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Ross LL, Shortino D, Shaefer MS. Changes from 2000 to 2009 in the Prevalence of HIV-1 Containing Drug Resistance-Associated Mutations from Antiretroviral Therapy-Naive, HIV-1-Infected Patients in the United States. AIDS Res Hum Retroviruses 2018; 34:672-679. [PMID: 29732898 PMCID: PMC6080107 DOI: 10.1089/aid.2017.0295] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pre-existing HIV drug resistance can jeopardize first-line antiretroviral therapy (ART) success. Changes in the prevalence of drug resistance-associated mutations (DRMs) were analyzed from HIV-infected, ART-naive, U.S. individuals seeking ART treatment from 2000 to 2009. HIV DRM data from 3,829 ART-naive subjects were analyzed by year of sample collection using International Antiviral Society-United States (IAS-USA) and World Health Organization (WHO) “surveillance” DRM definitions; minor IAS-USA-defined DRMs were excluded. IAS-USA DRM prevalence between 2000 and 2009 was 14%, beginning with 8% in 2000 and 13% in 2009. The greatest incidence was observed in 2007 (17%). Overall, IAS-USA-defined non-nucleoside reverse transcriptase inhibitor (NNRTI) DRMs were 9.5%; nucleoside reverse transcriptase inhibitor (NRTI): 4%, and major protease inhibitor (PI): 3%. The most frequently detected IAS-USA-defined DRMs by class were NNRTI: K103N/S (4%), NRTI: M41L (1.5%), and PI: L90M (1%). Overall, WHO-defined DRM prevalence was 13% (5% in 2000; 13% in 2009). By class, NNRTI prevalence was 6%, NRTI: 6%, and PI: 3.2%. The most frequent WHO-defined DRMs were NRTI: codon T215 (3.0%), NNRTI: K103N/S (4%), and PI: L90 (1%). WHO-defined NNRTI DRMs declined significantly (p = .0412) from 2007 to 2009. The overall prevalence of HIV-1 containing major IAS-USA or WHO-defined DRMs to ≥2 or ≥3 classes was 2% and <1%, respectively. The prevalence of HIV-1 with WHO-defined dual- or triple-class resistance significantly declined (p = .0461) from 2008 (4%) to 2009 (<1%). In this U.S. cohort, the prevalence of HIV-1 DRMs increased from 2000 onward, peaked between 2005 and 2007, and then declined between 2008 and 2009; the detection of WHO-defined dual- or triple-class DRM similarly decreased from 2008 to 2009.
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Affiliation(s)
- Lisa L. Ross
- ViiV Healthcare, Research Triangle Park, North Carolina
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52
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Pinto AN, Hawke K, Castley A, Chibo D, Giallonardo FD, Cooper C, Sawleshwarkar S, Kelleher A, Dwyer DE. HIV-1 subtype diversity, transmitted drug resistance and phylogenetics in Australia. Future Virol 2018. [DOI: 10.2217/fvl-2018-0031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Australia has maintained a low prevalence of HIV, with a mainly concentrated epidemic and successful public health response. With the widespread availability of HIV genotyping for resistance testing, and development of phylogenetic methodologies, the field of molecular epidemiology has evolved a deeper understanding of diversity and transmission dynamics of HIV. Studies combining HIV genotype with epidemiological data have allowed insights to be gained into the changing subtype diversity, rates of transmitted drug resistance and transmission networks of HIV in Australia. This review provides an overview of HIV molecular epidemiology studies in Australia.
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Affiliation(s)
- Angie N Pinto
- The Kirby Institute, The University of New South Wales, UNSW Sydney, Australia
| | - Karen Hawke
- South Australian Health & Medical Research Institute, Adelaide, South Australia
| | - Allison Castley
- PathWest, Clinical Immunology, Department of Health, Murdoch, Western Australia, Australia
| | - Doris Chibo
- HIV Characterization Laboratory, Victorian Infectious Diseases Reference Laboratory, Doherty Institute, Melbourne, Victoria, Australia
| | | | - Craig Cooper
- Positive Life NSW, Sydney, New South Wales, Australia
| | - Shailendra Sawleshwarkar
- The University of Sydney, Faculty of Medicine & Health, Westmead Clinical School, Western Sydney Sexual Health Centre, Parramatta, New South Wales, Australia
| | - Anthony Kelleher
- The Kirby Institute, The University of New South Wales, UNSW Sydney, Australia
| | - Dominic E Dwyer
- NSWHP-ICPMR, Westmead Hospital, Westmead, NSW, Australia
- Westmead Clinical School, University of Sydney, Westmead, Australia
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53
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Zitzmann C, Kaderali L. Mathematical Analysis of Viral Replication Dynamics and Antiviral Treatment Strategies: From Basic Models to Age-Based Multi-Scale Modeling. Front Microbiol 2018; 9:1546. [PMID: 30050523 PMCID: PMC6050366 DOI: 10.3389/fmicb.2018.01546] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 06/21/2018] [Indexed: 12/14/2022] Open
Abstract
Viral infectious diseases are a global health concern, as is evident by recent outbreaks of the middle east respiratory syndrome, Ebola virus disease, and re-emerging zika, dengue, and chikungunya fevers. Viral epidemics are a socio-economic burden that causes short- and long-term costs for disease diagnosis and treatment as well as a loss in productivity by absenteeism. These outbreaks and their socio-economic costs underline the necessity for a precise analysis of virus-host interactions, which would help to understand disease mechanisms and to develop therapeutic interventions. The combination of quantitative measurements and dynamic mathematical modeling has increased our understanding of the within-host infection dynamics and has led to important insights into viral pathogenesis, transmission, and disease progression. Furthermore, virus-host models helped to identify drug targets, to predict the treatment duration to achieve cure, and to reduce treatment costs. In this article, we review important achievements made by mathematical modeling of viral kinetics on the extracellular, intracellular, and multi-scale level for Human Immunodeficiency Virus, Hepatitis C Virus, Influenza A Virus, Ebola Virus, Dengue Virus, and Zika Virus. Herein, we focus on basic mathematical models on the population scale (so-called target cell-limited models), detailed models regarding the most important steps in the viral life cycle, and the combination of both. For this purpose, we review how mathematical modeling of viral dynamics helped to understand the virus-host interactions and disease progression or clearance. Additionally, we review different types and effects of therapeutic strategies and how mathematical modeling has been used to predict new treatment regimens.
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Affiliation(s)
- Carolin Zitzmann
- Institute of Bioinformatics and Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald, Germany
| | - Lars Kaderali
- Institute of Bioinformatics and Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald, Germany
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54
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Fabeni L, Alteri C, Di Carlo D, Orchi N, Carioti L, Bertoli A, Gori C, Forbici F, Continenza F, Maffongelli G, Pinnetti C, Vergori A, Mondi A, Ammassari A, Borghi V, Giuliani M, De Carli G, Pittalis S, Grisetti S, Pennica A, Mastroianni CM, Montella F, Cristaudo A, Mussini C, Girardi E, Andreoni M, Antinori A, Ceccherini-Silberstein F, Perno CF, Santoro MM. Dynamics and phylogenetic relationships of HIV-1 transmitted drug resistance according to subtype in Italy over the years 2000-14. J Antimicrob Chemother 2018; 72:2837-2845. [PMID: 29091206 DOI: 10.1093/jac/dkx231] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/09/2017] [Indexed: 11/14/2022] Open
Abstract
Background Transmitted drug-resistance (TDR) remains a critical aspect for the management of HIV-1-infected individuals. Thus, studying the dynamics of TDR is crucial to optimize HIV care. Methods In total, 4323 HIV-1 protease/reverse-transcriptase sequences from drug-naive individuals diagnosed in north and central Italy between 2000 and 2014 were analysed. TDR was evaluated over time. Maximum-likelihood and Bayesian phylogenetic trees with bootstrap and Bayesian-probability supports defined transmission clusters. Results Most individuals were males (80.2%) and Italian (72.1%), with a median (IQR) age of 37 (30-45) years. MSM accounted for 42.2% of cases, followed by heterosexuals (36.4%). Non-B subtype infections accounted for 30.8% of the overall population and increased over time (<2005-14: 19.5%-38.5%, P < 0.0001), particularly among Italians (<2005-14: 6.5%-28.8%, P < 0.0001). TDR prevalence was 8.8% and increased over time in non-B subtypes (<2005-14: 2%-7.1%, P = 0.018). Overall, 467 transmission clusters (involving 1207 individuals; 27.9%) were identified. The prevalence of individuals grouping in transmission clusters increased over time in both B (<2005-14: 12.9%-33.5%, P = 0.001) and non-B subtypes (<2005-14: 18.4%-41.9%, P = 0.006). TDR transmission clusters were 13.3% within the overall cluster observed and dramatically increased in recent years (<2005-14: 14.3%-35.5%, P = 0.005). This recent increase was mainly due to non-B subtype-infected individuals, who were also more frequently involved in large transmission clusters than those infected with a B subtype [median number of individuals in transmission clusters: 7 (IQR 6-19) versus 4 (3-4), P = 0.047]. Conclusions The epidemiology of HIV transmission changed greatly over time; the increasing number of transmission clusters (sometimes with drug resistance) shows that detection and proper treatment of the multi-transmitters is a major target for controlling HIV spread.
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Affiliation(s)
- L Fabeni
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - C Alteri
- University of Rome Tor Vergata, Rome, Italy
| | - D Di Carlo
- University of Rome Tor Vergata, Rome, Italy
| | - N Orchi
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - L Carioti
- University of Rome Tor Vergata, Rome, Italy
| | - A Bertoli
- University of Rome Tor Vergata, Rome, Italy
| | - C Gori
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - F Forbici
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - F Continenza
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | | | - C Pinnetti
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - A Vergori
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - A Mondi
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - A Ammassari
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - V Borghi
- Modena University Hospital, Modena, Italy
| | - M Giuliani
- San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - G De Carli
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - S Pittalis
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - S Grisetti
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | | | | | - F Montella
- S. Giovanni Addolorata Hospital, Rome, Italy
| | - A Cristaudo
- San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - C Mussini
- Modena University Hospital, Modena, Italy
| | - E Girardi
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - M Andreoni
- University Hospital Tor Vergata, Rome, Italy
| | - A Antinori
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | | | - C F Perno
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
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55
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Alidjinou EK, Deldalle J, Hallaert C, Robineau O, Ajana F, Choisy P, Hober D, Bocket L. RNA and DNA Sanger sequencing versus next-generation sequencing for HIV-1 drug resistance testing in treatment-naive patients. J Antimicrob Chemother 2018; 72:2823-2830. [PMID: 29091197 DOI: 10.1093/jac/dkx232] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/09/2017] [Indexed: 11/12/2022] Open
Abstract
Background Sanger sequencing of plasma RNA is the standard method for HIV-1 drug resistance testing in treatment-naive patients, but is limited by the non-detection of resistance-associated mutations (RAMs) with prevalence below approximately 20%. Objectives We compared RNA and DNA Sanger sequencing (RSS and DSS) with RNA next-generation sequencing (NGS) for RAM detection in HIV-1 reverse transcriptase (RT), protease (PR) and integrase (IN) genes. Methods Sanger sequencing was performed on RNA and DNA, following the recommendations of the French Agency for AIDS Research (ANRS). NGS was performed on RNA using the HIV-1 Drug Resistance Assay, v. 3.0 (Roche) on the 454 GS Junior sequencer. The IAS-USA list was used to identify RAMs. ANRS, Rega and Stanford algorithms were used for drug resistance interpretation. Results The study included 48 ART-naive patients. The number of patients with at least one major RAM was 3, 3, 4 and 8 when using RSS, DSS, NGS 20% and NGS 5%, respectively. Numerous minor mutations were detected in patients, especially in the protease gene. None of the methods detected any major mutation in the integrase gene. Overall, the mutation detection rate was similar between RSS and DSS, and higher with NGS 20%. Differences in drug resistance interpretation were found between algorithms. No impact of the minority RAMs detected by NGS was found on the short-term treatment outcome. Conclusions DSS does not clearly improve the detection of RAMs in ART-naive patients, as compared with RSS. NGS allows detection of additional minority RAMs; however, their clinical relevance requires further investigation.
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Affiliation(s)
- E K Alidjinou
- Univ Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, F-59000 Lille, France
| | - J Deldalle
- Univ Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, F-59000 Lille, France
| | - C Hallaert
- Univ Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, F-59000 Lille, France
| | - O Robineau
- Service Universitaire des Maladies Infectieuses, CH Dron, Tourcoing, France
| | - F Ajana
- Service Universitaire des Maladies Infectieuses, CH Dron, Tourcoing, France
| | - P Choisy
- Service Universitaire des Maladies Infectieuses, CH Dron, Tourcoing, France
| | - D Hober
- Univ Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, F-59000 Lille, France
| | - L Bocket
- Univ Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, F-59000 Lille, France
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56
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Gerry CJ, Schreiber SL. Chemical probes and drug leads from advances in synthetic planning and methodology. Nat Rev Drug Discov 2018; 17:333-352. [PMID: 29651105 PMCID: PMC6707071 DOI: 10.1038/nrd.2018.53] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Screening of small-molecule libraries is a productive method for identifying both chemical probes of disease-related targets and potential starting points for drug discovery. In this article, we focus on strategies such as diversity-oriented synthesis that aim to explore novel areas of chemical space efficiently by populating small-molecule libraries with compounds containing structural features that are typically under-represented in commercially available screening collections. Drawing from more than a decade's worth of examples, we highlight how the design and synthesis of such libraries have been enabled by modern synthetic chemistry, and we illustrate the impact of the resultant chemical probes and drug leads in a wide range of diseases.
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Affiliation(s)
- Christopher J Gerry
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- The Broad Institute of Harvard & MIT, Cambridge, MA, USA
| | - Stuart L Schreiber
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- The Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
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57
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Kityo C, Boerma RS, Sigaloff KCE, Kaudha E, Calis JCJ, Musiime V, Balinda S, Nakanjako R, Boender TS, Mugyenyi PN, Rinke de Wit TF. Pretreatment HIV drug resistance results in virological failure and accumulation of additional resistance mutations in Ugandan children. J Antimicrob Chemother 2018; 72:2587-2595. [PMID: 28673027 PMCID: PMC5890670 DOI: 10.1093/jac/dkx188] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 05/23/2017] [Indexed: 01/05/2023] Open
Abstract
Background Pretreatment HIV drug resistance (PDR) can impair virological response to ART, jeopardizing effective treatment for children. Methods Children aged ≤12 years initiated first-line ART in Uganda during 2010-11. Baseline and 6 monthly viral load (VL) and genotypic resistance testing if VL >1000 copies/mL was done. The 2015 IAS-USA mutation list and Stanford algorithm were used to score drug resistance mutations (DRMs) and susceptibility. Virological failure (VF) was defined as two consecutive VLs >1000 copies/mL or death after 6 months of ART. Factors associated with failure and acquired drug resistance (ADR) were assessed in a logistic regression analysis. Results Among 317 children enrolled, median age was 4.9 years and 91.5% received NNRTI-based regimens. PDR was detected in 47/278 (16.9%) children, of whom 22 (7.9%) had resistance against their first-line regimen and were therefore on a partially active regimen. After 24 months of follow-up, 92/287 (32.1%) had experienced VF. Children with PDR had a higher risk of VF (OR 15.25, P < 0.001) and ADR (OR 3.58, P = 0.01). Conclusions Almost one-third of children experienced VF within 24 months of NNRTI-based first-line treatment. PDR was the strongest predictor of VF and ADR, and therefore presents a major threat in children. There is a need for ART regimens that maximize effectiveness of first-line therapy for long-term treatment success in the presence of PDR or incorporation of routine VL testing to detect VF and change treatment in time, in order to prevent clinical deterioration and accumulation of additional drug resistance. Children ≤3 years should be initiated on a PI-based regimen as per WHO guidelines.
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Affiliation(s)
- Cissy Kityo
- Joint Clinical Research Centre (JCRC), Kampala, Uganda
| | - Ragna S Boerma
- Amsterdam Institute for Global Health and Development, Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands.,Global Child Health Group, Emma Children's Hospital, Academic Medical Centre Amsterdam, Amsterdam, The Netherlands
| | - Kim C E Sigaloff
- Amsterdam Institute for Global Health and Development, Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands.,Department of Infectious Diseases, Division of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Job C J Calis
- Global Child Health Group, Emma Children's Hospital, Academic Medical Centre Amsterdam, Amsterdam, The Netherlands.,Department of Pediatric Intensive Care, Emma Children's Hospital, Academic Medical Centre Amsterdam, Amsterdam, The Netherlands
| | - Victor Musiime
- Joint Clinical Research Centre (JCRC), Kampala, Uganda.,Department of Pediatrics and Child Health, Makerere University College of Health Sciences, Kampala, Uganda
| | | | | | - T Sonia Boender
- Amsterdam Institute for Global Health and Development, Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands.,Global Child Health Group, Emma Children's Hospital, Academic Medical Centre Amsterdam, Amsterdam, The Netherlands.,Stichting HIV Monitoring, Amsterdam, The Netherlands
| | | | - Tobias F Rinke de Wit
- Amsterdam Institute for Global Health and Development, Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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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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Xu Y, Peng X, Peng X, Ji S, Chen B, Wang L, Lu X, Xie T, Sun T, Wang H, Wu N. Characterization of HIV-1 subtypes and transmitted drug resistance among treatment-naive HIV-infected individuals in Zhejiang, China, 2014-2017. Arch Virol 2018; 163:2233-2237. [PMID: 29637428 DOI: 10.1007/s00705-018-3839-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/04/2018] [Indexed: 01/26/2023]
Abstract
In recent years, transmitted drug resistance (TDR) has adversely impacted upon first-line therapy for HIV-infected individuals. To understand the current subtype distribution and TDR level in Zhejiang, China we performed phylogenetic analysis and genotypic drug resistance testing of treatment-naive HIV-infected individuals. A total of 153 HIV-1 Pol genes were successfully amplified. The distribution of HIV-1 genotypes was as follows: CRF01_AE (43.8%); CRF07_BC (37.9%); subtype B/B' (7.2%); CRF08_BC (5.2%); and others (5.9%). Drug resistance analysis demonstrated that 11.1% of isolates contained at least one NRTI or NNRTI resistance-associated mutations while 2.0% were identified to be resistant to PIs. These findings enhance our understanding of the genetic diversity of HIV-1 strains circulating in Zhejiang and provide some guidelines for HIV initial treatment therapy.
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Affiliation(s)
- Yufan Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, China
| | - Xiaorong Peng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, China
| | - Xiuming Peng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, China
| | - Shujing Ji
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, China
| | - Bin Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, China
| | - Liyan Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, China
| | - Xiangyun Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, China
| | - Tiansheng Xie
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, China
| | - Tao Sun
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, China
| | - Hui Wang
- The Third People's Hospital of Shenzhen, Shenzhen, 518112, China
| | - Nanping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, China.
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Mehraj V, Cox J, Lebouché B, Costiniuk C, Cao W, Li T, Ponte R, Thomas R, Szabo J, Baril J, Trottier B, Côté P, LeBlanc R, Bruneau J, Tremblay C, Routy J. Socio-economic status and time trends associated with early ART initiation following primary HIV infection in Montreal, Canada: 1996 to 2015. J Int AIDS Soc 2018; 21:e25034. [PMID: 29412520 PMCID: PMC5804015 DOI: 10.1002/jia2.25034] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 11/17/2017] [Indexed: 12/20/2022] Open
Abstract
INTRODUCTION Guidelines regarding antiretroviral therapy (ART) initiation in HIV infection have varied over time, with the 2015 World Health Organization recommendation suggesting ART initiation at the time of diagnosis regardless of CD4 T-cell counts. Herein, we investigated the influence of socio-demographic and clinical factors in addition to time trends on early ART initiation among participants of the Montreal Primary HIV Infection Study. METHODS The Montreal Primary HIV Infection Study is a prospective cohort established in three community medical centres (CMCs) and two university medical centres (UMCs). Recently diagnosed HIV-infected adults were categorized as receiving early (vs. delayed) ART if ART was initiated within 180 days of the baseline visit. Associations between early ART initiation and socio-demographic, socio-economic and behavioural information were examined. Independent associations of factors linked with early ART initiation were determined using multivariable binary logistic regression analysis. RESULTS A total of 348 participants had a documented date of HIV acquisition of <180 days. The median interquartile range (IQR) age of participants was 35 (28; 42) years and the majority were male (96%), having paid employment (63%), men who have sex with men (MSM) (78%) and one to four sexual partners in the last three months (70%). Participants presented with a median IQR HIV plasma viral load of 4.6 (3.7; 5.3) log10 copies/ml, CD4 count of 510 (387; 660) cells/μl and were recruited in CMCs (52%) or UMCs (48%). Early ART initiation was observed in 47% of the participants and the trend followed a V-shaped curve with peaks in 1996 to 1997 (89%) and 2013 to 2015 (88%) with a dip in 2007 to 2009 (22%). Multivariable analyses showed that having a paid employment adjusted odds ratio (aOR: 2.43; 95% CI: 1.19, 4.95), lower CD4 count (aOR per 50 cell increase: 0.93; 95% CI: 0.87, 0.99) and care at UMCs (aOR: 2.03; 95% CI: 1.06 to 3.90) were independently associated with early ART initiation. CONCLUSIONS Early ART initiation during primary HIV infection was associated with diminished biological prognostic factors and calendar time mirroring evolution of treatment guidelines. In addition, socio-economic factors such as having a paid employment, contribute to early ART initiation in the context of universal access to care in Canada.
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Affiliation(s)
- Vikram Mehraj
- Chronic Viral Illness ServiceMcGill University Health CentreMontrealQCCanada
- Research Institute of the McGill University Health CentreMontrealQCCanada
| | - Joseph Cox
- Chronic Viral Illness ServiceMcGill University Health CentreMontrealQCCanada
- Research Institute of the McGill University Health CentreMontrealQCCanada
- Department of Epidemiology, Biostatistics and Occupational HealthMcGill UniversityMontrealQCCanada
| | - Bertrand Lebouché
- Chronic Viral Illness ServiceMcGill University Health CentreMontrealQCCanada
- Research Institute of the McGill University Health CentreMontrealQCCanada
- Department of Family MedicineMcGill UniversityMontrealQCCanada
| | - Cecilia Costiniuk
- Chronic Viral Illness ServiceMcGill University Health CentreMontrealQCCanada
- Research Institute of the McGill University Health CentreMontrealQCCanada
| | - Wei Cao
- Chronic Viral Illness ServiceMcGill University Health CentreMontrealQCCanada
- Research Institute of the McGill University Health CentreMontrealQCCanada
- Department of Infectious DiseasesPeking Union Medical College HospitalBeijingChina
| | - Taisheng Li
- Department of Infectious DiseasesPeking Union Medical College HospitalBeijingChina
| | - Rosalie Ponte
- Chronic Viral Illness ServiceMcGill University Health CentreMontrealQCCanada
- Research Institute of the McGill University Health CentreMontrealQCCanada
| | | | - Jason Szabo
- Chronic Viral Illness ServiceMcGill University Health CentreMontrealQCCanada
- Clinique Médicale l'ActuelMontréalQCCanada
| | | | | | - Pierre Côté
- Clinique Médicale Quartier LatinMontréalQCCanada
| | | | - Julie Bruneau
- Centre de recherche du Centre Hospitalier de l'Université de MontréalMontréalQCCanada
| | - Cécile Tremblay
- Centre de recherche du Centre Hospitalier de l'Université de MontréalMontréalQCCanada
- Département de microbiologie infectiologie et immunologieUniversité de MontréalMontréalQCCanada
| | - Jean‐Pierre Routy
- Chronic Viral Illness ServiceMcGill University Health CentreMontrealQCCanada
- Research Institute of the McGill University Health CentreMontrealQCCanada
- Division of HematologyMcGill University Health CentreMontrealQCCanada
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Chehadeh W, Albaksami O, John SE, Al-Nakib W. Drug Resistance-Associated Mutations in Antiretroviral Treatment-Experienced Patients in Kuwait. Med Princ Pract 2018; 27:152-157. [PMID: 29506011 PMCID: PMC5968259 DOI: 10.1159/000488108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 03/05/2018] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES To investigate the prevalence of nonpolymorphic resistance-associated mutations (RAM) in HIV-1 patients on first-line antiretroviral therapy in Kuwait. SUBJECTS AND METHODS Total RNA was isolated from plasma samples of 42 patients who received a first-line nonnucleoside reverse transcriptase inhibitor (NNRTI)-based regimen. HIV-1 protease and reverse transcriptase genetic regions were then amplified by nested reverse transcription-polymerase chain reaction and directly sequenced. The HIV-1 subtype was identified using the Bayesian phylogenetic method, and RAM were identified using the Stanford University genotypic resistance interpretation algorithm. RESULTS The HIV-1 viral load at sampling ranged from < 20 to 8.25 × 104 copies/ml. CRF01_AE, C, and B were the most predominant HIV-1 subtypes. Nonpolymorphic mutations associated with resistance to antiretroviral drugs were detected in 11 (26.2%) of the 42 patients; 5 (11.9%) patients had mutations associated with a high-level resistance to nucleoside reverse transcriptase inhibitors (NRTI), 4 (9.5%) patients had mutations associated with resistance to NNRTI, 1 (2.4%) patient had mutations associated with resistance to both NRTI and NNRTI, and 1 (2.4%) patient had mutations potentially associated with low-level resistance to both protease inhibitors and NNRTI. All patients with RAM had a detectable plasma HIV-1 RNA level. CONCLUSION Our results indicate the development of RAM during an NNRTI-based regimen and highlight the importance of considering other regimens to avoid treatment failure.
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Affiliation(s)
- Wassim Chehadeh
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
- *Dr. Wassim Chehadeh, Department of Microbiology, Faculty of Medicine, Kuwait University, Street Mubarak Al-Kabir Hospital, PO Box 24923, Safat, Kuwait City 13110 (Kuwait), E-Mail
| | - Osama Albaksami
- Infectious Diseases Hospital, Ministry of Health, Kuwait City, Kuwait
| | - Sonia Elezebeth John
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Widad Al-Nakib
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
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Dasgupta S, Hall HI, Hernandez AL, Ocfemia MCB, Saduvala N, Oster AM. Receipt and timing of HIV drug resistance testing in six U.S. jurisdictions. AIDS Care 2017; 29:1567-1575. [PMID: 28464705 PMCID: PMC5685490 DOI: 10.1080/09540121.2017.1316356] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The Department of Health and Human Services recommends drug resistance testing at linkage to HIV care. Because receipt and timing of testing are not well characterized, we examined testing patterns among persons with diagnosed HIV who are linked to care. Using surveillance data in six jurisdictions for persons aged ≥13 years with HIV infection diagnosed in 2013, we assessed the proportion receiving testing, and among these, the proportion receiving testing at linkage. Multivariable log-binomial regression modeling estimated associations between selected characteristics and receipt of testing (1) overall, and (2) at linkage among those tested. Of 9,408 persons linked to care, 66% received resistance testing, among whom 68% received testing at linkage. Less testing was observed among male persons who inject drugs (PWID), compared with men who have sex with men (adjusted prevalence ratio [aPR]: 0.88; 95% confidence interval [CI]: 0.81-0.97) and persons living in areas with population <500,000 compared with those in areas with population ≥2,500,000 (aPR: 0.88; CI: 0.84-0.93). In certain jurisdictions, testing was lower for persons with initial CD4 counts ≥500 cells/mm3, compared with those with CD4 counts <200 cells/mm3 (aPR range: 0.80-0.85). Of those tested, testing at linkage was lower among male PWID (aPR: 0.85; CI: 0.75-0.95) and, in some jurisdictions, persons with CD4 counts ≥500 cells/mm3 (aPR range: 0.63-0.73). Two-thirds of persons with diagnosed HIV who were linked to care received resistance testing, and most received testing at linkage as recommended. Improving receipt and timing of testing among male PWID, persons in less populous settings, and in all jurisdictions, regardless of CD4 count, may improve care outcomes.
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Affiliation(s)
- Sharoda Dasgupta
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, USA
| | - H. Irene Hall
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, USA
| | - Angela L. Hernandez
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, USA
| | | | | | - Alexandra M. Oster
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, USA
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Hendry AP, Gotanda KM, Svensson EI. Human influences on evolution, and the ecological and societal consequences. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0028. [PMID: 27920373 DOI: 10.1098/rstb.2016.0028] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2016] [Indexed: 01/08/2023] Open
Abstract
Humans have dramatic, diverse and far-reaching influences on the evolution of other organisms. Numerous examples of this human-induced contemporary evolution have been reported in a number of 'contexts', including hunting, harvesting, fishing, agriculture, medicine, climate change, pollution, eutrophication, urbanization, habitat fragmentation, biological invasions and emerging/disappearing diseases. Although numerous papers, journal special issues and books have addressed each of these contexts individually, the time has come to consider them together and thereby seek important similarities and differences. The goal of this special issue, and this introductory paper, is to promote and expand this nascent integration. We first develop predictions as to which human contexts might cause the strongest and most consistent directional selection, the greatest changes in evolutionary potential, the greatest genetic (as opposed to plastic) changes and the greatest effects on evolutionary diversification We then develop predictions as to the contexts where human-induced evolutionary changes might have the strongest effects on the population dynamics of the focal evolving species, the structure of their communities, the functions of their ecosystems and the benefits and costs for human societies. These qualitative predictions are intended as a rallying point for broader and more detailed future discussions of how human influences shape evolution, and how that evolution then influences species traits, biodiversity, ecosystems and humans.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.
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Affiliation(s)
- Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, 859 Sherbrooke Street West, Montréal, Québec, Canada H3A OC4
| | - Kiyoko M Gotanda
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Erik I Svensson
- Evolutionary Ecology Unit, Department of Biology, Lund University, Lund 223 62, Sweden
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Comparison of Population Pharmacokinetics Based on Steady-State Assumption Versus Electronically Monitored Adherence to Lopinavir, Atazanavir, Efavirenz, and Etravirine: A Retrospective Study. Ther Drug Monit 2017; 38:506-15. [PMID: 26937748 DOI: 10.1097/ftd.0000000000000297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Population pharmacokinetic (PopPK) analyses often rely on steady state and full adherence to prescribed dosage regimen assumptions from data gathered during therapeutic drug monitoring (TDM). Nonadherence is common in chronic diseases such as HIV. This study evaluates the impact of adherence measurement by electronic monitoring on PopPK parameter estimation and individual concentration profile predictions, and also the influence of adherence issues on the clinical interpretation of a concentration measurement. METHODS Published PopPK models for lopinavir, atazanavir, efavirenz, and etravirine were applied to estimate PK parameters and individual concentrations in 140 HIV patients taking part in a medication adherence program using 2 dosing data sets. The first set included the last dose reported by the patient with steady-state and full adherence assumptions; the second set used detailed electronic dosing history. PopPK parameter estimates and individual predictions were compared between the 2 dosing entries. RESULTS Clearance estimates and likewise predicted concentrations did not markedly differ between the 2 dosing histories. However, certain patterns of nonadherence such as sparse missed doses or consecutive missed doses lead to suboptimal drug exposure. The interpretation based on self-reported information would have concluded on a wrongly appropriate individual exposure. CONCLUSIONS PopPK analysis assuming steady state with full adherence produced similar results to those based on detailed electronic dosing history reconciled with patients' allegations. Self-reported last dose intake appeared reliable for concentration predictions and therapeutic drug monitoring interpretation for most patients followed at the medication adherence program. Yet, clinicians should be aware that concentration predictions based on self-reported last dose intake might be overestimated in case of undetected patterns of nonadherence, increasing the risk of forthcoming therapeutic failure.
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Andrade SDD, Sabidó M, Monteiro WM, Benzaken AS, Tanuri A. Drug resistance in antiretroviral-naive children newly diagnosed with HIV-1 in Manaus, Amazonas. J Antimicrob Chemother 2017; 72:1774-1783. [PMID: 28333295 DOI: 10.1093/jac/dkx025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/16/2017] [Indexed: 01/09/2023] Open
Abstract
Objectives To determine the prevalence of drug resistance mutations (DRM), the prevalence of drug susceptibility [transmitted drug resistance (TDR)] and the prevalence of HIV-1 variants among treatment-naive HIV-infected children in Manaus, Amazonas state, Brazil. Methods Children born to HIV-infected mothers and diagnosed with HIV in an HIV reference service centre and with available pol sequence between 2010 and 2015 prior to antiretroviral initiation were included. TDR was identified using the Calibrated Population Resistance Tool. HIV-1 subtypes were defined by Rega and phylogenetic analyses. Results One hundred and seventeen HIV-infected children with a median age of 3.7 years were included. Among them, 28.2% had been exposed to some form of prevention of mother-to-child transmission (PMTCT). HIV DRM were present in 21.4% of all children. Among PMTCT-exposed children, 3% had NRTI mutations, 15.2% had NNRTI mutations and 3% had PI mutations. Among PMTCT-unexposed children, 1.2% had NRTI mutations, 21.4% had non-NNRTI mutations and 1.2% had PI mutations. The most common DRM was E138A (8.5%). The prevalence of TDR was 16.2%; 21.1% among PMTCT-exposed children and 14.3% among PMTC-unexposed children. The analysis of HIV-1 subtypes revealed that 80.2% were subtype B, 6.0% were subtype C, 3.4% were subtype F1 and 10.3% were possible unique recombinant forms (BF1, 4.3%; DB, 4.3%; BC, 0.9%; KC, 0.9%). Conclusions We report a high prevalence of DRM in this population, including in almost a quarter of children with no reported PMTCT. The high prevalence of TDR observed might compromise ART effectiveness. Results show extensive HIV-1 diversity and expansion of subtype C, which highlights the need for surveillance of HIV-1 subtypes in Amazonas state.
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Affiliation(s)
- Solange Dourado de Andrade
- Tropical Medicine Foundation Doctor Heitor Vieira Dourado (FMT-HVD), Av. Pedro Teixeira 25, Manaus, Amazonas, CEP: 69040-000, Brazil.,Universidade do Estado do Amazonas, Avenida Djalma Batista, Manaus, Amazonas, CEP: 358-69005-010, Brazil
| | - Meritxell Sabidó
- Tropical Medicine Foundation Doctor Heitor Vieira Dourado (FMT-HVD), Av. Pedro Teixeira 25, Manaus, Amazonas, CEP: 69040-000, Brazil.,TransLab, Department of Medical Sciences, Universitat de Girona, Emili Grahit 77, Catalonia 17071, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Av. Monforte de Lemos 3-5, Pabellón 11, Planta 0, Madrid 28029, Spain
| | - Wuelton Marcelo Monteiro
- Tropical Medicine Foundation Doctor Heitor Vieira Dourado (FMT-HVD), Av. Pedro Teixeira 25, Manaus, Amazonas, CEP: 69040-000, Brazil
| | - Adele Schwartz Benzaken
- Tropical Medicine Foundation Doctor Heitor Vieira Dourado (FMT-HVD), Av. Pedro Teixeira 25, Manaus, Amazonas, CEP: 69040-000, Brazil.,Universidade do Estado do Amazonas, Avenida Djalma Batista, Manaus, Amazonas, CEP: 358-69005-010, Brazil.,Department of STI, AIDS and Viral Hepatitis, Secretary for Health Surveillance, Ministry of Health Brazil, Brasilia, Brazil
| | - Amilcar Tanuri
- Tropical Medicine Foundation Doctor Heitor Vieira Dourado (FMT-HVD), Av. Pedro Teixeira 25, Manaus, Amazonas, CEP: 69040-000, Brazil
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Stanga LL, Mujeeb A, Packel L, Martz T, Lemp G. The California HIV/AIDS Research Program: History, Impact, and HIV Cure Initiative. AIDS Res Hum Retroviruses 2017; 33:S1-S5. [PMID: 28851229 DOI: 10.1089/aid.2017.0149] [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: 11/13/2022] Open
Abstract
This Special Issue of AIDS Research and Human Retroviruses features results from the HIV Cure Initiative, funded by the California HIV/AIDS Research Program (CHRP). As a publicly funded grant maker, CHRP has served for more than three decades as a unique resource for innovative researchers in California, whose work seeks to address all aspects of the HIV epidemic and the communities affected by it. Early initiatives at CHRP pioneered what would become enduring cornerstones of HIV science: isolation of the virus; efficacy and toxicities of the first HIV treatments; the emergence of drug resistance; the first biospecimen banks for HIV-related research; the first community-based laboratory service for HIV diagnostic serology; and the first longitudinal case-control study of progression from HIV to AIDS-The San Francisco General Hospital Cohort. More recently, CHRP-funded conceptual studies of zinc-finger nuclease-mediated disruption of CCR5 genomic sequences and the safety of solid organ transplantation for HIV-positive patients have progressed from brilliant ideas to clinical realities, and CHRP is currently funding the first multisite trial of HIV preexposure prophylaxis for transgender persons in the United States. The present article outlines the founding of CHRP, our current grantmaking process, and our impact on HIV research over time. In 2013, CHRP launched a new initiative aimed at moving the then nascent frontier of HIV cure science forward: the CHRP HIV Cure Initiative provided over $1.4 million to multiple basic biomedical research projects, and selected results are presented in this Special Issue.
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Affiliation(s)
- Lisa Loeb Stanga
- California HIV/AIDS Research Program, University of California, Office of the President, Oakland, California
| | - Anwer Mujeeb
- Tobacco-Related Disease Research Program, University of California, Office of the President, Oakland, California
| | - Laura Packel
- California HIV/AIDS Research Program, University of California, Office of the President, Oakland, California
| | - Tyler Martz
- California HIV/AIDS Research Program, University of California, Office of the President, Oakland, California
| | - George Lemp
- California HIV/AIDS Research Program, University of California, Office of the President, Oakland, California
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Pessôa R, Sanabani SS. High prevalence of HIV-1 transmitted drug-resistance mutations from proviral DNA massively parallel sequencing data of therapy-naïve chronically infected Brazilian blood donors. PLoS One 2017; 12:e0185559. [PMID: 28953964 PMCID: PMC5617215 DOI: 10.1371/journal.pone.0185559] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/14/2017] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND An improved understanding of the prevalence of low-abundance transmitted drug-resistance mutations (TDRM) in therapy-naïve HIV-1-infected patients may help determine which patients are the best candidates for therapy. In this study, we aimed to obtain a comprehensive picture of the evolving HIV-1 TDRM across the massive parallel sequences (MPS) of the viral entire proviral genome in a well-characterized Brazilian blood donor naïve to antiretroviral drugs. MATERIALS AND METHODS The MPS data from 128 samples used in the analysis were sourced from Brazilian blood donors and were previously classified by less-sensitive (LS) or "detuned" enzyme immunoassay as non-recent or longstanding HIV-1 infections. The Stanford HIV Resistance Database (HIVDBv 6.2) and IAS-USA mutation lists were used to interpret the pattern of drug resistance. The minority variants with TDRM were identified using a threshold of ≥ 1.0% and ≤ 20% of the reads sequenced. The rate of TDRM in the MPS data of the proviral genome were compared with the corresponding published consensus sequences of their plasma viruses. RESULTS No TDRM were detected in the integrase or envelope regions. The overall prevalence of TDRM in the protease (PR) and reverse transcriptase (RT) regions of the HIV-1 pol gene was 44.5% (57/128), including any mutations to the nucleoside analogue reverse transcriptase inhibitors (NRTI) and non-nucleoside analogue reverse transcriptase inhibitors (NNRTI). Of the 57 subjects, 43 (75.4%) harbored a minority variant containing at least one clinically relevant TDRM. Among the 43 subjects, 33 (76.7%) had detectable minority resistant variants to NRTIs, 6 (13.9%) to NNRTIs, and 16 (37.2%) to PR inhibitors. The comparison of viral sequences in both sources, plasma and cells, would have detected 48 DNA provirus disclosed TDRM by MPS previously missed by plasma bulk analysis. CONCLUSION Our findings revealed a high prevalence of TDRM found in this group, as the use of MPS drastically increased the detection of these mutations. Sequencing proviral DNA provided additional information about TDRM, which may impact treatment decisions. The overall results emphasize the importance of continuous monitoring.
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Affiliation(s)
- Rodrigo Pessôa
- Laboratory of Dermatology and Immunodeficiencies, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo, São Paulo, Brazil
| | - Sabri S. Sanabani
- Laboratory of Dermatology and Immunodeficiencies, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo, São Paulo, Brazil
- Clinical Laboratory, Department of Pathology, Hospital das Clínicas, School of Medicine, University of São Paulo, São Paulo, Brazil
- * E-mail:
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Amano M, Miguel Salcedo-Gómez P, Yedidi RS, Delino NS, Nakata H, Venkateswara Rao K, Ghosh AK, Mitsuya H. GRL-09510, a Unique P2-Crown-Tetrahydrofuranylurethane -Containing HIV-1 Protease Inhibitor, Maintains Its Favorable Antiviral Activity against Highly-Drug-Resistant HIV-1 Variants in vitro. Sci Rep 2017; 7:12235. [PMID: 28947797 PMCID: PMC5613016 DOI: 10.1038/s41598-017-12052-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 08/30/2017] [Indexed: 11/12/2022] Open
Abstract
We report that GRL-09510, a novel HIV-1 protease inhibitor (PI) containing a newly-generated P2-crown-tetrahydrofuranylurethane (Crwn-THF), a P2′-methoxybenzene, and a sulfonamide isostere, is highly active against laboratory and primary clinical HIV-1 isolates (EC50: 0.0014–0.0028 μM) with minimal cytotoxicity (CC50: 39.0 μM). Similarly, GRL-09510 efficiently blocked the replication of HIV-1NL4-3 variants, which were capable of propagating at high-concentrations of atazanavir, lopinavir, and amprenavir (APV). GRL-09510 was also potent against multi-drug-resistant clinical HIV-1 variants and HIV-2ROD. Under the selection condition, where HIV-1NL4-3 rapidly acquired significant resistance to APV, an integrase inhibitor raltegravir, and a GRL-09510 congener (GRL-09610), no variants highly resistant against GRL-09510 emerged over long-term in vitro passage of the virus. Crystallographic analysis demonstrated that the Crwn-THF moiety of GRL-09510 forms strong hydrogen-bond-interactions with HIV-1 protease (PR) active-site amino acids and is bulkier with a larger contact surface, making greater van der Waals contacts with PR than the bis-THF moiety of darunavir. The present data demonstrate that GRL-09510 has favorable features for treating patients infected with wild-type and/or multi-drug-resistant HIV-1 variants, that the newly generated P2-Crwn-THF moiety confers highly desirable anti-HIV-1 potency. The use of the novel Crwn-THF moiety sheds lights in the design of novel PIs.
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Affiliation(s)
- Masayuki Amano
- Departments of Infectious Diseases and Hematology, Kumamoto University School of Medicine, Kumamoto, 860-8556, Japan
| | - Pedro Miguel Salcedo-Gómez
- Departments of Infectious Diseases and Hematology, Kumamoto University School of Medicine, Kumamoto, 860-8556, Japan
| | - Ravikiran S Yedidi
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Nicole S Delino
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hirotomo Nakata
- Departments of Infectious Diseases and Hematology, Kumamoto University School of Medicine, Kumamoto, 860-8556, Japan
| | | | - Arun K Ghosh
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Hiroaki Mitsuya
- Departments of Infectious Diseases and Hematology, Kumamoto University School of Medicine, Kumamoto, 860-8556, Japan. .,Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA. .,National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan.
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Aldous AM, Castel AD, Parenti DM. Prevalence and trends in transmitted and acquired antiretroviral drug resistance, Washington, DC, 1999-2014. BMC Res Notes 2017; 10:474. [PMID: 28893321 PMCID: PMC5594524 DOI: 10.1186/s13104-017-2764-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 08/31/2017] [Indexed: 11/29/2022] Open
Abstract
Background Drug resistance limits options for antiretroviral therapy (ART) and results in poorer health outcomes among HIV-infected persons. We sought to characterize resistance patterns and to identify predictors of resistance in Washington, DC. Methods We analyzed resistance in the DC Cohort, a longitudinal study of HIV-infected persons in care in Washington, DC. We measured cumulative drug resistance (CDR) among participants with any genotype between 1999 and 2014 (n = 3411), transmitted drug resistance (TDR) in ART-naïve persons (n = 1503), and acquired drug resistance (ADR) in persons with genotypes before and after ART initiation (n = 309). Using logistic regression, we assessed associations between patient characteristics and transmitted resistance to any antiretroviral. Results Prevalence of TDR was 20.5%, of ADR 40.5%, and of CDR 45.1% in the respective analysis groups. From 2004 to 2013, TDR prevalence decreased for nucleoside and nucleotide analogue reverse transcriptase inhibitors (15.0 to 5.5%; p = 0.0003) and increased for integrase strand transfer inhibitors (INSTIs) (0.0–1.4%; p = 0.04). In multivariable analysis, TDR was not associated with age, race/ethnicity, HIV risk group, or years from HIV diagnosis. Conclusions In this urban cohort of HIV-infected persons, almost half of participants tested had evidence of CDR; and resistance to INSTIs was increasing. If this trend continues, inclusion of the integrase-encoding region in baseline genotype testing should be strongly considered.
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Affiliation(s)
- Annette M Aldous
- Department of Epidemiology and Biostatistics, The George Washington University, Milken Institute School of Public Health, Washington, DC, 20037, USA
| | - Amanda D Castel
- Department of Epidemiology and Biostatistics, The George Washington University, Milken Institute School of Public Health, Washington, DC, 20037, USA
| | - David M Parenti
- Division of Infectious Diseases, The George Washington University School of Medicine, 2150 Pennsylvania Avenue, NW, Washington, DC, USA.
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Nakiganda LJ, Nakigozi G, Kagaayi J, Nalugoda F, Serwadda D, Sewankambo N, Gray R, Ndyanabo A, Muwanika R, Asamoah BO. Cross-sectional comparative study of risky sexual behaviours among HIV-infected persons initiated and waiting to start antiretroviral therapy in rural Rakai, Uganda. BMJ Open 2017; 7:e016954. [PMID: 28893749 PMCID: PMC5722091 DOI: 10.1136/bmjopen-2017-016954] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES To compare risky sexual behaviours between HIV-positive persons initiated on antiretroviral therapy (ART) (ART-experienced) and persons waiting to start on ART (ART-naive) and assess predictors of risky sexual behaviours among HIV-infected patients in rural Rakai district, Uganda. STUDY DESIGN This is a cross-sectional study that used data from the Rakai Community Cohort Study (RCCS) database between 2013 and 2014. A structured questionnaire was used for data collection. We used stepwise logistic regression as an index to estimate the adjusted ORs for the association between risky sexual behaviours and ART treatment status. STUDY SETTING This study was conducted in Rakai district, located in south-western Uganda. The data for this study were extracted from the RCCS. RCCS is an open prospective cohort of approximately 15 000 consenting participants aged 15-49 years. PARTICIPANTS HIV-positive participants aged 18-49 years who had sex at least once a month with any partner prior to the start of the study. MAIN OUTCOME MEASURES Inconsistent/no condom use in the last 12 months, alcohol use at last sexual encounter, and two or more sexual partners. RESULTS ART-naive participants were more likely to report inconsistent condom use (OR=1.74, 95% CI 1.11 to 2.73) and more likely to drink alcohol at last sexual encounter (OR=1.65, 95% CI 1.11 to 2.46), compared with ART-experienced patients. ART treatment status (p<0.001) was a significant predictor of risky sexual behaviours. Both marital status (p=0.016) and occupation level (p=0.009) were positively associated with inconsistent condom use, while sex (p<0.001) correlated with alcohol use at last sexual encounter. CONCLUSION ART-naive participants were more likely to exhibit risky sexual behaviours than the ART-experienced participants. The intensity of risk reduction counselling should be increased for HIV-positive persons waiting to start ART but already in HIV care.
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Affiliation(s)
- Lydia Jacenta Nakiganda
- International Master Programme in Public Health, Faculty of Medicine, Lund University, Malmö, Sweden
| | | | | | | | - David Serwadda
- Makerere University School of Public Health, Kampala, Uganda
| | | | - Ronald Gray
- School of Public Health, John Hopkins University, Maryland, USA
| | | | | | - Benedict Oppong Asamoah
- Department of Clinical Sciences, Division of Social Medicine and Global Health, Lund University, Malmö, Sweden
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Singh L, Kruger HG, Maguire GE, Govender T, Parboosing R. The role of nanotechnology in the treatment of viral infections. Ther Adv Infect Dis 2017; 4:105-131. [PMID: 28748089 PMCID: PMC5507392 DOI: 10.1177/2049936117713593] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Infectious diseases are the leading cause of mortality worldwide, with viruses in particular making global impact on healthcare and socioeconomic development. In addition, the rapid development of drug resistance to currently available therapies and adverse side effects due to prolonged use is a serious public health concern. The development of novel treatment strategies is therefore required. The interaction of nanostructures with microorganisms is fast-revolutionizing the biomedical field by offering advantages in both diagnostic and therapeutic applications. Nanoparticles offer unique physical properties that have associated benefits for drug delivery. These are predominantly due to the particle size (which affects bioavailability and circulation time), large surface area to volume ratio (enhanced solubility compared to larger particles), tunable surface charge of the particle with the possibility of encapsulation, and large drug payloads that can be accommodated. These properties, which are unlike bulk materials of the same compositions, make nanoparticulate drug delivery systems ideal candidates to explore in order to achieve and/or improve therapeutic effects. This review presents a broad overview of the application of nanosized materials for the treatment of common viral infections.
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Affiliation(s)
- Lavanya Singh
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | - Hendrik G. Kruger
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Durban, South Africa
| | - Glenn E.M. Maguire
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Durban, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Durban, South Africa
| | - Raveen Parboosing
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
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72
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Sapozhnikov J, Young JD, Patel M, Chiampas TD, Vaughn P, Badowski ME. Prevalence of HIV-1 transmitted drug resistance in the incarcerated population. HIV Med 2017; 18:756-763. [PMID: 28585361 DOI: 10.1111/hiv.12522] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2017] [Indexed: 11/28/2022]
Abstract
OBJECTIVES The aim of the study was to determine the prevalence of transmitted drug resistance (TDR)-associated mutations among treatment-naïve, incarcerated individuals with HIV-1 infection in the USA as well as the class TDR and antiretroviral (ARV) mutations present at baseline. METHODS Patients over the age of 18 years were included in the study if they had been diagnosed with HIV infection, if their HIV infection was managed through telemedicine and if they were incarcerated in the State of Illinois Department of Corrections between 10 July 2010 and 29 April 2016. Additionally, the patients were required to have a documented genotype and be ARV-naïve. A medical chart review was conducted to assess demographic information, disease burden, and risk factors for acquiring the virus. RESULTS The inclusion criteria were met for 105 patients. A total of 24 patients (23%) had a clinically significant mutation associated with resistance to any drug class. The prevalence of mutations conferring clinically significant resistance was 19% for nonnucleoside reverse transcriptase inhibitors (NNRTIs), 18% for nucleoside reverse transcriptase inhibitors (NRTIs), and 4% for protease inhibitors (PIs). Five per cent of patients had dual-class TDR to both NRTI and NNRTI drug classes and 2% of patients had mutations to both NNRTI and PI drug classes. There was no significant increase in the prevalence of clinically relevant drug resistance mutations based on demographics, burden of disease, or risk factors for acquiring the virus. CONCLUSIONS A high prevalence of TDR was identified in the ARV-naïve incarcerated population. The results of this study indicate an increased prevalence of TDR in a largely unstudied incarcerated population, demonstrating the need for increased monitoring of resistance in HIV-infected patients world-wide.
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Affiliation(s)
- J Sapozhnikov
- College of Pharmacy, Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, IL, USA
| | - J D Young
- Division of Infectious Diseases, Immunology and International Medicine, Department of Medicine, University of Illinois Hospital & Health Sciences System, Chicago, IL, USA
| | - M Patel
- Division of Infectious Diseases, Immunology and International Medicine, Department of Medicine, University of Illinois Hospital & Health Sciences System, Chicago, IL, USA
| | - T D Chiampas
- College of Pharmacy, Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, IL, USA
| | - P Vaughn
- College of Pharmacy, Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, IL, USA
| | - M E Badowski
- College of Pharmacy, Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, IL, USA
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The Role of Caveolin 1 in HIV Infection and Pathogenesis. Viruses 2017; 9:v9060129. [PMID: 28587148 PMCID: PMC5490806 DOI: 10.3390/v9060129] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/02/2017] [Accepted: 05/22/2017] [Indexed: 12/29/2022] Open
Abstract
Caveolin 1 (Cav-1) is a major component of the caveolae structure and is expressed in a variety of cell types including macrophages, which are susceptible to human immunodeficiency virus (HIV) infection. Caveolae structures are present in abundance in mechanically stressed cells such as endothelial cells and adipocytes. HIV infection induces dysfunction of these cells and promotes pathogenesis. Cav-1 and the caveolae structure are believed to be involved in multiple cellular processes that include signal transduction, lipid regulation, endocytosis, transcytosis, and mechanoprotection. Such a broad biological role of Cav-1/caveolae is bound to have functional cross relationships with several molecular pathways including HIV replication and viral-induced pathogenesis. The current review covers the relationship of Cav-1 and HIV in respect to viral replication, persistence, and the potential role in pathogenesis.
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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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Bai X, Yang Z, Zhu M, Dong B, Zhou L, Zhang G, Wang J, Wang Y. Design and synthesis of potent HIV-1 protease inhibitors with (S)-tetrahydrofuran-tertiary amine-acetamide as P2-ligand: Structure-activity studies and biological evaluation. Eur J Med Chem 2017; 137:30-44. [PMID: 28554091 DOI: 10.1016/j.ejmech.2017.05.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 10/19/2022]
Abstract
The design, synthesis, and SAR study of a new series of HIV-1 protease inhibitors incorporating stereochemically defined tetrahydrofuran-tertiary amine-acetamide P2-ligand are described. Various substituent effects on the tertiary amine P2-ligand and phenylsulfonamide P2'-ligand were investigated to maximize the ligand-binding site interactions in the protease active site. Most of inhibitors displayed low nanomolar to subnanomolar inhibitory potency. Inhibitor 20e containing N-(S-tetrahydrofuran)-N-(2-methoxyethyl)acetamide as P2-ligand along with 4-methoxylphenylsulfonamide as P2'-ligand displayed the most potent enzyme inhibitory activity (IC50 = 0.35 nM) and remarkably low cytotoxicity (CC50 = 305 μM).
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Affiliation(s)
- Xiaoguang Bai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Zhiheng Yang
- Department of Pharmacy, The First Affiliated Hospital, Zhengzhou University, Zhengzhou 450052, China
| | - Mei Zhu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Biao Dong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Lei Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Guoning Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Juxian Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China.
| | - Yucheng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China.
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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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A Modified P1 Moiety Enhances In Vitro Antiviral Activity against Various Multidrug-Resistant HIV-1 Variants and In Vitro Central Nervous System Penetration Properties of a Novel Nonpeptidic Protease Inhibitor, GRL-10413. Antimicrob Agents Chemother 2016; 60:7046-7059. [PMID: 27620483 DOI: 10.1128/aac.01428-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 08/22/2016] [Indexed: 11/20/2022] Open
Abstract
We report here that GRL-10413, a novel nonpeptidic HIV-1 protease inhibitor (PI) containing a modified P1 moiety and a hydroxyethylamine sulfonamide isostere, is highly active against laboratory HIV-1 strains and primary clinical isolates (50% effective concentration [EC50] of 0.00035 to 0.0018 μM), with minimal cytotoxicity (50% cytotoxic concentration [CC50] = 35.7 μM). GRL-10413 blocked the infectivity and replication of HIV-1NL4-3 variants selected by use of atazanavir, lopinavir, or amprenavir (APV) at concentrations of up to 5 μM (EC50 = 0.0021 to 0.0023 μM). GRL-10413 also maintained its strong antiviral activity against multidrug-resistant clinical HIV-1 variants isolated from patients who no longer responded to various antiviral regimens after long-term antiretroviral therapy. The development of resistance against GRL-10413 was significantly delayed compared to that against APV. In addition, GRL-10413 showed favorable central nervous system (CNS) penetration properties as assessed with an in vitro blood-brain barrier (BBB) reconstruction system. Analysis of the crystal structure of HIV-1 protease in complex with GRL-10413 demonstrated that the modified P1 moiety of GRL-10413 has a greater hydrophobic surface area and makes greater van der Waals contacts with active site amino acids of protease than in the case of darunavir. Moreover, the chlorine substituent in the P1 moiety interacts with protease in two distinct configurations. The present data demonstrate that GRL-10413 has desirable features for treating patients infected with wild-type and/or multidrug-resistant HIV-1 variants, with favorable CNS penetration capability, and that the newly modified P1 moiety may confer desirable features in designing novel anti-HIV-1 PIs.
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Li H, Chang S, Han Y, Zhuang D, Li L, Liu Y, Liu S, Bao Z, Zhang W, Song H, Li T, Li J. The prevalence of drug resistance among treatment-naïve HIV-1-infected individuals in China during pre- and post- 2004. BMC Infect Dis 2016; 16:605. [PMID: 27782811 PMCID: PMC5080753 DOI: 10.1186/s12879-016-1928-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 10/13/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The widespread use of antiretroviral therapies has led to considerable concerns about the prevalence of drug-resistant, as transmission of drug-resistant (TDR) strains poses a challenge for the control of the HIV-1 epidemic. METHODS We conducted an epidemiological study enrolling treatment-naïve HIV-1-positive subjects at the Peking Union Medical College Hospital since 1991. Drug resistance was determined by submitting the sequences to the Stanford University Network HIV-1 database. RESULTS Of 521 participants, 478 samples were amplified and sequenced successfully. HIV Transmitted drug resistance prevalence in China was determined to be 6.7 %. We did not find significant differences in the TDR rate by demographic characteristics. No significant time trend in the prevalence of overall TDR was observed (p > 0.05). CONCLUSIONS We identified an intermediate prevalence of transmitted drug resistance (TDR), exhibiting a stable time trend. These findings enhance our understanding of HIV-1 drug resistance prevalence and time trend, and provide some guidelines for the comprehensive public health strategy of TDR prevention.
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Affiliation(s)
- Hanping Li
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, No. 20 East Street, Fengtai district, Beijing, 100071, China
| | - Shuai Chang
- Institute of Disease Control and Prevention, Academy of Military Medical Science, Beijing, 100071, China.,Department of Clinical Laboratory, PLA Army General Hospital, Beijing, 100700, China
| | - Yang Han
- Department of Infectious Disease, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan Wangfujing, Dongcheng district, Beijing, 100730, China
| | - Daomin Zhuang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, No. 20 East Street, Fengtai district, Beijing, 100071, China
| | - Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, No. 20 East Street, Fengtai district, Beijing, 100071, China
| | - Yongjian Liu
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, No. 20 East Street, Fengtai district, Beijing, 100071, China
| | - Siyang Liu
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, No. 20 East Street, Fengtai district, Beijing, 100071, China
| | - Zuoyi Bao
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, No. 20 East Street, Fengtai district, Beijing, 100071, China
| | - Wenfu Zhang
- Institute of Disease Control and Prevention, Academy of Military Medical Science, Beijing, 100071, China
| | - Hongbin Song
- Institute of Disease Control and Prevention, Academy of Military Medical Science, Beijing, 100071, China
| | - Taisheng Li
- Department of Infectious Disease, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan Wangfujing, Dongcheng district, Beijing, 100730, China.
| | - Jingyun Li
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, No. 20 East Street, Fengtai district, Beijing, 100071, China.
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Cunningham E, Chan YT, Aghaizu A, Bibby DF, Murphy G, Tosswill J, Harris RJ, Myers R, Field N, Delpech V, Cane PA, Gill ON, Mbisa JL. Enhanced surveillance of HIV-1 drug resistance in recently infected MSM in the UK. J Antimicrob Chemother 2016; 72:227-234. [PMID: 27742812 DOI: 10.1093/jac/dkw404] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 08/19/2016] [Accepted: 08/26/2016] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To determine the prevalence of inferred low-frequency HIV-1 transmitted drug resistance (TDR) in MSM in the UK and its predicted effect on first-line therapy. METHODS The HIV-1 pol gene was amplified from 442 newly diagnosed MSM identified as likely recently infected by serological avidity testing in 2011-13. The PCR products were sequenced by next-generation sequencing with a mutation frequency threshold of >2% and TDR mutations defined according to the 2009 WHO surveillance drug resistance mutations list. RESULTS The majority (75.6%) were infected with subtype B and 6.6% with rare complex or unique recombinant forms. At a mutation frequency threshold of >20%, 7.2% (95% CI 5.0%-10.1%) of the sequences had TDR and this doubled to 15.8% (95% CI 12.6%-19.6%) at >2% mutation frequency (P < 0.0001). The majority (26/42, 62%) of low-frequency variants were against PIs. The most common mutations detected at >20% and 2%-20% mutation frequency differed for each drug class, these respectively being: L90M (n = 7) and M46IL (n = 10) for PIs; T215rev (n = 9) and D67GN (n = 4) for NRTIs; and K103N (n = 5) and G190E (n = 2) for NNRTIs. Combined TDR was more frequent in subtype B than non-B (OR = 0.38; 95% CI = 0.17-0.88; P = 0.024) and had minimal predicted effect on recommended first-line therapies. CONCLUSIONS The data suggest differences in the types of low-frequency compared with majority TDR variants that require a better understanding of the origins and clinical significance of low-frequency variants. This will better inform diagnostic and treatment strategies.
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Affiliation(s)
- Emma Cunningham
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Yuen-Ting Chan
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Adamma Aghaizu
- HIV and STI Department, National Infection Service, Public Health England, London, UK
| | - David F Bibby
- Virus Reference Department, National Infection Service, Public Health England, London, UK.,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
| | - Gary Murphy
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Jennifer Tosswill
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Ross J Harris
- Statistics, Modelling and Economics Department, National Infection Service, Public Health England, London, UK
| | - Richard Myers
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Nigel Field
- HIV and STI Department, National Infection Service, Public Health England, London, UK
| | - Valerie Delpech
- HIV and STI Department, National Infection Service, Public Health England, London, UK.,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
| | - Patricia A Cane
- Virus Reference Department, National Infection Service, Public Health England, London, UK.,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
| | - O Noel Gill
- HIV and STI Department, National Infection Service, Public Health England, London, UK.,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
| | - Jean L Mbisa
- Virus Reference Department, National Infection Service, Public Health England, London, UK .,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
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HIV-1 drug resistance and resistance testing. INFECTION GENETICS AND EVOLUTION 2016; 46:292-307. [PMID: 27587334 DOI: 10.1016/j.meegid.2016.08.031] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/24/2016] [Accepted: 08/27/2016] [Indexed: 12/23/2022]
Abstract
The global scale-up of antiretroviral (ARV) therapy (ART) has led to dramatic reductions in HIV-1 mortality and incidence. However, HIV drug resistance (HIVDR) poses a potential threat to the long-term success of ART and is emerging as a threat to the elimination of AIDS as a public health problem by 2030. In this review we describe the genetic mechanisms, epidemiology, and management of HIVDR at both individual and population levels across diverse economic and geographic settings. To describe the genetic mechanisms of HIVDR, we review the genetic barriers to resistance for the most commonly used ARVs and describe the extent of cross-resistance between them. To describe the epidemiology of HIVDR, we summarize the prevalence and patterns of transmitted drug resistance (TDR) and acquired drug resistance (ADR) in both high-income and low- and middle-income countries (LMICs). We also review to two categories of HIVDR with important public health relevance: (i) pre-treatment drug resistance (PDR), a World Health Organization-recommended HIVDR surveillance metric and (ii) and pre-exposure prophylaxis (PrEP)-related drug resistance, a type of ADR that can impact clinical outcomes if present at the time of treatment initiation. To summarize the implications of HIVDR for patient management, we review the role of genotypic resistance testing and treatment practices in both high-income and LMIC settings. In high-income countries where drug resistance testing is part of routine care, such an understanding can help clinicians prevent virological failure and accumulation of further HIVDR on an individual level by selecting the most efficacious regimens for their patients. Although there is reduced access to diagnostic testing and to many ARVs in LMIC, understanding the scientific basis and clinical implications of HIVDR is useful in all regions in order to shape appropriate surveillance, inform treatment algorithms, and manage difficult cases.
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Basuyau F, Josset V, Merle V, Czernichow P. Case Fatality and Health Care Costs in HIV-Infected Patients: Evolution from 1992 to 2000 at Rouen University Hospital, France. Int J STD AIDS 2016; 15:679-84. [PMID: 15479505 DOI: 10.1177/095646240401501009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Vital prognosis in HIV-infected patients has been improved by new therapies, leading to an increase in treatment and outpatient costs but lower inpatient care costs. The aim of the study was to compare the health care costs between 1992–1996 (first half) and 1996–2000 (second half) in HIV-infected patients at Rouen University Hospital. Hospitalization costs (including inpatient and outpatient care), infectious complication treatment and antiretroviral therapy costs were evaluated from a National Health Insurance viewpoint. Between 1992 and 2000, 1212 patients were admitted at least once. Total expenditure increased between the two periods from €13,660 to €27,567, i.e., a two-fold increase. During the same period, 125 deaths were avoided, and 3602 years of life were gained. The cost of one avoided death was €108,320 and the cost per life-year gained was €3776.
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Affiliation(s)
- F Basuyau
- Department of Epidemiology and Public Health, Rouen University Hospital-Charles Nicolle, 1 rue de Germont, 76031 Rouen Cedex, France.
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Bethell RC, Lie YS, Parkin NT. In Vitro Activity of SPD754, a New Deoxycytidine Nucleoside Reverse Transcriptase Inhibitor (NRTI), against 215 HIV-1 Isolates Resistant to Other NRTIs. ACTA ACUST UNITED AC 2016; 16:295-302. [PMID: 16245645 DOI: 10.1177/095632020501600502] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
SPD754 (also known as AVX-754) is a deoxycytidine analogue nucleoside reverse transcriptase inhibitor (NRTI) with antiretroviral activity against HIV-1 and HIV-2 in vitro and against recombinant viruses containing thymidine analogue mutations (TAMs). In order to better establish the activity of SPD754 against HIV-1 containing TAMs, twelve panels of up to twenty clinical isolates with defined TAM combinations were selected from the ViroLogic database. Phenotypic viral susceptibility to SPD754 and five other NRTIs was tested using the PhenoSense HIV assay and expressed as median fold-change compared with a reference strain. In total, 215 isolates were selected, representing four TAM patterns in both pathways by which TAMs accumulate clinically. The presence of five TAMs in the 41, 215 pathway, at codons 41, 67, 210, 215, and 219 of reverse transcriptase (RT), produced a median 1.8-fold reduction in SPD754 susceptibility, compared with fold reductions to zidovudine, lamivudine, abacavir, didanosine and tenofovir of 438, 4.8, 4.5, 1.4 and 3.6, respectively. Five TAMs in the 67, 70, 219 pathway (at codons 41, 67, 70, 215 and 219) reduced SPD754 susceptibility by a median 1.3-fold, compared with fold reductions for the aforementioned NRTIs of 108, 3.2, 3.0, 1.3 and 2.5, respectively. M184V addition reduced SPD754 susceptibility by 1.8-fold in the presence or absence of TAMs. SPD754 retains a substantial proportion of its antiviral activity against HIV-1 containing multiple TAMs, with or without the M184V mutation. These data suggest that SPD754 is a promising new NRTI for the treatment of NRTI-experienced HIV-infected patients.
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83
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Grusky O, Duan N, Swanson AN, Woodbridge M, Leich J. Evaluating the Accessibility of HIV Testing Organizations. Eval Health Prof 2016; 27:189-205. [PMID: 15140294 DOI: 10.1177/0163278704264048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Consumer-based indicators were developed to evaluate the accessibility of private and public nonhospital HIV testing organizations. A comprehensive roster of 148 nonhospital HIV testing organizations in Los Angeles County was constructed from publicly available listings. A telephone survey protocol was used to contact sites and assess consumer relevant accessibility measures. Only 50% of the sites could be contacted and indicated that HIV testing was available. Hence, a consumer who tried to reach one site had only a 50-50 chance of success. HIV testing sites differed with regard to how frequently they offered testing; whether they offered anonymous and/or confidential testing; what types of counseling they provided; how quickly test results were available; and how friendly, helpful, attentive, and knowledgeable about testing procedures their attendants were. HIV testing sites must make their services accessible and be perceived by consumers as responsive if they are to be effective service providers.
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Affiliation(s)
- Oscar Grusky
- Department of Sociology, University of California, Los Angeles 90095-1551, USA.
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84
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Bussmann H, Novitsky V, Wester W, Peter T, Masupu K, Gabaitiri L, Kim S, Gaseitsiwe S, Ndungú T, Marlink R, Thior I, Essex M. HIV-1 Subtype C Drug-Resistance Background among ARV-Naive Adults in Botswana. ACTA ACUST UNITED AC 2016; 16:103-15. [PMID: 15889533 DOI: 10.1177/095632020501600203] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Current HIV-1 antiretroviral (ARV) drug resistance knowledge is limited to HIV-1 subtype B (HIV-1B). We addressed whether unique genetic and phenotypic properties of HIV-1 subtype C (HIV-1C), southern Africa's most prevalent subtype, may foment earlier and/or distinct resistance mutations. Population-level HIV-1C genotypes were evaluated with respect to drug resistance prevalence before Botswana's public ARV treatment programme began. Viruses were genotyped from 11 representative districts of northern and southern Botswana, and consensus sequences from these 71 individuals and 51 previously reported sequences from HIV-positive blood donors were constructed. Phylogenetic analysis classified all 71 sequences but one, which exhibited pol gene mosaicism, as HIV-1C. The protease and reverse transcriptase coding region had no detectable known primary mutations associated with HIV-1B protease inhibitor (PI) drug resistance. Secondary mutations associated with PI drug resistance were found in all sequences. Several HIV-1C—specific polymorphic sites were found across the pol gene. Northern and southern Botswana viral sequences showed no significant differences from each other. Population genotyping shows that, without countrywide ARV treatment, HIV-1C—infected Batswana harbour virtually no primary mutations known to confer resistance to the three major HIV-1B ARV drug classes. Some secondary PI mutations and polymorphic sites in the protease enzyme necessitate continuous population monitoring, particularly after introduction of countrywide ARV treatment in Botswana. Although its PI resistance development rate and kinetics are not known, our data may suggest increased susceptibility and readiness of HIV-1C to develop resistance under drug pressure when the PI class of drugs is used.
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Affiliation(s)
- Hermann Bussmann
- Botswana-Harvard School of Public Health AIDS Initiative Partnership, Gaborone, Botswana
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85
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Prevalence of Transmitted HIV Drug Resistance Among Recently Infected Persons in San Diego, CA 1996-2013. J Acquir Immune Defic Syndr 2016; 71:228-36. [PMID: 26413846 DOI: 10.1097/qai.0000000000000831] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Transmitted drug resistance (TDR) remains an important concern when initiating antiretroviral therapy (ART). Here, we describe the prevalence and phylogenetic relationships of TDR among ART-naive, HIV-infected individuals in San Diego from 1996 to 2013. METHODS Data were analyzed from 496 participants of the San Diego Primary Infection Cohort who underwent genotypic resistance testing before initiating therapy. Mutations associated with drug resistance were identified according to the WHO-2009 surveillance list. Network and phylogenetic analyses of the HIV-1 pol sequences were used to evaluate the relationships of TDR within the context of the entire cohort. RESULTS The overall prevalence of TDR was 13.5% (67/496), with an increasing trend over the study period (P = 0.005). TDR was predominantly toward nonnucleoside reverse transcriptase inhibitors (NNRTIs) [8.5% (42/496)], also increasing over the study period (P = 0.005). By contrast, TDR to protease inhibitors and nucleos(t)ide reverse transcriptase inhibitors were 4.4% (22/496) and 3.8% (19/496), respectively, and did not vary with time. TDR prevalence did not differ by age, gender, race/ethnicity, or risk factors. Using phylogenetic analysis, we identified 52 transmission clusters, including 8 with at least 2 individuals sharing the same mutation, accounting for 23.8% (16/67) of the individuals with TDR. CONCLUSIONS Between 1996 and 2013, the prevalence of TDR significantly increased among recently infected ART-naive individuals in San Diego. Around one-fourth of TDR occurred within clusters of recently infected individuals. These findings highlight the importance of baseline resistance testing to guide selection of ART and for public health monitoring.
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86
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Cho MC, Park CW, Park BG, Oh HB, Choi SH, Choi SE, Cho NS. Detecting primary drug-resistant mutations in Korean HIV patients using ultradeep pyrosequencing. J Virol Methods 2016; 234:115-22. [PMID: 27109046 DOI: 10.1016/j.jviromet.2016.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 03/24/2016] [Accepted: 04/10/2016] [Indexed: 12/13/2022]
Abstract
HIV primary resistance, drug resistance in treatment-naïve patients, is an emerging public health issue. The prevalence of HIV primary resistance mutations down to the level of 1% minor variants was investigated using ultradeep pyrosequencing (UDPS) in HIV-positive Korean blood donors and in treatment naïve chronic patients for the comparison. The entire pol region was sequenced from 25 HIV-positive blood donors, and 18 treatment-naïve chronic HIV patients. UDPS was successful in 19 blood donors and 18 chronic patients. In total, 1,011,338 sequence reads were aligned, and 28,093 sequence reads were aligned on average per sample. The prevalence of HIV primary resistance mutations in the HIV-positive blood donors and chronic HIV patients were 63.2% and 44.4% according to UDPS, respectively. Protease inhibitor (PI) drugs demonstrated different patterns in HIV-positive blood donors and chronic HIV patients, whereas non-nucleoside reverse transcriptase inhibitors (NNRTI), nucleoside reverse transcriptase inhibitors (NRTI), and integrase inhibitor (INI) drugs showed similar patterns between the two groups. Higher level of primary resistance prevalence was observed mainly because UDPS method could detect mutations in minor variants with 1-10% frequency. The higher resistance prevalence was observed in HIV-positive blood donors than in chronic patients. Considering that treatments for HIV-infected patients were recently amended to start at an earlier stage, information about degree of drug resistance to each drug between the two groups would help to establish future policies, design additional clinical trials, assess HIV patient care in Korea.
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Affiliation(s)
- Min-Chul Cho
- Department of Laboratory Medicine, Gyeongsang National University Hospital and Gyeongsang National University School of Medicine, Jinju, Korea, South Korea
| | - Chang-Wook Park
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea
| | - Borae G Park
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea
| | - Heung-Bum Oh
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea.
| | - Sang-Ho Choi
- Department of Infectious Diseases, University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea
| | - Sung-Eun Choi
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea
| | - Nam-Sun Cho
- Korea Red Cross Blood Service, Korean Red Cross, Seoul, South Korea
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Punyacharoensin N, Edmunds WJ, De Angelis D, Delpech V, Hart G, Elford J, Brown A, Gill ON, White RG. Effect of pre-exposure prophylaxis and combination HIV prevention for men who have sex with men in the UK: a mathematical modelling study. Lancet HIV 2016; 3:e94-e104. [PMID: 26847231 DOI: 10.1016/s2352-3018(15)00056-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/18/2015] [Accepted: 03/24/2015] [Indexed: 02/02/2023]
Abstract
BACKGROUND HIV transmission in men who have sex with men (MSM) in the UK has shown no sign of decreasing in the past decade. Additional prevention measures are needed. We aimed to estimate the effect of various potential interventions implemented individually and in combination on prevention of HIV infection. METHODS We extended a deterministic partnership-based mathematical model for HIV transmission, informed by detailed behavioural and surveillance data, to assess the effect of seven different HIV interventions implemented in MSM (aged 15-64 years) in the UK during 2014-20, including increasing rates of HIV testing, test-and-treat programmes, pre-exposure prophylaxis (PrEP), and sexual behavioural changes. We did sensitivity analyses on risk compensation. FINDINGS We predicted a baseline of 16 955 new infections (IQR 13 156-21 669) in MSM in the UK during 2014-20. At a coverage of ≤50%, testing twice a year outperformed all other interventions. Of all intervention combinations, only the combined effect of test and treat and annual HIV testing (61·8%, IQR 47·2-81·8, of total incidence) was greater than the sum of effects of the two interventions individually (32·6%, 23·7-46·0, and 23·9%, 16·5-33·3, respectively). Simultaneous PrEP, expansion of HIV testing, and initiation of test-and-treat programme in 25% of high-activity MSM could save 7399 (IQR 5587-9813) UK MSM from HIV infection (43·6%, IQR 32·9-57·9, of total incidence). An increase in unsafe sex or sexual partners to 50% or more could substantially reduce the effect of interventions, but is unlikely to negate the prevention benefit completely. INTERPRETATION PrEP could prevent a large number of new HIV infections if other key strategies including HIV testing and treatment are simultaneously expanded and improved. Without PrEP, HIV incidence in MSM in the UK is unlikely to decrease substantially by the end of this decade. FUNDING Health Protection Agency (now Public Health England).
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Affiliation(s)
- Narat Punyacharoensin
- Centre for the Mathematical Modelling of Infectious Diseases and Department of Infectious Diseases Epidemiology, London School of Hygiene & Tropical Medicine, London, UK.
| | - William John Edmunds
- Centre for the Mathematical Modelling of Infectious Diseases and Department of Infectious Diseases Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Valerie Delpech
- HIV and STI Department of Public Health England's Centre for Infectious Disease Surveillance and Control, London, UK
| | - Graham Hart
- Centre for Sexual Health and HIV Research, Department of Infection and Population Health, Mortimer Market Centre, University College London, London, UK
| | - Jonathan Elford
- School of Health Sciences, City University London, London, UK
| | - Alison Brown
- HIV and STI Department of Public Health England's Centre for Infectious Disease Surveillance and Control, London, UK
| | - O Noel Gill
- HIV and STI Department of Public Health England's Centre for Infectious Disease Surveillance and Control, London, UK
| | - Richard Guy White
- Centre for the Mathematical Modelling of Infectious Diseases and Department of Infectious Diseases Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
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88
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Comparative analysis of drug resistance mutations in the human immunodeficiency virus reverse transcriptase gene in patients who are non-responsive, responsive and naive to antiretroviral therapy. Arch Virol 2016; 161:1101-13. [PMID: 26801790 DOI: 10.1007/s00705-016-2760-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 01/11/2016] [Indexed: 11/27/2022]
Abstract
Drug resistance mutations in the Pol gene of human immunodeficiency virus 1 (HIV-1) are one of the critical factors associated with antiretroviral therapy (ART) failure in HIV-1 patients. The issue of resistance to reverse transcriptase inhibitors (RTIs) in HIV infection has not been adequately addressed in the Indian subcontinent. We compared HIV-1 reverse transcriptase (RT) gene sequences to identify mutations present in HIV-1 patients who were ART non-responders, ART responders and drug naive. Genotypic drug resistance testing was performed by sequencing a 655-bp region of the RT gene from 102 HIV-1 patients, consisting of 30 ART-non-responding, 35 ART-responding and 37 drug-naive patients. The Stanford HIV Resistance Database (HIVDBv 6.2), IAS-USA mutation list, ANRS_09/2012 algorithm, and Rega v8.02 algorithm were used to interpret the pattern of drug resistance. The majority of the sequences (96 %) belonged to subtype C, and a few of them (3.9 %) to subtype A1. The frequency of drug resistance mutations observed in ART-non-responding, ART-responding and drug-naive patients was 40.1 %, 10.7 % and 20.58 %, respectively. It was observed that in non-responders, multiple mutations were present in the same patient, while in responders, a single mutation was found. Some of the drug-naive patients had more than one mutation. Thymidine analogue mutations (TAMs), however, were found in non-responders and naive patients but not in responders. Although drug resistance mutations were widely distributed among ART non-responders, the presence of resistance mutations in the viruses of drug-naive patients poses a big concern in the absence of a genotyping resistance test.
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89
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Calvez V, Marcelin AG, Vingerhoets J, Hill A, Hadacek B, Moecklinghoff C. Systematic review to determine the prevalence of transmitted drug resistance mutations to rilpivirine in HIV-infected treatment-naive persons. Antivir Ther 2016; 21:405-12. [PMID: 26761642 DOI: 10.3851/imp3024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2016] [Indexed: 10/22/2022]
Abstract
BACKGROUND Transmitted drug resistance to antiretrovirals in HIV-1-infected individuals is rising in some regions and could compromise the effectiveness of first-line treatment. It is important to understand the prevalence of resistance to rilpivirine to inform treatment provision. METHODS A PUBMED/EMBASE search identified analyses of transmitted genotypic resistance to specific non-nucleoside reverse transcriptase inhibitor mutations worldwide. Patients were to be HIV-1-infected and antiretroviral-naive. Rilpivirine mutations assessed were: L100I, K101E/P, E138A/G/K/Q/R, V179L, Y181C/I/V, Y188L, H221Y, F227C and M230I/L. Additionally, frequency of resistance mutations were extracted and pooled by HIV subtype from the Stanford HIV drug resistance database. RESULTS 138 eligible articles from 65 countries were identified (n=64,466). Among these 64,466 samples, 7 of the 9 genotypic rilpivirine mutations had a prevalence <0.1%. Two mutations were more prevalent: E138A/G/K/Q/R (0.7%, 95% CI 0.2, 1.3) and Y181C/I/V (0.3%, 95% CI 0.2, 0.4). Prevalence of E138 rilpivirine-related mutations varied between regions: highest in Latin America/Caribbean (3.6%, 95% CI 1.0, 7.6) and in Europe (3.2%, 95% CI 0.7, 6.9). Pooled results from the Stanford database (n=52,680) correlated with these findings indicating a low prevalence of 8/9 rilpivirine mutations (<0.1%), except for E138A/G/K/Q/R (2.9%, 95% CI 1.8, 4.4). Prevalence of the mutations at E138 varied significantly by HIV subtype and was highest for subtype-C (6.1%), subtype-F (5.1%) and subtype-A (3.3%). CONCLUSIONS The prevalence of most transmitted rilpivirine-related HIV mutations is generally low in treatment-naive HIV-1-infected individuals (<0.1%). The prevalence of E138A/G/K/Q/R mutations is higher (0.7%) and varies according to geographical region and HIV subtype.
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Affiliation(s)
- Vincent Calvez
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, INSERM, UMR_S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, F-75013, France
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90
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Panpradist N, Beck IA, Chung MH, Kiarie JN, Frenkel LM, Lutz BR. Simplified Paper Format for Detecting HIV Drug Resistance in Clinical Specimens by Oligonucleotide Ligation. PLoS One 2016; 11:e0145962. [PMID: 26751207 PMCID: PMC4713472 DOI: 10.1371/journal.pone.0145962] [Citation(s) in RCA: 24] [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: 05/20/2015] [Accepted: 12/10/2015] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus (HIV) is a chronic infection that can be managed by antiretroviral treatment (ART). However, periods of suboptimal viral suppression during lifelong ART can select for HIV drug resistant (DR) variants. Transmission of drug resistant virus can lessen or abrogate ART efficacy. Therefore, testing of individuals for drug resistance prior to initiation of treatment is recommended to ensure effective ART. Sensitive and inexpensive HIV genotyping methods are needed in low-resource settings where most HIV infections occur. The oligonucleotide ligation assay (OLA) is a sensitive point mutation assay for detection of drug resistance mutations in HIV pol. The current OLA involves four main steps from sample to analysis: (1) lysis and/or nucleic acid extraction, (2) amplification of HIV RNA or DNA, (3) ligation of oligonucleotide probes designed to detect single nucleotide mutations that confer HIV drug resistance, and (4) analysis via oligonucleotide surface capture, denaturation, and detection (CDD). The relative complexity of these steps has limited its adoption in resource-limited laboratories. Here we describe a simplification of the 2.5-hour plate-format CDD to a 45-minute paper-format CDD that eliminates the need for a plate reader. Analysis of mutations at four HIV-1 DR codons (K103N, Y181C, M184V, and G190A) in 26 blood specimens showed a strong correlation of the ratios of mutant signal to total signal between the paper CDD and the plate CDD. The assay described makes the OLA easier to perform in low resource laboratories.
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Affiliation(s)
- Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Ingrid A. Beck
- Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Michael H. Chung
- Department of Internal Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - James N. Kiarie
- Departments of Obstetrics and Gynecology, University of Nairobi, Nairobi, Kenya
| | - Lisa M. Frenkel
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Departments of Pediatrics and Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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91
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Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing. Viruses 2016; 8:v8010012. [PMID: 26751471 PMCID: PMC4728572 DOI: 10.3390/v8010012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/08/2015] [Accepted: 12/15/2015] [Indexed: 12/24/2022] Open
Abstract
Genetic analyses play a central role in infectious disease research. Massively parallelized “mechanical cloning” and sequencing technologies were quickly adopted by HIV researchers in order to broaden the understanding of the clinical importance of minor drug-resistant variants. These efforts have, however, remained largely limited to small genomic regions. The growing need to monitor multiple genome regions for drug resistance testing, as well as the obvious benefit for studying evolutionary and epidemic processes makes complete genome sequencing an important goal in viral research. In addition, a major drawback for NGS applications to RNA viruses is the need for large quantities of input DNA. Here, we use a generic overlapping amplicon-based near full-genome amplification protocol to compare low-input enzymatic fragmentation (Nextera™) with conventional mechanical shearing for Roche 454 sequencing. We find that the fragmentation method has only a modest impact on the characterization of the population composition and that for reliable results, the variation introduced at all steps of the procedure—from nucleic acid extraction to sequencing—should be taken into account, a finding that is also relevant for NGS technologies that are now more commonly used. Furthermore, by applying our protocol to deep sequence a number of pre-therapy plasma and PBMC samples, we illustrate the potential benefits of a near complete genome sequencing approach in routine genotyping.
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92
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Wu S, Yin Q, Zhao L, Fan N, Tang X, Zhao J, Sheng T, Guo Y, Tian C, Zhang Z, Xu W, Liu Z, Jiang S, Ma L, Liu J, Wang X. A stereo configuration-activity study of 3-iodo-4-(2-methylcyclohexyloxy)-6-phenethylpyridin-2(2H)-ones as potency inhibitors of HIV-1 variants. Org Biomol Chem 2016; 14:1413-20. [DOI: 10.1039/c5ob02154e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The trans-(S, S)-enantiomer 2e turned out to be significantly more potent than its enantiomer 2d against wild-type and mutant strains with high selectivity indexes.
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93
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Martin F, Lee J, Thomson E, Tarrant N, Hale A, Lacey CJ. Two cases of possible transmitted drug-resistant HIV: likely HIV superinfection and unmasking of pre-existing resistance. Int J STD AIDS 2016; 27:66-9. [PMID: 25663247 PMCID: PMC4674743 DOI: 10.1177/0956462415571671] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 01/05/2015] [Indexed: 11/17/2022]
Abstract
In the UK, patients undergo HIV viral load and genotype testing before they are prescribed antiretroviral therapy. The genotype test guides clinicians in prescribing antiretroviral therapy with maximum efficacy against the patient's specific viral strain. HIV viral load escape under antiretroviral drug therapy, to which the virus was thought to be genotypically susceptible, is commonly observed in patients with poor adherence. We observed early viral escapes in two-newly diagnosed patients, during antiretroviral treatment, with different sequences compared to their original viral resistance test and who reported excellent adherence to and tolerance of their therapy. HIV superinfection with a new viral strain was identified in a patient with multiple risk factors and co-infections with sexually transmitted infections. The second patient was a case of the emergence of primary resistant virus under drug pressure. Both suppressed their virus promptly after treatment switch.
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Affiliation(s)
- Fabiola Martin
- Centre for Immunology and Infection, Department of Biology, University of York, York, UK
| | - John Lee
- Genitourinary Department, Josephine Butler Centre King Street Health Centre, Wakefield, UK
| | - Emma Thomson
- Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Nick Tarrant
- Genitourinary Department, York Teaching Hospital, York, UK
| | - Antony Hale
- Department of Virology, Leeds Teaching Hospitals Trust, Leeds, UK
| | - Charles J Lacey
- Centre for Immunology and Infection, Department of Biology, University of York, York, UK
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94
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Hamacher K, McCammon JA. Computing the Amino Acid Specificity of Fluctuations in Biomolecular Systems. J Chem Theory Comput 2015; 2:873-8. [PMID: 26626694 DOI: 10.1021/ct050247s] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We developed a new amino acid specific method for the computation of spatial fluctuations of proteins around their native structures. We show the consistency with experimental values and the increased performance in comparison to an established model, based on statistical estimates for a set of test proteins. We apply the new method to HIV-1 protease in its wild-type form and to a V82F-I84V mutant that shows resistance to protease inhibitors. We further show how the method can be successfully used to explain the molecular biophysics of drug resistance of the mutant.
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Affiliation(s)
- K Hamacher
- Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, Department of Pharmacology, and Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California 92093-0365
| | - J A McCammon
- Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, Department of Pharmacology, and Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California 92093-0365
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Hofstra LM, Sauvageot N, Albert J, Alexiev I, Garcia F, Struck D, Van de Vijver DAMC, Åsjö B, Beshkov D, Coughlan S, Descamps D, Griskevicius A, Hamouda O, Horban A, Van Kasteren M, Kolupajeva T, Kostrikis LG, Liitsola K, Linka M, Mor O, Nielsen C, Otelea D, Paraskevis D, Paredes R, Poljak M, Puchhammer-Stöckl E, Sönnerborg A, Staneková D, Stanojevic M, Van Laethem K, Zazzi M, Zidovec Lepej S, Boucher CAB, Schmit JC, Wensing AMJ, Puchhammer-Stockl E, Sarcletti M, Schmied B, Geit M, Balluch G, Vandamme AM, Vercauteren J, Derdelinckx I, Sasse A, Bogaert M, Ceunen H, De Roo A, De Wit S, Echahidi F, Fransen K, Goffard JC, Goubau P, Goudeseune E, Yombi JC, Lacor P, Liesnard C, Moutschen M, Pierard D, Rens R, Schrooten Y, Vaira D, Vandekerckhove LPR, Van den Heuvel A, Van Der Gucht B, Van Ranst M, Van Wijngaerden E, Vandercam B, Vekemans M, Verhofstede C, Clumeck N, Van Laethem K, Beshkov D, Alexiev I, Lepej SZ, Begovac J, Kostrikis L, Demetriades I, Kousiappa I, Demetriou V, Hezka J, Linka M, Maly M, Machala L, Nielsen C, Jørgensen LB, Gerstoft J, Mathiesen L, Pedersen C, Nielsen H, Laursen A, Kvinesdal B, Liitsola K, Ristola M, Suni J, Sutinen J, Descamps D, Assoumou L, Castor G, Grude M, Flandre P, Storto A, Hamouda O, Kücherer C, Berg T, Braun P, Poggensee G, Däumer M, Eberle J, Heiken H, Kaiser R, Knechten H, Korn K, Müller H, Neifer S, Schmidt B, Walter H, Gunsenheimer-Bartmeyer B, Harrer T, Paraskevis D, Hatzakis A, Zavitsanou A, Vassilakis A, Lazanas M, Chini M, Lioni A, Sakka V, Kourkounti S, Paparizos V, Antoniadou A, Papadopoulos A, Poulakou G, Katsarolis I, Protopapas K, Chryssos G, Drimis S, Gargalianos P, Xylomenos G, Lourida G, Psichogiou M, Daikos GL, Sipsas NV, Kontos A, Gamaletsou MN, Koratzanis G, Sambatakou H, Mariolis H, Skoutelis A, Papastamopoulos V, Georgiou O, Panagopoulos P, Maltezos E, Coughlan S, De Gascun C, Byrne C, Duffy M, Bergin C, Reidy D, Farrell G, Lambert J, O'Connor E, Rochford A, Low J, Coakely P, O'Dea S, Hall W, Mor O, Levi I, Chemtob D, Grossman Z, Zazzi M, de Luca A, Balotta C, Riva C, Mussini C, Caramma I, Capetti A, Colombo MC, Rossi C, Prati F, Tramuto F, Vitale F, Ciccozzi M, Angarano G, Rezza G, Kolupajeva T, Vasins O, Griskevicius A, Lipnickiene V, Schmit JC, Struck D, Sauvageot N, Hemmer R, Arendt V, Michaux C, Staub T, Sequin-Devaux C, Wensing AMJ, Boucher CAB, van de Vijver DAMC, van Kessel A, van Bentum PHM, Brinkman K, Connell BJ, van der Ende ME, Hoepelman IM, van Kasteren M, Kuipers M, Langebeek N, Richter C, Santegoets RMWJ, Schrijnders-Gudde L, Schuurman R, van de Ven BJM, Åsjö B, Kran AMB, Ormaasen V, Aavitsland P, Horban A, Stanczak JJ, Stanczak GP, Firlag-Burkacka E, Wiercinska-Drapalo A, Jablonowska E, Maolepsza E, Leszczyszyn-Pynka M, Szata W, Camacho R, Palma C, Borges F, Paixão T, Duque V, Araújo F, Otelea D, Paraschiv S, Tudor AM, Cernat R, Chiriac C, Dumitrescu F, Prisecariu LJ, Stanojevic M, Jevtovic D, Salemovic D, Stanekova D, Habekova M, Chabadová Z, Drobkova T, Bukovinova P, Shunnar A, Truska P, Poljak M, Lunar M, Babic D, Tomazic J, Vidmar L, Vovko T, Karner P, Garcia F, Paredes R, Monge S, Moreno S, Del Amo J, Asensi V, Sirvent JL, de Mendoza C, Delgado R, Gutiérrez F, Berenguer J, Garcia-Bujalance S, Stella N, de Los Santos I, Blanco JR, Dalmau D, Rivero M, Segura F, Elías MJP, Alvarez M, Chueca N, Rodríguez-Martín C, Vidal C, Palomares JC, Viciana I, Viciana P, Cordoba J, Aguilera A, Domingo P, Galindo MJ, Miralles C, Del Pozo MA, Ribera E, Iribarren JA, Ruiz L, de la Torre J, Vidal F, Clotet B, Albert J, Heidarian A, Aperia-Peipke K, Axelsson M, Mild M, Karlsson A, Sönnerborg A, Thalme A, Navér L, Bratt G, Karlsson A, Blaxhult A, Gisslén M, Svennerholm B, Bergbrant I, Björkman P, Säll C, Mellgren Å, Lindholm A, Kuylenstierna N, Montelius R, Azimi F, Johansson B, Carlsson M, Johansson E, Ljungberg B, Ekvall H, Strand A, Mäkitalo S, Öberg S, Holmblad P, Höfer M, Holmberg H, Josefson P, Ryding U. Transmission of HIV Drug Resistance and the Predicted Effect on Current First-line Regimens in Europe. Clin Infect Dis 2015; 62:655-663. [PMID: 26620652 PMCID: PMC4741360 DOI: 10.1093/cid/civ963] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 11/06/2015] [Indexed: 11/13/2022] Open
Abstract
Transmitted human immunodeficiency virus drug resistance in Europe is stable at around 8%. The impact of baseline mutation patterns on susceptibility to antiretroviral drugs should be addressed using clinical guidelines. The impact on baseline susceptibility is largest for nonnucleoside reverse transcriptase inhibitors. Background. Numerous studies have shown that baseline drug resistance patterns may influence the outcome of antiretroviral therapy. Therefore, guidelines recommend drug resistance testing to guide the choice of initial regimen. In addition to optimizing individual patient management, these baseline resistance data enable transmitted drug resistance (TDR) to be surveyed for public health purposes. The SPREAD program systematically collects data to gain insight into TDR occurring in Europe since 2001. Methods. Demographic, clinical, and virological data from 4140 antiretroviral-naive human immunodeficiency virus (HIV)–infected individuals from 26 countries who were newly diagnosed between 2008 and 2010 were analyzed. Evidence of TDR was defined using the WHO list for surveillance of drug resistance mutations. Prevalence of TDR was assessed over time by comparing the results to SPREAD data from 2002 to 2007. Baseline susceptibility to antiretroviral drugs was predicted using the Stanford HIVdb program version 7.0. Results. The overall prevalence of TDR did not change significantly over time and was 8.3% (95% confidence interval, 7.2%–9.5%) in 2008–2010. The most frequent indicators of TDR were nucleoside reverse transcriptase inhibitor (NRTI) mutations (4.5%), followed by nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations (2.9%) and protease inhibitor mutations (2.0%). Baseline mutations were most predictive of reduced susceptibility to initial NNRTI-based regimens: 4.5% and 6.5% of patient isolates were predicted to have resistance to regimens containing efavirenz or rilpivirine, respectively, independent of current NRTI backbones. Conclusions. Although TDR was highest for NRTIs, the impact of baseline drug resistance patterns on susceptibility was largest for NNRTIs. The prevalence of TDR assessed by epidemiological surveys does not clearly indicate to what degree susceptibility to different drug classes is affected.
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Affiliation(s)
- L Marije Hofstra
- Luxembourg Institute of Health, Luxembourg.,Department of Virology, University Medical Center Utrecht, The Netherlands
| | | | - Jan Albert
- Karolinska Institute, Solna.,Karolinska University Hospital, Stockholm, Sweden
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Federico Garcia
- Complejo Hospitalario Universitario de Granada, Instituto de Investigación IBS Granada; on behalf of Cohorte de Adultos de la Red de Investigación en SIDA, Spain
| | | | | | | | - Danail Beshkov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Diane Descamps
- AP-HP Groupe hospitalier Bichat-Claude Bernard, IAME INSERM UMR 1137, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | | | | | | | | | | | | | - Kirsi Liitsola
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland
| | - Marek Linka
- National Reference Laboratory for HIV/AIDS, National Institute of Public Health, Prague, Czech Republic
| | - Orna Mor
- National HIV Reference Laboratory, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | | | - Dan Otelea
- National Institute for Infectious Diseases "Prof. dr. Matei Bals", Bucharest, Romania
| | | | | | - Mario Poljak
- Faculty of Medicine, Slovenian HIV/AIDS Reference Centre, University of Ljubljana, Slovenia
| | | | - Anders Sönnerborg
- Karolinska Institute, Solna.,Karolinska University Hospital, Stockholm, Sweden
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96
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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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97
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Chauhan J, Chen SE, Fenstermacher KJ, Naser-Tavakolian A, Reingewertz T, Salmo R, Lee C, Williams E, Raje M, Sundberg E, DeStefano JJ, Freire E, Fletcher S. Synthetic, structural mimetics of the β-hairpin flap of HIV-1 protease inhibit enzyme function. Bioorg Med Chem 2015; 23:7095-109. [PMID: 26474665 DOI: 10.1016/j.bmc.2015.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/20/2015] [Accepted: 09/03/2015] [Indexed: 01/11/2023]
Abstract
Small-molecule mimetics of the β-hairpin flap of HIV-1 protease (HIV-1 PR) were designed based on a 1,4-benzodiazepine scaffold as a strategy to interfere with the flap-flap protein-protein interaction, which functions as a gated mechanism to control access to the active site. Michaelis-Menten kinetics suggested our small-molecules are competitive inhibitors, which indicates the mode of inhibition is through binding the active site or sterically blocking access to the active site and preventing flap closure, as designed. More generally, a new bioactive scaffold for HIV-1PR inhibition has been discovered, with the most potent compound inhibiting the protease with a modest K(i) of 11 μM.
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Affiliation(s)
- Jay Chauhan
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA
| | - Shen-En Chen
- Department of Biology, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Katherine J Fenstermacher
- Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Aurash Naser-Tavakolian
- Department of Biology, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Tali Reingewertz
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 725 West Lombard St., Baltimore, MD 21201, USA
| | - Rosene Salmo
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA
| | - Christian Lee
- PharmD Program, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA
| | - Emori Williams
- Vivien T Thomas Medical Arts Academy, 100 N Calhoun St., Baltimore, MD 21223, USA
| | - Mithun Raje
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA
| | - Eric Sundberg
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 725 West Lombard St., Baltimore, MD 21201, USA
| | - Jeffrey J DeStefano
- Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Ernesto Freire
- Department of Biology, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA; University of Maryland Greenebaum Cancer Center, 22 S. Greene St., Baltimore, MD 21201, USA.
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98
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Burgess MJ, Zeuli JD, Kasten MJ. Management of HIV/AIDS in older patients-drug/drug interactions and adherence to antiretroviral therapy. HIV AIDS (Auckl) 2015; 7:251-64. [PMID: 26604826 PMCID: PMC4629973 DOI: 10.2147/hiv.s39655] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Patients with human immunodeficiency virus (HIV) are living longer with their disease, as HIV has become a chronic illness managed with combination antiretroviral therapy (cART). This has led to an increasing number of patients greater than 50 years old living successfully with HIV. As the number of older adults with HIV has increased, there are special considerations for the management of HIV. Older adults with HIV must be monitored for drug side effects and toxicities. Their other non-HIV comorbidities should also be considered when choosing a cART regimen. Older adults with HIV have unique issues related to medication compliance. They are more likely than the younger HIV patients to have vision loss, cognitive impairment, and polypharmacy. They may have lower expectations of their overall health status. Depression and financial concerns, especially if they are on a fixed income, may also contribute to noncompliance in the aging HIV population.
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Affiliation(s)
- Mary J Burgess
- Division of Infectious Diseases, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - John D Zeuli
- Department of Pharmacy, Mayo Clinic, Rochester, MN, USA
| | - Mary J Kasten
- Divisions of General Internal Medicine and Infectious Diseases, Mayo Clinic, Rochester, MN, USA
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99
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Abstract
More than 75 million people worldwide have been infected with human immunodeficiency virus (HIV), and there are now approximately 37 million individuals living with the infection. Untreated HIV replication causes progressive CD4(+) T cell loss and a wide range of immunological abnormalities, leading to an increased risk of infectious and oncological complications. HIV infection also contributes to cardiovascular disease, bone disease, renal and hepatic dysfunction and several other common morbidities. Antiretroviral drugs are highly effective at inhibiting HIV replication, and for individuals who can access and adhere to these drugs, combination antiretroviral therapy leads to durable (and probably lifelong) suppression of viral replication. Viral suppression enables immune recovery and the near elimination of the risk for developing acquired immune deficiency syndrome (AIDS). Despite effective treatment, HIV-infected individuals have a higher than expected risk of heart, bone, liver, kidney and neurological disease. When used optimally by an infected (or by an uninfected) person, antiretroviral drugs can virtually eliminate the risk of HIV transmission. Despite major advances in prevention sciences, HIV transmission remains common in many vulnerable populations, including men who have sex with men, injection drug users and sex workers. Owing to a lack of widespread HIV testing and the costs and toxicities associated with antiretroviral drugs, the majority of the infected population is not on effective antiretroviral therapy. To reverse the pandemic, improved prevention, treatment and implementation approaches are necessary.
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Affiliation(s)
- Steven G Deeks
- University of California, San Francisco, Department of Medicine, 995 Potrero Avenue, San Francisco, California 94110, USA
| | - Julie Overbaugh
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Andrew Phillips
- Department of Infection and Population Health, University College London, London, UK
| | - Susan Buchbinder
- University of California, San Francisco, Department of Medicine, 995 Potrero Avenue, San Francisco, California 94110, USA.,San Francisco Department of Health, San Francisco, California, USA
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100
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In vitro antiretroviral activity and in vivo toxicity of the potential topical microbicide copper phthalocyanine sulfate. Virol J 2015; 12:132. [PMID: 26319137 PMCID: PMC4552998 DOI: 10.1186/s12985-015-0358-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 08/13/2015] [Indexed: 11/10/2022] Open
Abstract
Background Copper has antimicrobial properties and has been studied for its activity against viruses, including HIV. Copper complexed within a phthalocyanine ring, forming copper (II) phthalocyanine sulfate (CuPcS), may have a role in microbicide development when used intravaginally. Methods CuPcS toxicity was tested against cervical epithelial cells, TZM-BL cells, peripheral blood mononuclear cells (PBMC), and cervical explant tissues using cell viability assays. In vivo toxicity was assessed following intravaginal administration of CuPcS in female BALB/C mice and measured using a standardized histology grading system on reproductive tract tissues. Efficacy studies for preventing infection with HIV in the presence of various non-toxic concentrations of CuPcS were carried out in TZM-BL, PBMC, and cervical explant cultures using HIV-1BAL and various pseudovirus subtypes. Non-linear regression was applied to the data to determine the EC50/90 and CC50/90. Results CuPcS demonstrated inhibition of HIV infection in PBMCs at concentrations that were non-toxic in cervical epithelial cells and PBMCs with EC50 values of approximately 50 μg/mL. Reproductive tract tissue analysis revealed no toxicity at 100 mg/mL. Human cervical explant tissues challenged with HIV in the presence of CuPcS also revealed a dose–response effect at preventing HIV infection at non-toxic concentrations with an EC50 value of 65 μg/mL. Conclusion These results suggest that CuPcS may be useful as a topical microbicide in concentrations that can be achieved in the female genital tract. Electronic supplementary material The online version of this article (doi:10.1186/s12985-015-0358-5) contains supplementary material, which is available to authorized users.
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