4336490 DOI: 10.1186/s12981-015-0046-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 02/10/2015] [Indexed: 11/16/2022] Open
Abstract
Background The emergence of transmitted drug resistance (TDR) compromises the effect of antiretroviral therapy (ART), resulting in treatment failure of human immunodeficiency virus (HIV) disease. Although more than a decade has passed since ART was introduced into Indonesia, information on TDR is limited. Here, a genotypic study of TDR among ART-naïve individuals was conducted in Surabaya, Indonesia. Method HIV-1 seropositive participants were recruited from the communities of commercial sex workers and intravenous drug users as well as from the university teaching hospital in Surabaya. Protease (PR) and reverse transcriptase (RT) genes were sequenced in order to conduct HIV-1 subtyping and phylogenetic analysis and to detect TDR. TDR was defined as the presence of at least one surveillance drug resistance mutation on the WHO list or major drug resistance mutations in the International AIDS Society-USA panel. Result Fifty two and 47 of the PR and RT genes, respectively, were successfully sequenced in the 58 samples. HIV-1 subtyping revealed that 86.3% (50/58) of the sequenced samples were classified as CRF01_AE, 8.6% as subtype B, 3.4% as B/CRF01_AE, and 1.7% as A/G/CRF01_AE. TDR of PR inhibitors was not detected in this study. In contrast, TDR of RT inhibitors was detected in 4.3% (2/47) of samples. In addition, minor drug resistance mutations were detected in 98.1% (51/52) and 12.8% (6/47) of PR and RT genes, respectively. Conclusion This study clarified the predominance of the CRF01_AE strain in Surabaya, Indonesia. The prevalence of TDR was below 5%, indicating that the currently available first-line regimen is still effective in Surabaya. However, the prevalence might be underestimated since we detected only major population of HIV-1 in individuals. Therefore, continuous surveillance is required in order to detect the emergence of TDR in the early phase. Electronic supplementary material The online version of this article (doi:10.1186/s12981-015-0046-y) contains supplementary material, which is available to authorized users.
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Mulu A, Lange T, Liebert UG, Maier M. Clade homogeneity and Pol gene polymorphisms in chronically HIV-1 infected antiretroviral treatment naive patients after the roll out of ART in Ethiopia. BMC Infect Dis 2014; 14:158. [PMID: 24655349 PMCID: PMC3976149 DOI: 10.1186/1471-2334-14-158] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 03/18/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Despite the increasing use of antiretroviral treatment (ART) recent data on frequency and pattern of drug resistance mutations in Ethiopia is not available. Furthermore with increasing mobility of people HIV-1 subtypes other than the predominant subtype C may likely be introduced from the neighbouring countries. This study was aimed to determine the molecular characterization and pre-antiretroviral treatment resistance mutations among HIV-1 chronically infected ART naïve patients after the roll out of ART in Ethiopia. METHODS Viral RNA was determined in 160 baseline plasma samples. The entire PR and the first 335 codons (76%) of the RT regions of the pol gene of the HIV-1 genome (N = 160) were amplified and sequenced using an in-house assay. Genotypic drug resistance was defined as the presence of one or more resistance-related mutations as specified by the consensus mutation of Stanford University HIVDB and the International Antiviral Society (IAS) mutation lists. RESULTS A predominance of HIV-1 subtype C (98.7%) was observed. The level of drug resistance is found to be 5.6% and 13.1% according to the Stanford University HIVDB drug resistance interpretation algorithms and the International Antiviral Society mutation lists, respectively. Mutations conferring simultaneous resistance to NRTIs and NNRTIs were not detected and no major PR mutation was found. However, a high rate of polymorphic changes both in PR and RT regions were observed. Moreover, twenty four (15%) monophyletic transmission clusters with bootstrap value of 99% were found. CONCLUSIONS Strong evidence for consistent HIV-1C clade homogeneity and low influx of other variant into the country was found. The level of drug resistance observed in chronically infected treatment naïve patients which exceeds the WHO estimates suggests the need for incorporation of HIV-1 drug resistance testing prior to ART initiation. The occurrence of monophyletic transmission clusters affecting (24/160) individuals indicates their potential risk related practice. Thus, an intensified public health intervention program and monitoring of HIV drug resistance testing appears indispensible.
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Affiliation(s)
- Andargachew Mulu
- Institute of Virology, Leipzig University Leipzig, Germany
- Department of Microbiology, College of Medicine and Health Sciences, University of Gondar Gondar, Ethiopia
| | - Thomas Lange
- Institute of Virology, Leipzig University Leipzig, Germany
| | | | - Melanie Maier
- Institute of Virology, Leipzig University Leipzig, Germany
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Miron RE, Smith RJ. Resistance to protease inhibitors in a model of HIV-1 infection with impulsive drug effects. Bull Math Biol 2013; 76:59-97. [PMID: 24194434 DOI: 10.1007/s11538-013-9903-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 09/02/2013] [Indexed: 02/05/2023]
Abstract
BACKGROUND The emergence of drug resistance is one of the most prevalent reasons for treatment failure in HIV therapy. This has severe implications for the cost of treatment, survival and quality of life. METHODS We use mathematical modelling to describe the interaction between T cells, HIV-1 and protease inhibitors. We use impulsive differential equations to examine the effects of different levels of protease inhibitors in a T cell. We classify three different regimes according to whether the drug efficacy is low, intermediate or high. The model includes two strains: the wild-type strain, which initially dominates in the absence of drugs, and the mutant strain, which is the less efficient competitor, but has more resistance to the drugs. RESULTS Drug regimes may take trajectories through one, two or all three regimes, depending on the dosage and the dosing schedule. Stability analysis shows that resistance does not emerge at low drug levels. At intermediate drug levels, drug resistance is guaranteed to emerge. At high drug levels, either the drug-resistant strain will dominate or, in the absence of longer-lived reservoirs of infected cells, a region exists where viral elimination could theoretically occur. We provide estimates of a range of dosages and dosing schedules where the trajectories lie either solely within a region or cross multiple regions. CONCLUSION Under specific circumstances, if the drug level is physiologically tolerable, elimination of free virus is theoretically possible. This forms the basis for theoretical control using combination therapy and for understanding the effects of partial adherence.
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Affiliation(s)
- Rachelle E Miron
- Department of Mathematics, The University of Ottawa, 585 King Edward Ave, Ottawa, ON, K1N 6N5, Canada
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Prevalence of transmitted antiretroviral drug resistance differs between acutely and chronically HIV-infected patients. J Acquir Immune Defic Syndr 2012; 61:258-62. [PMID: 22692092 DOI: 10.1097/qai.0b013e3182618f05] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The associations of acute HIV infection (AHI) and other predictors with transmitted drug resistance (TDR) prevalence were assessed in a cohort of HIV-infected, antiretroviral-naïve patients. AHI was defined as being seronegative with detectable HIV RNA. Binomial regression was used to estimate prevalence ratios and 95% confidence intervals for associations with TDR. Among 43 AHI patients, TDR prevalence was 20.9%, whereas prevalence was 8.6% among 677 chronically infected patients. AHI was associated with 1.9 times the prevalence of TDR (95% confidence intervals: 1.0 to 3.6) in multivariable analysis. AHI patients may represent a vanguard group that portends increasing TDR in the future.
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Buskin SE, Zhang S, Thibault CS. Prevalence of and viral outcomes associated with primary HIV-1 drug resistance. Open AIDS J 2012; 6:181-7. [PMID: 23049668 PMCID: PMC3462330 DOI: 10.2174/1874613601206010181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 08/18/2011] [Accepted: 09/19/2011] [Indexed: 11/26/2022] Open
Abstract
Primary, or transmitted, HIV antiretroviral resistance is an ongoing concern despite continuing development of
new antiretroviral therapies. We examined HIV surveillance data, including both patient demographic characteristics and
laboratory data, combined with HIV genotypic test results to evaluate the comprehensiveness of drug resistance
surveillance, prevalence of primary drug resistance, and impact, if any, of primary resistance on population-based
virological outcomes. The King County, WA Variant, Atypical, and Resistant HIV Surveillance (VARHS) system
increased coverage of eligible genotypic testing – within three months of an HIV diagnosis among antiretroviral naïve
individuals -- from – 15% in 2003 to 69% in 2010. VARHS under-represented females, Blacks, Native Americans, and
injection drug users. Primary drug resistance was more common among males, individuals aged 20 – 29 years, men who
had sex with men, and individuals with an initial CD4+ lymphocyte count of 200 cells/µL and higher. High level
resistance to two or three antiretroviral classes declined over time. Over 90% of sequences were HIV-1 subtype B. The
proportion of individuals with a most recent viral load (closest to April 2011) that was undetectable (<50 copies/mL) was
not statistically significantly associated with primary drug resistance. This was true for both number and type of
antiretroviral drug class; although small numbers of specimens with drug resistance may have limited our statistical
power. In summary, although we found disparities in testing coverage and prevalence of drug resistance, we were unable
to detect a significantly deleterious impact of primary drug resistance based on a most recent viral load.
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Affiliation(s)
- S E Buskin
- Public Health - Seattle & King County, Seattle, WA, USA ; University of Washington, Seattle, WA, USA
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Factors limiting the transmission of HIV mutations conferring drug resistance: fitness costs and genetic bottlenecks. Sci Rep 2012; 2:320. [PMID: 22432052 PMCID: PMC3307053 DOI: 10.1038/srep00320] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 02/20/2012] [Indexed: 11/08/2022] Open
Abstract
Transmission of HIV strains with drug-resistance mutations (DRMs) causes public health problems in resource-rich countries. We use a stochastic model, with data from viral competition experiments, to analyze the effect of fitness costs (FCs) and genetic bottlenecks on limiting transmission of 10 clinically significant DRMs. Transmission of DRMs with low FCs (∼0.2%) is similar to wild-type; transmission chains last ∼8 generations causing clusters of ∼60 infected individuals. Genetic bottlenecks substantially limit transmission of DRMs with moderately high FCs (∼0.6%); chains last ∼1–3 generations with transmission clusters of 2–7. Transmission of DRMs with extremely high FCs (>6%) only occurs from ∼5% of index cases. DRMs can revert to wild-type and remain as minority strains, within treatment-naïve individuals, undetectable by current resistance assays. We calculate, based on assay sensitivity, the length of time each DRM is detectable within individuals. Taken together, our results imply a hidden epidemic of transmitted resistance may exist.
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Taniguchi T, Nurutdinova D, Grubb JR, Önen NF, Shacham E, Donovan M, Overton ET. Transmitted drug-resistant HIV type 1 remains prevalent and impacts virologic outcomes despite genotype-guided antiretroviral therapy. AIDS Res Hum Retroviruses 2012; 28:259-64. [PMID: 21877906 DOI: 10.1089/aid.2011.0022] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Trends in transmitted drug resistance-associated mutations (TDRM) in HIV-1infection vary depending on geographic and cohort characteristics. The impact of TDRM among patients receiving fully active combination antiretroviral therapy (cART) is poorly characterized. This was a retrospective study of 801 HIV-1-infected treatment-naive patients from 2001 to 2009 who had pre-cART genotype resistance test results available. The prevalence of TDRM was compared for each year strata. Multivariate Cox proportional hazards regression models were used to assess factors associated with virologic failure at 48 weeks. TDRM was detected in 136 (17%) patients with ≥2 class TDRM in 20 patients. K103N/S was the most frequent (n=77). There were no changes in the prevalence of mutations over time (P(trend)=0.67). Six hundred and eleven patients were started on cART. Virologic failure occurred in 38% of those with TDRM and 24% of those without (p<0.01). In multivariate analysis, nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance was associated with a 1.5-fold increased risk of virologic failure. TDRM remains common among treatment-naive HIV-1-infected patients, affecting one in six patients. Transmission of NNRTI drug resistance was associated with risk of virologic failure despite initiation of genotype-guided cART.
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Affiliation(s)
- Toshibumi Taniguchi
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri
| | | | - Jessica R. Grubb
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri
| | - Nur F. Önen
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri
| | - Enbal Shacham
- Health Communication Research Laboratory, George Warren Brown School of Social Work, Washington University, St. Louis, Missouri
| | - Michael Donovan
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri
| | - Edgar Turner Overton
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri
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Lai CC, Hung CC, Chen MY, Sun HY, Lu CL, Tseng YT, Chang SF, Su YC, Liu WC, Hsieh CY, Wu PY, Chang SY, Chang SC. Trends of transmitted drug resistance of HIV-1 and its impact on treatment response to first-line antiretroviral therapy in Taiwan. J Antimicrob Chemother 2012; 67:1254-60. [DOI: 10.1093/jac/dkr601] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Effect of pretreatment HIV-1 drug resistance on immunological, virological, and drug-resistance outcomes of first-line antiretroviral treatment in sub-Saharan Africa: a multicentre cohort study. THE LANCET. INFECTIOUS DISEASES 2011; 12:307-17. [PMID: 22036233 DOI: 10.1016/s1473-3099(11)70255-9] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND The effect of pretreatment HIV-1 drug resistance on the response to first-line combination antiretroviral therapy (ART) in sub-Saharan Africa has not been assessed. We studied pretreatment drug resistance and virological, immunological, and drug-resistance treatment outcomes in a large prospective cohort. METHODS HIV-1 infected patients in the PharmAccess African Studies to Evaluate Resistance Monitoring (PASER-M) cohort started non-nucleoside reverse transcriptase inhibitor-based ART at 13 clinical sites in six countries, from 2007 to 2009. We used the International Antiviral Society-USA drug resistance mutation list and the Stanford algorithm to classify participants into three pretreatment drug resistance categories: no pretreatment drug resistance, pretreatment drug resistance with fully active ART prescribed, or pretreatment drug resistance with reduced susceptibility to at least one prescribed drug. We assessed risk factors of virological failure (≥400 copies per mL) and acquired drug resistance after 12 months of ART by use of multilevel logistic regression with multiple imputations for missing data. CD4 cell count increase was estimated with linear mixed models. FINDINGS Pretreatment drug resistance results were available for 2579 (94%) of 2733 participants; 2404 (93%) had no pretreatment drug resistance, 123 (5%) had pretreatment drug resistance to at least one prescribed drug, and 52 (2%) had pretreatment drug resistance and received fully active ART. Compared with participants without pretreatment drug resistance, the odds ratio (OR) for virological failure (OR 2·13, 95% CI 1·44-3·14; p<0·0001) and acquired drug-resistance (2·30, 1·55-3·40; p<0·0001) was increased in participants with pretreatment drug resistance to at least one prescribed drug, but not in those with pretreatment drug resistance and fully active ART. CD4 count increased less in participants with pretreatment drug resistance than in those without (35 cells per μL difference after 12 months; 95% CI 13-58; p=0·002). INTERPRETATION At least three fully active antiretroviral drugs are needed to ensure an optimum response to first-line regimens and to prevent acquisition of drug resistance. Improved access to alternative combinations of antiretroviral drugs in sub-Saharan Africa is warranted. FUNDING The Netherlands Ministry of Foreign Affairs.
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Hightow-Weidman LB, Jones K, Phillips G, Wohl A, Giordano, for The YMSM of Color SPN TP. Baseline clinical characteristics, antiretroviral therapy use, and viral load suppression among HIV-positive young men of color who have sex with men. AIDS Patient Care STDS 2011; 25 Suppl 1:S9-14. [PMID: 21711145 DOI: 10.1089/apc.2011.9881] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Given the continued high incidence of HIV infection in the United States among racial/ethnic minority young men who have sex with men (YMSM), and an appreciation that antiretroviral therapy (ART) can provide personal and public health benefits, attention is needed to enhance the detection of HIV-infected youth and engage them in medical care and support services that encourage sustained HIV treatment and suppression of viremia. Poor retention in clinical care has been associated with higher mortality, an increase in HIV RNA, and decreased CD4 cell count. The goal of the current study was to evaluate the health care utilization and health outcomes of HIV-infected racial/ethnic minority YMSM enrolled in an outreach, linkage, and retention study funded by the Health Resources and Services Administration (HRSA) HIV/AIDS Bureau (HAB). We hypothesized that among racial/ethnic minority YMSM, baseline CD4 counts and usage of ART are influenced by age, race, drug and alcohol use, and mental health symptoms. Overall, 155 subjects had at least a baseline CD4 count recorded at study entry. There was a low rate of ART use in this population with only one-half of the cohort with CD4 counts ≤ 350 cells/mm(3) being prescribed ART to treat their infection. However, of those youth who were started on ART, the majority (74%) did achieve undetectable viral loads (< 400 copies). Given the continued increase in cases of HIV infection among racial/ethnic minority YMSM, efforts to increase both the provision of ART and support services that encourage adherence in this population are warranted.
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Affiliation(s)
| | - Karen Jones
- The George Washington University School of Public Health and Health Services, Washington, District of Columbia
| | - Gregory Phillips
- The George Washington University School of Public Health and Health Services, Washington, District of Columbia
| | - Amy Wohl
- Los Angeles County Department of Public Health, Los Angeles, California
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Hurt CB. Transmitted resistance to HIV integrase strand-transfer inhibitors: right on schedule. Antivir Ther 2011; 16:137-40. [PMID: 21447861 DOI: 10.3851/imp1750] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Transmitted drug resistance (TDR), the primary acquisition of an HIV variant already resistant to antiretrovirals, affects approximately 15% of all new infections in the United States. Historically, from the time initial agents in the reverse transcriptase, protease and entry inhibitor classes were introduced, it took 3-5 years before the first case reports of TDR appeared. With the description of the first two cases of transmitted integrase stand-transfer inhibitor resistance, it is only a matter of time before the prevalence of TDR affecting this newest antiretroviral class reaches a level warranting baseline resistance testing for all patients entering care.
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Affiliation(s)
- Christopher B Hurt
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, USA.
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31
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Poon AFY, Aldous JL, Mathews WC, Kitahata M, Kahn JS, Saag MS, Rodríguez B, Boswell SL, Frost SDW, Haubrich RH. Transmitted drug resistance in the CFAR network of integrated clinical systems cohort: prevalence and effects on pre-therapy CD4 and viral load. PLoS One 2011; 6:e21189. [PMID: 21701595 PMCID: PMC3118815 DOI: 10.1371/journal.pone.0021189] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 05/22/2011] [Indexed: 01/16/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) genomes often carry one or more mutations associated with drug resistance upon transmission into a therapy-naïve individual. We assessed the prevalence and clinical significance of transmitted drug resistance (TDR) in chronically-infected therapy-naïve patients enrolled in a multi-center cohort in North America. Pre-therapy clinical significance was quantified by plasma viral load (pVL) and CD4+ cell count (CD4) at baseline. Naïve bulk sequences of HIV-1 protease and reverse transcriptase (RT) were screened for resistance mutations as defined by the World Health Organization surveillance list. The overall prevalence of TDR was 14.2%. We used a Bayesian network to identify co-transmission of TDR mutations in clusters associated with specific drugs or drug classes. Aggregate effects of mutations by drug class were estimated by fitting linear models of pVL and CD4 on weighted sums over TDR mutations according to the Stanford HIV Database algorithm. Transmitted resistance to both classes of reverse transcriptase inhibitors was significantly associated with lower CD4, but had opposing effects on pVL. In contrast, position-specific analyses of TDR mutations revealed substantial effects on CD4 and pVL at several residue positions that were being masked in the aggregate analyses, and significant interaction effects as well. Residue positions in RT with predominant effects on CD4 or pVL (D67 and M184) were re-evaluated in causal models using an inverse probability-weighting scheme to address the problem of confounding by other mutations and demographic or risk factors. We found that causal effect estimates of mutations M184V/I (-1.7 log₁₀pVL) and D67N/G (-2.1[³√CD4] and 0.4 log₁₀pVL) were compensated by K103N/S and K219Q/E/N/R. As TDR becomes an increasing dilemma in this modern era of highly-active antiretroviral therapy, these results have immediate significance for the clinical management of HIV-1 infections and our understanding of the ongoing adaptation of HIV-1 to human populations.
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Affiliation(s)
- Art F. Y. Poon
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Jeannette L. Aldous
- Department of Medicine, University of California San Diego, San Diego, California, United States of America
| | - W. Christopher Mathews
- Department of Medicine, University of California San Diego, San Diego, California, United States of America
| | - Mari Kitahata
- University of Washington, Seattle, Washington, United States of America
| | - James S. Kahn
- University of California San Francisco, San Francisco, California, United States of America
| | - Michael S. Saag
- University of Alabama Birmingham, Birmingham, Alabama, United States of America
| | - Benigno Rodríguez
- Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Stephen L. Boswell
- Fenway Community Health/Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Richard H. Haubrich
- Department of Medicine, University of California San Diego, San Diego, California, United States of America
- * E-mail:
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Ceccherini-Silberstein F, Cento V, Calvez V, Perno CF. The use of human immunodeficiency virus resistance tests in clinical practice. Clin Microbiol Infect 2011; 16:1511-7. [PMID: 20731678 DOI: 10.1111/j.1469-0691.2010.03353.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Important progress has been made in recent years in the development and clinical use of drugs for the treatment of human immunodeficiency virus type 1 (HIV-1) infection. Nevertheless, when antiretroviral therapy fails to be fully suppressive, new viral variants emerge, thus allowing HIV-1 to escape from drug pressure by accumulating mutations. Between 50% and 70% of treated patients with virological rebound harbour some form of drug-resistant virus; transmitted drug resistance in drug-naïve populations has reached 5-20% in areas of the world with access to treatment. The emergence of drug-resistant viruses remains the limiting factor in HIV-1 management, being a major cause of treatment failure, and being associated with clinical progression and death. All international guidelines focus on the importance of tailoring antiretroviral therapy to the individual patient, on the basis onf HIV-1 genetic data, integrated with clinical, laboratory and therapeutic information. The aim of this review is to provide useful information to clinicians and virologists about how and when to use genotypic resistance testing in clinical practice, especially in the management of the first stages of HIV-1 patient care and treatment decisions.
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Detection of minority resistance during early HIV-1 infection: natural variation and spurious detection rather than transmission and evolution of multiple viral variants. J Virol 2011; 85:8359-67. [PMID: 21632754 DOI: 10.1128/jvi.02582-10] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Reports of a high frequency of the transmission of minority viral populations with drug-resistant mutations (DRM) are inconsistent with evidence that HIV-1 infections usually arise from mono- or oligoclonal transmission. We performed ultradeep sequencing (UDS) of partial HIV-1 gag, pol, and env genes from 32 recently infected individuals. We then evaluated overall and per-site diversity levels, selective pressure, sequence reproducibility, and presence of DRM and accessory mutations (AM). To differentiate biologically meaningful mutations from those caused by methodological errors, we obtained multinomial confidence intervals (CI) for the proportion of DRM at each site and fitted a binomial mixture model to determine background error rates for each sample. We then examined the association between detected minority DRM and the virologic failure of first-line antiretroviral therapy (ART). Similar to other studies, we observed increased detection of DRM at low frequencies (average, 0.56%; 95% CI, 0.43 to 0.69; expected UDS error, 0.21 ± 0.08% mutations/site). For 8 duplicate runs, there was variability in the proportions of minority DRM. There was no indication of increased diversity or selection at DRM sites compared to other sites and no association between minority DRM and AM. There was no correlation between detected minority DRM and clinical failure of first-line ART. It is unlikely that minority viral variants harboring DRM are transmitted and maintained in the recipient host. The majority of low-frequency DRM detected using UDS are likely errors inherent to UDS methodology or a consequence of error-prone HIV-1 replication.
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34
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A novel methodology for large-scale phylogeny partition. Nat Commun 2011; 2:321. [PMID: 21610724 PMCID: PMC6045912 DOI: 10.1038/ncomms1325] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 04/21/2011] [Indexed: 01/24/2023] Open
Abstract
Understanding the determinants of virus transmission is a fundamental step for effective design of screening and intervention strategies to control viral epidemics. Phylogenetic analysis can be a valid approach for the identification of transmission chains, and very-large data sets can be analysed through parallel computation. Here we propose and validate a new methodology for the partition of large-scale phylogenies and the inference of transmission clusters. This approach, on the basis of a depth-first search algorithm, conjugates the evaluation of node reliability, tree topology and patristic distance analysis. The method has been applied to identify transmission clusters of a phylogeny of 11,541 human immunodeficiency virus-1 subtype B pol gene sequences from a large Italian cohort. Molecular transmission chains were characterized by means of different clinical/demographic factors, such as the interaction between male homosexuals and male heterosexuals. Our method takes an advantage of a flexible notion of transmission cluster and can become a general framework to analyse other epidemics.
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Wittkop L, Günthard HF, de Wolf F, Dunn D, Cozzi-Lepri A, de Luca A, Kücherer C, Obel N, von Wyl V, Masquelier B, Stephan C, Torti C, Antinori A, García F, Judd A, Porter K, Thiébaut R, Castro H, van Sighem AI, Colin C, Kjaer J, Lundgren JD, Paredes R, Pozniak A, Clotet B, Phillips A, Pillay D, Chêne G. Effect of transmitted drug resistance on virological and immunological response to initial combination antiretroviral therapy for HIV (EuroCoord-CHAIN joint project): a European multicohort study. THE LANCET. INFECTIOUS DISEASES 2011; 11:363-71. [DOI: 10.1016/s1473-3099(11)70032-9] [Citation(s) in RCA: 297] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Integrase and Fusion Inhibitors Transmitted Drug Resistance in Naive Patients With Recent Diagnosis of HIV-1 Infection. J Acquir Immune Defic Syndr 2011; 56:e51-4. [DOI: 10.1097/qai.0b013e3181fcc0f1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Ghosh AK, Chapsal BD, Baldridge A, Steffey MP, Walters DE, Koh Y, Amano M, Mitsuya H. Design and synthesis of potent HIV-1 protease inhibitors incorporating hexahydrofuropyranol-derived high affinity P(2) ligands: structure-activity studies and biological evaluation. J Med Chem 2011; 54:622-34. [PMID: 21194227 PMCID: PMC3024462 DOI: 10.1021/jm1012787] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The design, synthesis, and evaluation of a new series of hexahydrofuropyranol-derived HIV-1 protease inhibitors are described. We have designed a stereochemically defined hexahydrofuropyranol-derived urethane as the P2-ligand. The current ligand is designed based upon the X-ray structure of 1a-bound HIV-1 protease. The synthesis of (3aS,4S,7aR)-hexahydro-2H-furo[2,3-b]pyran-4-ol, (-)-7, was carried out in optically active form. Incorporation of this ligand provided inhibitor 35a, which has shown excellent enzyme inhibitory activity and antiviral potency. Our structure-activity studies have indicated that the stereochemistry and the position of oxygens in the ligand are important to the observed potency of the inhibitor. Inhibitor 35a has maintained excellent potency against multidrug-resistant HIV-1 variants. An active site model of 35a was created based upon the X-ray structure of 1b-bound HIV-1 protease. The model offers molecular insights regarding ligand-binding site interactions of the hexahydrofuropyranol-derived novel P2-ligand.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.
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Transmitted HIV-1 drug resistance among young men of color who have sex with men: a multicenter cohort analysis. J Adolesc Health 2011; 48:94-9. [PMID: 21185530 DOI: 10.1016/j.jadohealth.2010.05.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Revised: 05/14/2010] [Accepted: 05/18/2010] [Indexed: 11/22/2022]
Abstract
BACKGROUND Given the elevated potential for primary or transmitted drug resistance (TDR) among newly HIV-infected individuals, there is a need for a deeper understanding of the baseline resistance patterns present in young men of color who have sex with men. METHODS Genotypic data were collected for participants aged 13-24 who were enrolled from seven sites. Univariate and bivariate methods were used to describe the prevalence of TDR and characteristics associated with TDR. RESULTS Of the 296 individuals participating in the substudy, 145 (49%) had baseline genotypes. The majority of the individuals were African American (65%) and gay-identified (70%). There was significant variation in genotype availability by site (p < .001). Major surveillance drug resistance mutations were present in 28 subjects (19.3%); the majority were non-nucleoside reverse transcriptase inhibitor mutations (12.4%). Subjects with TDR were less likely to have used alcohol on 1 or more days in the prior 2 weeks. Location was not associated with acquisition of TDR. CONCLUSIONS There was a high rate of TDR in a geographically and racially diverse sample of HIV-infected young men of color who have sex with men. This represents a serious public health concern given the young age of this sample and the potential need for long-term antiretroviral therapy. These findings underscore the critical roles of both early case identification and secondary prevention.
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Pando M, Gómez-Carrillo M, Vignoles M, Rubio A, dos Ramos Farias M, Vila M, Rossi D, Ralón G, Marone R, Reynaga E, Sosa J, Torres O, Maestri M, Ávila M, Salomón H. Incidence of HIV type 1 infection, antiretroviral drug resistance, and molecular characterization in newly diagnosed individuals in Argentina: A Global Fund Project. AIDS Res Hum Retroviruses 2011; 27:17-23. [PMID: 20860532 DOI: 10.1089/aid.2010.0013] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An HIV incidence estimation was performed among men who have sex with men (MSM), drug users (DUs), sex workers (SWs), and pregnant women (PW) from Argentina. Volunteers older than 18 years old without a previous HIV-positive diagnosis were included. HIV-positive samples were analyzed by the Serological Testing Algorithm for Recent HIV Seroconversion (STARHS) to estimate incidence. By partial RT-PCR and sequencing of the HIV pol gene, an HIV subtype and resistance profile were determined. A total of 12,192 volunteers were recruited from October 2006 to September 2008. A higher HIV prevalence was detected among trans SWs (33.9%, 38/112), male SWs (10.8%, 12/111), and MSM 10.4% (161/1549). HIV incidence estimates by STARHS was also higher on trans SWs (11.31 per 100 person-years), male SWs (6.06 per 100 person-years), and MSM (6.36 per 100 person-years). Antiretroviral primary resistant mutations were detected in 8.4% of the study group, with a higher frequency in female DUs (33.3%). Phylogenetic analysis showed that 124 (57.9%) samples were subtype B, 84 (39.3%) intersubtype BF recombinants, 5 (2.3%) subtype C, and 1 (0.5%) subtype F in the pol region. Subtype B was most commonly found in MSM and male SWs whereas the intersubtype BF recombinant was more prevalent in female DUs, female SWs, and PW. Given the high HIV prevalence and incidence found in most of these groups, monitoring the continuing spread of the HIV epidemic is essential for determining public health priorities, assessing the impact of interventions, and estimating current and future health care needs.
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Affiliation(s)
- M.A. Pando
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - M. Gómez-Carrillo
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - M. Vignoles
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - A.E. Rubio
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - M.S. dos Ramos Farias
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - M. Vila
- Intercambios Asociación Civil, Buenos Aires, Argentina
| | - D. Rossi
- Intercambios Asociación Civil, Buenos Aires, Argentina
| | - G. Ralón
- Intercambios Asociación Civil, Buenos Aires, Argentina
| | - R. Marone
- Nexo Asociación Civil, Buenos Aires, Argentina
| | - E. Reynaga
- AMMAR, Asociación de Mujeres Meretrices de Argentina, Buenos Aires, Argentina
| | - J. Sosa
- AMMAR, Asociación de Mujeres Meretrices de Argentina, Buenos Aires, Argentina
| | - O. Torres
- Hospital Materno Infantil Ramón Sardá, Buenos Aires, Argentina
| | - M. Maestri
- Hospital Materno Infantil Ramón Sardá, Buenos Aires, Argentina
| | - M.M. Ávila
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - H. Salomón
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
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Ghosh AK, Xu CX, Rao KV, Baldridge A, Agniswamy J, Wang YF, Weber IT, Aoki M, Miguel SGP, Amano M, Mitsuya H. Probing multidrug-resistance and protein-ligand interactions with oxatricyclic designed ligands in HIV-1 protease inhibitors. ChemMedChem 2010; 5:1850-4. [PMID: 20827746 PMCID: PMC3523686 DOI: 10.1002/cmdc.201000318] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Indexed: 11/12/2022]
Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA.
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Bell SK, Little SJ, Rosenberg ES. Clinical management of acute HIV infection: best practice remains unknown. J Infect Dis 2010; 202 Suppl 2:S278-88. [PMID: 20846034 DOI: 10.1086/655655] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Best practice for the clinical management of acute human immunodeficiency virus (HIV) infection remains unknown. Although some data suggest possible immunologic, virologic, or clinical benefit of early treatment, other studies show no difference in these outcomes over time, after early treatment is discontinued. The literature on acute HIV infection is predominantly small nonrandomized studies, which further limits interpretation. As a result, the physician is left to grapple with these uncertainties while making clinical decisions for patients with acute HIV infection. Here we review the literature, focusing on the potential advantages and disadvantages of treating acute HIV infection outlined in treatment guidelines, and summarize the presentations on clinical management of acute HIV infection from the 2009 Acute HIV Infection Meeting in Boston, Massachusetts.
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Affiliation(s)
- Sigall K Bell
- Divisions of Infectious Diseases, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
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Abstract
Minor drug-resistant variants exist in every patient infected with human immunodeficiency virus (HIV). Because these minority variants are usually present at very low levels, they cannot be detected and quantified using conventional genotypic and phenotypic tests. Recently, several assays have been developed to characterize these low-abundance drug-resistant variants in the large, genetically complex population that is present in every HIV-infected individual. The most important issue is what results generated by these assays can predict clinical or treatment outcomes and might guide the management of patients in clinical practice. Cutoff values for the detection of these low-abundance viral variants that predict an increased risk of treatment failure should be determined. These thresholds may be specific for each mutation and treatment regimen. In this review, we summarize the attributes and limitations of the currently available detection assays and review the existing information about both acquired and transmitted drug-resistant minority variants.
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Affiliation(s)
- Sara Gianella
- Departments of Pathology and Medicine, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0679, USA
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43
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Ragonnet-Cronin M, Ofner-Agostini M, Merks H, Pilon R, Rekart M, Archibald CP, Sandstrom PA, Brooks JI. Longitudinal Phylogenetic Surveillance Identifies Distinct Patterns of Cluster Dynamics. J Acquir Immune Defic Syndr 2010; 55:102-8. [DOI: 10.1097/qai.0b013e3181e8c7b0] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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44
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The Impact of Transmitted Drug-Resistance on Treatment Selection and Outcome of First-Line Highly Active Antiretroviral Therapy (HAART). J Acquir Immune Defic Syndr 2010. [DOI: 10.1097/qai.0b013e3181c070d2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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45
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Riva C, Lai A, Caramma I, Corvasce S, Violin M, Dehò L, Prati F, Rossi C, Colombo MC, Capetti A, Franzetti M, Rossini V, Tambussi G, Ciccozzi M, Suligoi B, Mussini C, Rezza G, Balotta C. Transmitted HIV Type 1 drug resistance and Non-B subtypes prevalence among seroconverters and newly diagnosed patients from 1992 to 2005 in Italy. AIDS Res Hum Retroviruses 2010; 26:41-9. [PMID: 20055587 DOI: 10.1089/aid.2009.0057] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The patterns of transmitted drug-resistant (TDR) HIV-1 variants, non-B subtype spread, and epidemiological trends were evaluated either in seroconverters or in newly diagnosed individuals in Italy over a 13-year period. We analyzed 119 seroconverters, enrolled from 1992 to 2003 for the CASCADE study, and 271 newly diagnosed individuals of the SPREAD study (2002-2005), of whom 42 had a known seroconversion date. Overall, TDR was 15.1% in the CASCADE and 12.2% in the SPREAD study. In the 1992-2003 period, men having sex with men (MSMs) and heterosexuals (HEs) were 48.7% and 36.8%, respectively; TDR was found to be higher in MSMs compared to HEs (78.9% vs. 21%, p = 0.006). The same groups were 39.1% and 53.3% in the SPREAD study; however, no association was detected between modality of infection and TDR. Overall, 9.2% and 22.1% of individuals harbored a non-B clade virus in the CASCADE and SPREAD study, respectively. As evidence of onward transmission, 40% (24/60) of non-B variants were carried by European individuals in the latter study; among these patients the F1 subtype was highly prevalent (p = 0.00001). One of every eight patients who received a diagnosis of HIV-1 in recent years harbored a resistant variant, reinforcing the arguments for baseline resistance testing to customize first-line therapy in newly infected individuals. The spread of non-B clades may act as a dilution factor of TDR concealing the proportion of TDR in seroconverters and MSMs.
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Affiliation(s)
- Chiara Riva
- Department of Clinical Sciences ‘L. Sacco’ Hospital, Section of Infectious Diseases and Immunopathology, University of Milan, Milan, Italy
| | - Alessia Lai
- Department of Clinical Sciences ‘L. Sacco’ Hospital, Section of Infectious Diseases and Immunopathology, University of Milan, Milan, Italy
| | - Ilaria Caramma
- Department of Clinical Sciences ‘L. Sacco’ Hospital, Section of Infectious Diseases and Immunopathology, University of Milan, Milan, Italy
| | - Stefano Corvasce
- Department of Clinical Sciences ‘L. Sacco’ Hospital, Section of Infectious Diseases and Immunopathology, University of Milan, Milan, Italy
| | - Michela Violin
- Department of Clinical Sciences ‘L. Sacco’ Hospital, Section of Infectious Diseases and Immunopathology, University of Milan, Milan, Italy
| | - Lorenzo Dehò
- Department of Clinical Sciences ‘L. Sacco’ Hospital, Section of Infectious Diseases and Immunopathology, University of Milan, Milan, Italy
| | - Francesca Prati
- Clinic of Infectious and Tropical Diseases, University Hospital, Modena, Italy
| | - Cristina Rossi
- Infectious Diseases Unit, San Camillo Hospital of Treviso, Treviso, Italy
| | | | - Amedeo Capetti
- 1st Infectious Diseases Clinic, ‘L. Sacco’ Hospital, Milan, Italy
| | - Marco Franzetti
- Department of Clinical Sciences ‘L. Sacco’ Hospital, Section of Infectious Diseases and Immunopathology, University of Milan, Milan, Italy
| | - Valeria Rossini
- Department of Clinical Sciences ‘L. Sacco’ Hospital, Section of Infectious Diseases and Immunopathology, University of Milan, Milan, Italy
| | | | - Massimo Ciccozzi
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy
| | - Barbara Suligoi
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy
| | - Cristina Mussini
- Clinic of Infectious and Tropical Diseases, University Hospital, Modena, Italy
| | - Giovanni Rezza
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy
| | - Claudia Balotta
- Department of Clinical Sciences ‘L. Sacco’ Hospital, Section of Infectious Diseases and Immunopathology, University of Milan, Milan, Italy
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Low-frequency K103N strengthens the impact of transmitted drug resistance on virologic responses to first-line efavirenz or nevirapine-based highly active antiretroviral therapy. J Acquir Immune Defic Syndr 2009; 52:569-73. [PMID: 19779307 DOI: 10.1097/qai.0b013e3181ba11e8] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND There are conflicting data on the impact of low-frequency transmitted drug-resistant mutants on responses to first-line highly active antiretroviral therapy (HAART). METHODS Patients started nevirapine or efavirenz with two or more nucleoside/nucleotide reverse transcriptase inhibitors in 1998-2007 without a prior resistance test at a median 1.0 (interquartile range, 0.0-3.4) year after diagnosis and with a median 218 (interquartile range, 131-296) CD4 cells/mm3, and had at least 24 weeks of follow up. Pre-HAART plasma samples were tested retrospectively by bulk genotyping and sensitive real-time polymerase chain reaction targeting reverse transcriptase K65R, K103N, Y181C, M184V, and G190A (interpretative cutoff 0.3%-0.9%). RESULTS Among 93 patients, seven of 18 who experienced virologic failure and zero of 75 who maintained virologic suppression showed pre-HAART resistance, including three with high-frequency mutations detectable by bulk genotyping (two K103N, one G190A) and four with low-frequency K103N detectable only by polymerase chain reaction. Detection of either bulk (P = 0.006) or low-frequency (P = 0.001) resistance was significantly associated with the odds of virologic failure; combining the two markedly increased the strength of the association (P < 0.0001). At failure, the pre-HAART mutations were detected by bulk genotyping in five of seven patients alongside additional reverse transcriptase mutations. CONCLUSIONS Low-frequency K103N mutants were as prevalent as bulk-detectable variants before starting HAART. Both high- and low-frequency mutants were significantly associated with virologic failure.
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47
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Ghosh AK, Gemma S, Simoni E, Baldridge A, Walters DE, Ide K, Tojo Y, Koh Y, Amano M, Mitsuya H. Synthesis and biological evaluation of novel allophenylnorstatine-based HIV-1 protease inhibitors incorporating high affinity P2-ligands. Bioorg Med Chem Lett 2009; 20:1241-6. [PMID: 20034787 DOI: 10.1016/j.bmcl.2009.11.123] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 11/20/2009] [Accepted: 11/23/2009] [Indexed: 11/28/2022]
Abstract
A series of stereochemically defined cyclic ethers as P2-ligands were incorporated in an allophenylnorstatine-based isostere to provide a new series of HIV-1 protease inhibitors. Inhibitors 3b and 3c, containing conformationally constrained cyclic ethers, displayed impressive enzymatic and antiviral properties and represent promising lead compounds for further optimization.
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Affiliation(s)
- Arun K Ghosh
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, United States.
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48
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Paredes R, Clotet B. Clinical management of HIV-1 resistance. Antiviral Res 2009; 85:245-65. [PMID: 19808056 DOI: 10.1016/j.antiviral.2009.09.015] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2009] [Revised: 09/28/2009] [Accepted: 09/30/2009] [Indexed: 11/18/2022]
Abstract
Antiretroviral drug resistance is a fundamental survival strategy for the virus that stems from its vast capacity to generate diversity. With the recent availability of new ARV drugs and classes, it is now possible to prescribe fully active ART to most HIV-infected subjects and achieve viral suppression even in those with multidrug-resistant HIV. It is uncertain, however, if this scenario will endure. Given that ART must be given for life, and new compounds other than second-generation integrase inhibitors may not reach the clinic soon, all efforts must be done to avoid the development of resistance to the new agents. Here, we discuss relevant aspects for the clinical management of antiretroviral drug resistance, leaving detailed explanations of mechanisms and mutation patterns to other articles in this issue. This article forms part of a special issue of Antiviral Research marking the 25th anniversary of antiretroviral drug discovery and development, vol. 85, issue 1, 2010.
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Affiliation(s)
- Roger Paredes
- Institut de Recerca de SIDA - irsiCaixa & Fundació Lluita contra SIDA, Servei de Medicina Interna, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain.
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49
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Ghosh AK, Dawson ZL. Synthesis of Bioactive Natural Products by Asymmetric syn- and anti-Aldol Reactions. SYNTHESIS-STUTTGART 2009; 2009:2992-3002. [PMID: 30443084 PMCID: PMC6233898 DOI: 10.1055/s-0029-1216941] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The use of several variants of the asymmetric aldol reaction as key steps in the syntheses of bioactive target molecules is described.
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Affiliation(s)
- Arun K Ghosh
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA Fax +1(765)4961612;
| | - Zachary L Dawson
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA Fax +1(765)4961612;
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50
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Ghosh AK, Leshchenko-Yashchuk S, Anderson DD, Baldridge A, Noetzel M, Miller HB, Tie Y, Wang YF, Koh Y, Weber IT, Mitsuya H. Design of HIV-1 protease inhibitors with pyrrolidinones and oxazolidinones as novel P1'-ligands to enhance backbone-binding interactions with protease: synthesis, biological evaluation, and protein-ligand X-ray studies. J Med Chem 2009; 52:3902-14. [PMID: 19473017 PMCID: PMC2745609 DOI: 10.1021/jm900303m] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Structure-based design, synthesis, and biological evaluation of a series of novel HIV-1 protease inhibitors are described. In an effort to enhance interactions with protease backbone atoms, we have incorporated stereochemically defined methyl-2-pyrrolidinone and methyl oxazolidinone as the P1'-ligands. These ligands are designed to interact with Gly-27' carbonyl and Arg-8 side chain in the S1'-subsite of the HIV protease. We have investigated the potential of these ligands in combination with our previously developed bis-tetrahydrofuran (bis-THF) and cyclopentanyltetrahydrofuran (Cp-THF) as the P2-ligands. Inhibitor 19b with a (R)-aminomethyl-2-pyrrolidinone and a Cp-THF was shown to be the most potent compound. This inhibitor maintained near full potency against multi-PI-resistant clinical HIV-1 variants. A high resolution protein-ligand X-ray crystal structure of 19b-bound HIV-1 protease revealed that the P1'-pyrrolidinone heterocycle and the P2-Cp-ligand are involved in several critical interactions with the backbone atoms in the S1' and S2 subsites of HIV-1 protease.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
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