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Adawaye C, Fokam J, Kamangu EN, Ngwese DTA, Susin F, Moussa AM, Hig-Zounet B, Mad-Toingué J, Tidjani A, Vaira D, Moutschen M. Performance characteristics of Allele-Specific PCR (ASPCR) in detecting drug resistance mutations among non-B HIV-1 Variants. J Virol Methods 2024; 323:114856. [PMID: 38000668 DOI: 10.1016/j.jviromet.2023.114856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
Allele-Specific Polymerase Chain Reaction (ASPCR) is an affordable point-mutation assay whose validation could improve the detection of HIV-1 drug resistance mutations (DRMs) in resource-limited settings (RLS). We assessed the performance of ASPCR onforty-four non-B HIV-1 plasma samples from patients who were ARV treated in failure in N'Djamena-Chad. Viral RNA was reverse-transcribed and amplified using LightCycler® FastStart DNA MasterPLUS SYBR Green I. Detection of six major DRMs (K70R, K103N, Y181C, M184V, T215F, T215Y) was evaluated on Roche LightCycler®480 automated system (with dilutions 0.01-100%). ASPCR-results were compared to Sanger-sequencing (gold-standard). Correlations of mutation curves were excellent (R2 >0.97); all DRMs were detected with desirable mutant/wild-type threshold differences (ΔCt≥9) except K70R(ΔCtK70R=6; ΔCtK103N=13; ΔCtM184V=9; ΔCtT215F=12; ΔCtT215Y=12; ΔCtY181C=9) and positive controls were below required thresholds. Also, ASPCR reproducibility on DRMs was assessed by using dilutions of intra-assay and inter-assay coefficient of variations respectively with a threshold of less than 50(i.e.<0.50 variation) which are;: K70R (0.02-0.28 vs. 0.12-0.37), K103N (0.08-0.42 vs. 0.12-0.37), Y181C (0.12-0.39 vs. 0.31-0.37), M184V (0.13-0.39 vs. 0.23-0.42), T215F (0.05-0.43 vs. 0.04-0.45) and T215Y (0.13-0.41 vs. 0.19-0.41). DRM detection-rate by ASPCR vs Sanger was respectively: M184V (63.6% vs. 38.6%); T215F (18.1% vs. 9.1%); T215Y (6.8% vs. 2.3%); K70R (4.5% vs. 2.3%). K103N (22.7% vs. 13.6%); Y181C (13.6% vs. 11.4%). Correlations of mutation curves were excellent (R2 >0.97); all DRMs were detected with desirable mutant/wild-type threshold differences (ΔCt≥9) except K70R(ΔCtK70R=6; ΔCtK103N=13; ΔCtM184V=9; ΔCtT215F=12; ΔCtT215Y=12; ΔCtY181C=9) and positive controls were below required thresholds. Also, ASPCR reproducibility on DRMs was assessed by using dilutions of intra-assay and inter-assay coefficient of variations respectively with a threshold of less than 50(i.e.<0.50 variation) which are;: K70R (0.02-0.28 vs. 0.12-0.37), K103N (0.08-0.42 vs. 0.12-0.37), Y181C (0.12-0.39 vs. 0.31-0.37), M184V (0.13-0.39 vs. 0.23-0.42), T215F (0.05-0.43 vs. 0.04-0.45) and T215Y (0.13-0.41 vs. 0.19-0.41). DRM detection-rate by ASPCR vs Sanger was respectively: M184V (63.6% vs. 38.6%); T215F (18.1% vs. 9.1%); T215Y (6.8% vs. 2.3%); K70R (4.5% vs. 2.3%). K103N (22.7% vs. 13.6%); Y181C (13.6% vs. 11.4%). ASPCR appears more efficient for detecting DRMs on diverse HIV-1 non-B circulating in RLS like Chad.
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Affiliation(s)
- Chatté Adawaye
- National Institute of Sciences and Techniques of Abeche (INSTA), Abeche, Chad; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium.
| | - Joseph Fokam
- Virology Laboratory, Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management, Yaoundé, Cameroon; Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Buea, Cameroon; Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaounde, Cameroon; National HIV Drug Resistance Surveillance and Prevention Working Group (HIVDRWG), Ministry of Public Health, Yaounde, Cameroon.
| | - Erick Ntambwe Kamangu
- Department of Basic Sciences, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
| | - Derrick Tambe Ayuk Ngwese
- Virology Laboratory, Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management, Yaoundé, Cameroon; Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaounde, Cameroon; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
| | - Fabrice Susin
- Department of Basic Sciences, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
| | - Ali Mahamat Moussa
- AIDS Reference Laboratory of Liege, CHU de Liege, Liege, Belgium; Faculty of Human Health Sciences, University of N'Djamena, N'Djamena, Chad; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
| | - BertinTchombou Hig-Zounet
- AIDS Reference Laboratory of Liege, CHU de Liege, Liege, Belgium; Faculty of Human Health Sciences, University of N'Djamena, N'Djamena, Chad; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
| | - Joseph Mad-Toingué
- AIDS Reference Laboratory of Liege, CHU de Liege, Liege, Belgium; Faculty of Human Health Sciences, University of N'Djamena, N'Djamena, Chad; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
| | - Abdelsalam Tidjani
- AIDS Reference Laboratory of Liege, CHU de Liege, Liege, Belgium; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
| | - Dolores Vaira
- Department of Basic Sciences, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
| | - Michel Moutschen
- Department of Basic Sciences, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo; National Reference General Hospital, N'Djamena, Chad; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
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Colson P, Bader W, Fantini J, Dudouet P, Levasseur A, Pontarotti P, Devaux C, Raoult D. From viral democratic genomes to viral wild bunch of quasispecies. J Med Virol 2023; 95:e29209. [PMID: 37937701 DOI: 10.1002/jmv.29209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/05/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023]
Abstract
The tremendous majority of RNA genomes from pathogenic viruses analyzed and deposited in databases are consensus or "democratic" genomes. They represent the genomes most frequently found in the clinical samples of patients but do not account for the huge genetic diversity of coexisting genomes, which is better described as quasispecies. A viral quasispecies is defined as the dynamic distribution of nonidentical but closely related mutants, variants, recombinant, or reassortant viral genomes. Viral quasispecies have collective behavior and dynamics and are the subject of internal interactions that comprise interference, complementation, or cooperation. In the setting of SARS-CoV-2 infection, intrahost SARS-CoV-2 genetic diversity was recently notably reported for immunocompromised, chronically infected patients, for patients treated with monoclonal antibodies targeting the viral spike protein, and for different body compartments of a single patient. A question that deserves attention is whether such diversity is generated postinfection from a clonal genome in response to selection pressure or is already present at the time of infection as a quasispecies. In the present review, we summarize the data supporting that hosts are infected by a "wild bunch" of viruses rather than by multiple virions sharing the same genome. Each virion in the "wild bunch" may have different virulence and tissue tropisms. As the number of viruses replicated during host infections is huge, a viral quasispecies at any time of infection is wide and is also influenced by host-specific selection pressure after infection, which accounts for the difficulty in deciphering and predicting the appearance of more fit variants and the evolution of epidemics of novel RNA viruses.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Wahiba Bader
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Jacques Fantini
- INSERM UMR_S 1072, Aix-Marseille Université, Marseille, France
| | - Pierre Dudouet
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
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Foka FET, Mufhandu HT. Current ARTs, Virologic Failure, and Implications for AIDS Management: A Systematic Review. Viruses 2023; 15:1732. [PMID: 37632074 PMCID: PMC10458198 DOI: 10.3390/v15081732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Antiretroviral therapies (ARTs) have revolutionized the management of human immunodeficiency virus (HIV) infection, significantly improved patient outcomes, and reduced the mortality rate and incidence of acquired immunodeficiency syndrome (AIDS). However, despite the remarkable efficacy of ART, virologic failure remains a challenge in the long-term management of HIV-infected individuals. Virologic failure refers to the persistent detectable viral load in patients receiving ART, indicating an incomplete suppression of HIV replication. It can occur due to various factors, including poor medication adherence, drug resistance, suboptimal drug concentrations, drug interactions, and viral factors such as the emergence of drug-resistant strains. In recent years, extensive efforts have been made to understand and address virologic failure in order to optimize treatment outcomes. Strategies to prevent and manage virologic failure include improving treatment adherence through patient education, counselling, and supportive interventions. In addition, the regular monitoring of viral load and resistance testing enables the early detection of treatment failure and facilitates timely adjustments in ART regimens. Thus, the development of novel antiretroviral agents with improved potency, tolerability, and resistance profiles offers new options for patients experiencing virologic failure. However, new treatment options would also face virologic failure if not managed appropriately. A solution to virologic failure requires a comprehensive approach that combines individualized patient care, robust monitoring, and access to a range of antiretroviral drugs.
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Affiliation(s)
- Frank Eric Tatsing Foka
- Department of Microbiology, Virology Laboratory, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North West University, Mafikeng, Private Bag, Mmabatho X2046, South Africa
| | - Hazel Tumelo Mufhandu
- Department of Microbiology, Virology Laboratory, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North West University, Mafikeng, Private Bag, Mmabatho X2046, South Africa
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Yan J, Zhang W, Luo H, Wang X, Ruan L. Development and validation of a scoring system for the prediction of HIV drug resistance in Hubei province, China. Front Cell Infect Microbiol 2023; 13:1147477. [PMID: 37234779 PMCID: PMC10208424 DOI: 10.3389/fcimb.2023.1147477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Objective The present study aimed to build and validate a new nomogram-based scoring system for the prediction of HIV drug resistance (HIVDR). Design and methods Totally 618 patients with HIV/AIDS were included. The predictive model was created using a retrospective set (N = 427) and internally validated with the remaining cases (N = 191). Multivariable logistic regression analysis was carried out to fit a model using candidate variables selected by Least absolute shrinkage and selection operator (LASSO) regression. The predictive model was first presented as a nomogram, then transformed into a simple and convenient scoring system and tested in the internal validation set. Results The developed scoring system consisted of age (2 points), duration of ART (5 points), treatment adherence (4 points), CD4 T cells (1 point) and HIV viral load (1 point). With a cutoff value of 7.5 points, the AUC, sensitivity, specificity, PLR and NLR values were 0.812, 82.13%, 64.55%, 2.32 and 0.28, respectively, in the training set. The novel scoring system exhibited a favorable diagnostic performance in both the training and validation sets. Conclusion The novel scoring system can be used for individualized prediction of HIVDR patients. It has satisfactory accuracy and good calibration, which is beneficial for clinical practice.
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Affiliation(s)
- Jisong Yan
- Department of Respiratory and Critical Care Medicine, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology and Wuhan Jinyintan Hospital, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Wenyuan Zhang
- Department of Infectious Diseases, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology and Wuhan Jinyintan Hospital, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Hong Luo
- Department of Respiratory and Critical Care Medicine, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology and Wuhan Jinyintan Hospital, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xianguang Wang
- Department of Respiratory and Critical Care Medicine, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology and Wuhan Jinyintan Hospital, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Lianguo Ruan
- Department of Infectious Diseases, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology and Wuhan Jinyintan Hospital, Chinese Academy of Sciences, Wuhan, Hubei, China
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5
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Bareng OT, Choga WT, Maphorisa ST, Seselamarumo S, Seatla KK, Mokgethi PT, Maruapula D, Mogwele ML, Ditshwanelo D, Moraka NO, Gobe I, Motswaledi MS, Makhema JM, Musonda R, Shapiro R, Essex M, Novitsky V, Moyo S, Gaseitsiwe S. HIV-1C in-House RNA-Based Genotyping Assay for Detection of Drug Resistance Mutations in Samples with Low-Level Viral Loads. Infect Drug Resist 2022; 15:7565-7576. [PMID: 36582452 PMCID: PMC9792565 DOI: 10.2147/idr.s388816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/08/2022] [Indexed: 12/24/2022] Open
Abstract
Purpose Monitoring HIV-1 drug resistance mutations (DRM) in treated patients on combination antiretroviral therapy (cART) with a detectable HIV-1 viral load (VL) is important for the selection of appropriate cART. Currently, there is limited data on HIV DRM at low-level viremia (LLV) (VL 401-999 copies/mL) due to the use of a threshold of VL ≥1000 copies/mL for HIV DRM testing. We here assess the performance of an in-house HIV drug resistance genotyping assay using plasma for the detection of DRM at LLV. Methods We used a total of 96 HIV plasma samples from the population-based Botswana Combination Prevention Project (BCPP). The samples were stratified by VL groups: 50 samples had LLV, defined as 401-999 copies/mL, and 46 had ≥1000 copies/mL. HIV pol (PR and RT) region was amplified and sequenced using an in-house genotyping assay with BigDye sequencing chemistry. Known HIV DRMs were identified using the Stanford HIV Drug Resistance Database. Genotyping success rate between the two groups was estimated and compared using the comparison of proportions test. Results The overall genotyping success rate was 79% (76/96). For VL groups, the genotyping success was 72% (36/50) at LLV and 87% (40/46) at VL ≥1000 copies/mL. Among generated sequences, the overall prevalence of individuals with at least 1 major or intermediate-associated DRM was 24% (18/76). The proportions of NNRTI-, NRTI- and PI-associated resistance mutations were 28%, 24%, and 0%, respectively. The most predominant mutations detected were K103N (18%) and M184V (12%) in NNRTI- and NRTI-associated mutations, respectively. The prevalence of DRM was 17% (6/36) at LLV and 30% (12/40) at VL ≥1000 copies/mL. Conclusion The in-house HIV genotyping assay successfully genotyped 72% of LLV samples and was able to detect 17% of DRM amongst them. Our results highlight the possibility and clinical significance of genotyping HIV among individuals with LLV.
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Affiliation(s)
- Ontlametse T Bareng
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Wonderful T Choga
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | | | | | - Kaelo K Seatla
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Patrick T Mokgethi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | | | - Doreen Ditshwanelo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Biological Science and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
| | | | - Irene Gobe
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Modisa S Motswaledi
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Joseph M Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Max Essex
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Vlad Novitsky
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Correspondence: Simani Gaseitsiwe, Botswana Harvard AIDS Institute Partnership, Private Bag BO320, Bontleng, Gaborone, Botswana, Tel +267 390 2671, Fax +267 390 1284, Email
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Durability of switched therapy after failure of WHO-recommended antiretroviral therapy regimens in a resource-limited setting. AIDS 2022; 36:1791-1800. [PMID: 35876663 DOI: 10.1097/qad.0000000000003340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The study investigated the durability of switched therapy and factors associated with the viral rebound among patients on second-line antiretroviral therapy (ART) in Uganda. DESIGN A retrospective dynamic cohort of adults initiated on second-line ART after virological failure to first-line ART. METHODS Patients on second-line treatment for at least 6 months between 2007 and 2017 were included. Patients were followed, until they experienced a viral rebound (viral load ≥200 copies/ml). Cumulative probability of viral rebounds and factors associated with viral rebound were determined using Kaplan-Meier methods and Cox proportional hazard models. RESULTS One thousand, one hundred and one participants were enrolled of which 64% were women, the median age was 37 years [interquartile range (IQR) 31-43]. The preswitch median CD4 + cell count and viral load were 128 cells/μl (IQR 58-244) and 45 978 copies/ml (IQR 13 827-139 583), respectively. During the 4190.37 person-years, the incidence rate of viral rebound was 83.29 [95% confidence interval (CI) 74.99-92.49] per 1000 person-years. The probability of viral rebound at 5 and 10 years was 0.29 (95% CI 0.26-0.32) and 0.62 (95% CI 0.55-0.69), respectively. The median rebound-free survival was 8.7 years. Young adults (18-24 years) [adjusted hazard ratio (aHR) 2.49, 95% CI 1.32-4.67], preswitch viral load at least 100 000 copies/ml (aHR 1.53, 95% CI 1.22-1.92), and atazanavir/ritonavir (ATV/r)-based second-line (aHR 1.73, 95% CI 1.29-2.32) were associated with an increased risk of viral rebound. CONCLUSION Switched therapies are durable for 8 years after failure of recommended regimens. A high preswitch viral load, ATV/r-based regimens, and young adulthood are risk factors for viral rebound, which underscores the need for more durable regimens and differentiated care services.
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Amblard F, Patel D, Michailidis E, Coats SJ, Kasthuri M, Biteau N, Tber Z, Ehteshami M, Schinazi RF. HIV nucleoside reverse transcriptase inhibitors. Eur J Med Chem 2022; 240:114554. [PMID: 35792384 DOI: 10.1016/j.ejmech.2022.114554] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/28/2022]
Abstract
More than 40 years into the pandemic, HIV remains a global burden and as of now, there is no cure in sight. Fortunately, highly active antiretroviral therapy (HAART) has been developed to manage and suppress HIV infection. Combinations of two to three drugs targeting key viral proteins, including compounds inhibiting HIV reverse transcriptase (RT), have become the cornerstone of HIV treatment. This review discusses nucleoside reverse transcriptase inhibitors (NRTIs), including chain terminators, delayed chain terminators, nucleoside reverse transcriptase translocation inhibitors (NRTTIs), and nucleotide competing RT inhibitors (NcRTIs); focusing on their history, mechanism of action, resistance, and current clinical application, including long-acting regimens.
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Affiliation(s)
- Franck Amblard
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Dharmeshkumar Patel
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Eleftherios Michailidis
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Steven J Coats
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Mahesh Kasthuri
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Nicolas Biteau
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Zahira Tber
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Maryam Ehteshami
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Raymond F Schinazi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA, 30322, USA.
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8
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Omooja J, Bbosa N, Lule DB, Nannyonjo M, Lunkuse S, Nassolo F, Nabirye SE, Suubi HN, Kaleebu P, Ssemwanga D. HIV-1 drug resistance genotyping success rates and correlates of Dried-blood spots and plasma specimen genotyping failure in a resource-limited setting. BMC Infect Dis 2022; 22:474. [PMID: 35581555 PMCID: PMC9112432 DOI: 10.1186/s12879-022-07453-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND HIV-1 drug resistance genotyping is critical to the monitoring of antiretroviral treatment. Data on HIV-1 genotyping success rates of different laboratory specimen types from multiple sources is still scarce. METHODS In this cross-sectional study, we determined the laboratory genotyping success rates (GSR) and assessed the correlates of genotyping failure of 6837 unpaired dried blood spot (DBS) and plasma specimens. Specimens from multiple studies in a resource-constrained setting were analysed in our laboratory between 2016 and 2019. RESULTS We noted an overall GSR of 65.7% and specific overall GSR for DBS and plasma of 49.8% and 85.9% respectively. The correlates of genotyping failure were viral load (VL) < 10,000 copies/mL (aOR 0.3 95% CI: 0.24-0.38; p < 0.0001), lack of viral load testing prior to genotyping (OR 0.85 95% CI: 0.77-0.94; p = 0.002), use of DBS specimens (aOR 0.10 95% CI: 0.08-0.14; p < 0.0001) and specimens from routine clinical diagnosis (aOR 1.4 95% CI: 1.10-1.75; p = 0.005). CONCLUSIONS We report rapidly decreasing HIV-1 genotyping success rates between 2016 and 2019 with increased use of DBS specimens for genotyping and note decreasing median viral loads over the years. We recommend improvement in DBS handling, pre-genotyping viral load testing to screen samples to enhance genotyping success and the development of more sensitive assays with well-designed primers to genotype specimens with low or undetectable viral load, especially in this era where virological suppression rates are rising due to increased antiretroviral therapy roll-out.
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Affiliation(s)
- Jonah Omooja
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda.
| | - Nicholas Bbosa
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Dan Bugembe Lule
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Maria Nannyonjo
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Sandra Lunkuse
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Faridah Nassolo
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Stella Esther Nabirye
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Hamidah Namagembe Suubi
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, UK
| | - Deogratius Ssemwanga
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda.
- Uganda Virus Research Institute, Entebbe, Uganda.
- London School of Hygiene and Tropical Medicine, London, UK.
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9
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Antiretroviral (ARV) Drug Resistance and HIV-1 Subtypes among Injecting Drug Users in the Coastal Region of Kenya. Adv Virol 2022; 2022:3217749. [PMID: 35186083 PMCID: PMC8853818 DOI: 10.1155/2022/3217749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/18/2022] [Indexed: 11/21/2022] Open
Abstract
HIV-1 genetic diversity results into the development of widespread drug-resistant mutations (DRMs) for the first-line retroviral therapy. Nevertheless, few studies have investigated the relationship between DRMs and HIV-1 subtypes among HIV-positive injecting drug users (IDUs). This study therefore determined the association between HIV-1 genotypes and DRMs among the 200 IDUs. Stanford HIV Drug Resistance Database was used to interpret DRMs. The five HIV-1 genotypes circulating among the IDUs were A1 (25 (53.2%)), A2 (2 (4.3%)), B (2 (4.3%)), C (9 (19.1%)), and D (9 (19.1%)). The proportions of DRMs were A1 (12 (52.2%)), A2 (1 (4.3%)), B (0 (0.0%)), C (5 (21.7%)), and D (5 (21.7%)). Due to the large proportion of drug resistance across all HIV-1 subtypes, surveillance and behavioral studies need to be explored as IDUs may be spreading the drug resistance to the general population. In addition, further characterization of DRMs including all the relevant clinical parameters among the larger population of IDUs is critical for effective drug resistance surveillance.
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10
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Lan Y, Li F, Li L, Deng X, Li L, Li J, Cai X, Ling X, Hu F. OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1960-1968. [PMID: 35484082 DOI: 10.1093/jac/dkac132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/01/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yun Lan
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, 8 Huaying Road, Baiyun District, Guangzhou, 510440, China
| | - Feng Li
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, 8 Huaying Road, Baiyun District, Guangzhou, 510440, China
| | - Linghua Li
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, 8 Huaying Road, Baiyun District, Guangzhou, 510440, China
| | - Xizi Deng
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, 8 Huaying Road, Baiyun District, Guangzhou, 510440, China
| | - Liya Li
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, 8 Huaying Road, Baiyun District, Guangzhou, 510440, China
| | - Junbin Li
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, 8 Huaying Road, Baiyun District, Guangzhou, 510440, China
- Guangdong Center for Diagnosis and Treatment of AIDS, 627 Dongfeng East Road, Yuexiu District, Guangzhou, 510060, China
| | - Xiaoli Cai
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, 8 Huaying Road, Baiyun District, Guangzhou, 510440, China
| | - Xuemei Ling
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, 8 Huaying Road, Baiyun District, Guangzhou, 510440, China
- Guangdong Center for Diagnosis and Treatment of AIDS, 627 Dongfeng East Road, Yuexiu District, Guangzhou, 510060, China
| | - Fengyu Hu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, 8 Huaying Road, Baiyun District, Guangzhou, 510440, China
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11
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Fokam J, Mpouel Bala ML, Santoro MM, Takou D, Tala V, Beloumou G, Ngoufack ES, Chenwi C, Pabo Willy Leroi T, Njume D, Teto G, Dambaya B, Djupsa S, Sosso S, Ateba F, Kamta C, Bala L, Njom Nlend AE, Koki Ndombo P, Colizzi V, Perno CF, Ndjolo A. Archiving of mutations in HIV-1 cellular reservoirs among vertically infected adolescents is contingent with clinical stages and plasma viral load: Evidence from the EDCTP-READY study. HIV Med 2021; 23:629-638. [PMID: 34951111 DOI: 10.1111/hiv.13220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/09/2021] [Accepted: 12/06/2021] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Globally, HIV-related adolescent deaths have increased about 50%, especially for those who are vertically infected. This could be driven by archived drug resistance mutations (DRMs) as children grow up, which might jeopardize antiretroviral therapy (ART). Our objective was to compare HIV-1 genotypic variation between plasma RNA and proviral DNA of vertically infected adolescents (aged 10-19 years) failing ART. METHODS A comparative study was conducted in 2019 among 296 adolescents with perinatal HIV infection (ALPHI) failing ART in health facilities of the Centre Region of Cameroon. The WHO clinical stage, CD4 count and plasma viral load (PVL) were measured. For those failing ART (PVL ≥ 1000 copies/mL), RNA (plasma) and proviral DNA (buffy coat) were sequenced in the pol gene at Chantal BIYA International Reference Centre (CIRCB), Yaoundé, Cameroon. HIV-1 subtypes and DRMs were interpreted using Stanford HIVdb v.8.8 and MEGA-X. RESULTS Of the 30% (89/296) failing ART, 81 had both RNA and DNA sequences generated and three were excluded for APOBEC mutations: the mean age was 16 ± 3 years; female-to-male ratio was 3:5; median PVL was 46 856 copies/mL [interquartile range (IQR): 19 898-271 410]; median CD4 count was 264 cells/μL (IQR: 131-574); and 42% were at WHO clinical stage 3/4. Subtype concordance between RNA and DNA viral strains was 100%, with CRF02_AG being predominant (65%) and two potential new recombinants found (A1/G/K; F1/G). Adolescents with DRMs were significantly higher in plasma than in proviral DNA (92% vs. 86%, p < 0.0001). Prevalent DRMs by drug class (RNA vs. DNA respectively) were at position M184 (74% vs. 67%) for nucleoside reverse transcriptase inhibitors (NRTIs), K103 (63% vs. 59%) for non-NRTIs, and V82, L76 and M46 (2% vs. 2%) for protease inhibitors. A total of 35% (27/78) of adolescents had concordant DRM profiles in RNA and DNA, while 27% (21/78) had DRMs only in proviral DNA. The presence of archived DRMs was associated with advanced clinical stage 3/4 (OR = 0.14, p = 0.0003) and PVL < 5 Log (Copies/mL) (OR: 4.88, p = 0.006). CONCLUSIONS Although plasma RNA remains more sensitive for detecting HIV-1 DRMs, about a quarter of ALPHI experiencing ART failure in an African setting might have archived DRMs in viral reservoirs, indicating clinically occult resistance. Thus, to ensure effective ART success, proviral DNA profiling (alongside RNA genotyping) would provide additional DRMs for adolescents with advanced clinical stages and/or moderate PVL.
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Affiliation(s)
- Joseph Fokam
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Health Sciences, University of Buea, Buea, Cameroon.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon.,National HIV Drug Resistance Working Group, Ministry of Public Health, Yaoundé, Cameroon
| | - Marie Laure Mpouel Bala
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | | | - Désiré Takou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Valère Tala
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Grace Beloumou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Ezechiel Semengue Ngoufack
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,University of Rome Tor Vergata, Rome, Italy.,Evangelic University of Cameroon, Bandjoun, Cameroon
| | - Collins Chenwi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Togna Pabo Willy Leroi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Sciences, University of Buea, Buea, Cameroon
| | - Debimeh Njume
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Health Sciences, University of Buea, Buea, Cameroon
| | - Georges Teto
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Beatrice Dambaya
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Sandrine Djupsa
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Samuel Sosso
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Francis Ateba
- Mother and Child Centre of the Chantal BIYA's Foundation, Yaoundé, Cameroon
| | | | - Lionel Bala
- District Hospital of Mbalmayo, Mbalmayo, Cameroon
| | | | - Paul Koki Ndombo
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon.,Mother and Child Centre of the Chantal BIYA's Foundation, Yaoundé, Cameroon
| | - Vittorio Colizzi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,University of Rome Tor Vergata, Rome, Italy.,Evangelic University of Cameroon, Bandjoun, Cameroon
| | - Carlo Frederico Perno
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,University of Rome Tor Vergata, Rome, Italy.,Bambino Gesü Pediatric Hospital, Rome, Italy
| | - Alexis Ndjolo
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
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12
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Development of HIV Drug Resistance in a Cohort of Adults on First-Line Antiretroviral Therapy in Tanzania during the Stavudine Era. MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12040062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
As more HIV patients start combination antiretroviral therapy (cART), the emergence of HIV drug resistance (HIVDR) is inevitable. This will have consequences for the transmission of HIVDR, the success of ART, and the nature and trend of the epidemic. We recruited a cohort of 223 patients starting or continuing their first-line cART in Tanzania towards the end of the stavudine era in 2010. Patients were then followed for one year. Of those with a viral load test at baseline and follow-up time, 34% had a detectable viral load at the one-year endpoint. For 41 patients, protease and reverse transcriptase genotyping were successful. Eighteen samples were from cART-naïve patients, and 23 samples were taken under therapy either at baseline for cART-experienced patients or from follow-up samples for both cART–naïve and cART–experienced patients. The isolates were subtype A, followed by C and D in 41.5%, 22%, and 12.2% of the patients, respectively. No transmitted HIVDR was detected, as scored using the surveillance drug resistance mutations (DRMs) list. However, in 3 of the 18 samples from cART-naïve patients, the clinical Rega interpretation algorithm scored 44D or 138A as non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance-associated polymorphisms. The most observed nucleoside reverse transcriptase inhibitor (NRTI) mutation was 184V. The mutation was found in 16 patients, causing resistance to lamivudine and emtricitabine. Nineteen patients had NNRTI resistance mutations, the most common of which was 103N, observed in eight patients. These high levels of resistance call for regular drug resistance surveillance in Tanzania to inform the control of the emergence and transmission of HIVDR.
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13
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Zhang F, Liang B, Liang X, Lin Z, Yang Y, Liang N, Yang Y, Liang H, Jiang J, Huang J, Huang R, Zhong S, Qin C, Jiang J, Ye L, Liang H. Using Molecular Transmission Networks to Reveal the Epidemic of Pretreatment HIV-1 Drug Resistance in Guangxi, China. Front Genet 2021; 12:688292. [PMID: 34567064 PMCID: PMC8460771 DOI: 10.3389/fgene.2021.688292] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
Introduction Pretreatment drug resistance (PDR) is becoming an obstacle to the success of ART. This study investigated the prevalence of PDR and the transmission clusters (TCs) of drug resistance mutations (DRMs) in two cities where drug abuse used to be high to describe the local HIV-1 transmission dynamics. Methods Plasma samples were obtained from 1,027 ART-naïve patients in Guangxi. Viral subtypes and DRMs were identified. Transmission network and related factors were also determined. Results A total of 1,025 eligible sequences were obtained from Qinzhou (65.8%) and Baise (34.2%) cities. The predominant HIV-1 genotype was CRF08_BC (45.0%), followed by CRF01_AE (40.9%). The overall prevalence of PDR was 8.3%, and resistance to NNRTI was the most common. Putative links with at least one other sequence were found in 543/1,025 (53.0%) sequences, forming 111 clusters (2–143 individuals). The most prevalent shared DRMs included V106I (45.35%), V179D (15.1%), and V179E (15.1%). Clusters related to shared DRMs were more frequent and larger in CRF08_BC. The prevalence of shared DRMs increased with time, while the proportion of PDR gradually decreased. Age > 50 years was associated with clustering. Subtype CRF08_BC was more likely to have DRMs, PDR propagation, and DRM sharing. Conclusion PDR prevalence is moderate in this region. The association between PDR and subtype CRF08_BC suggested that DRMs spreading from injection drug users (IDUs) to heterosexuals (HETs) might be the major source of PDR in this region. Our findings highlight the significance of continuous surveillance of PDR.
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Affiliation(s)
- Fei Zhang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Bingyu Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Xu Liang
- Baise Center for Disease Control and Prevention, Baise, China
| | - Zhaosen Lin
- Qinzhou Center for Disease Control and Prevention, Qinzhou, China
| | - Yuan Yang
- Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Na Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Yao Yang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Huayue Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Jiaxiao Jiang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Jiegang Huang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Rongye Huang
- Qinzhou Center for Disease Control and Prevention, Qinzhou, China
| | - Shanmei Zhong
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Cai Qin
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Junjun Jiang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
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14
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Mbunkah HA, Bertagnolio S, Hamers RL, Hunt G, Inzaule S, Rinke De Wit TF, Paredes R, Parkin NT, Jordan MR, Metzner KJ. Low-Abundance Drug-Resistant HIV-1 Variants in Antiretroviral Drug-Naive Individuals: A Systematic Review of Detection Methods, Prevalence, and Clinical Impact. J Infect Dis 2021; 221:1584-1597. [PMID: 31809534 DOI: 10.1093/infdis/jiz650] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/04/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The presence of high-abundance drug-resistant HIV-1 jeopardizes success of antiretroviral therapy (ART). Despite numerous investigations, the clinical impact of low-abundance drug-resistant HIV-1 variants (LA-DRVs) at levels <15%-25% of the virus population in antiretroviral (ARV) drug-naive individuals remains controversial. METHODS We systematically reviewed 103 studies assessing prevalence, detection methods, technical and clinical detection cutoffs, and clinical significance of LA-DRVs in antiretroviral drug-naive adults. RESULTS In total, 14 919 ARV drug-naive individuals were included. Prevalence of LA-DRVs (ie, proportion of individuals harboring LA-DRVs) was 0%-100%. Technical detection cutoffs showed a 4 log range (0.001%-10%); 42/103 (40.8%) studies investigating the impact of LA-DRVs on ART; 25 studies included only individuals on first-line nonnucleoside reverse transcriptase inhibitor-based ART regimens. Eleven of those 25 studies (44.0%) reported a significantly association between preexisting LA-DRVs and risk of virological failure whereas 14/25 (56.0%) did not. CONCLUSIONS Comparability of the 103 studies is hampered by high heterogeneity of the studies' designs and use of different methods to detect LA-DRVs. Thus, evaluating clinical impact of LA-DRVs on first-line ART remains challenging. We, the WHO HIVResNet working group, defined central areas of future investigations to guide further efforts to implement ultrasensitive resistance testing in routine settings.
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Affiliation(s)
- Herbert A Mbunkah
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zürich, Switzerland.,Institute of Medical Virology, University of Zurich, Zürich, Switzerland.,Paul-Ehrlich-Institut, Langen, Germany
| | | | - Raph L Hamers
- Amsterdam Institute for Global Health and Development, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Eijkman-Oxford Clinical Research Unit, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gillian Hunt
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Seth Inzaule
- Amsterdam Institute for Global Health and Development, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Tobias F Rinke De Wit
- Amsterdam Institute for Global Health and Development, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Roger Paredes
- Infectious Diseases Service and IrsiCaixa AIDS Research Institute for AIDS Research, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | | | - Michael R Jordan
- Division of Geographic Medicine and Infectious Disease, Tufts University School of Medicine, Tufts Medical Center, Boston, Massachusetts, USA
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zürich, Switzerland.,Institute of Medical Virology, University of Zurich, Zürich, Switzerland
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15
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Ghiasifar Z, Salehabadi H, Adibpour N, Alipour E, Kobarfard F, Shoushizadeh MR. Synthesis of Biuret Derivatives as Potential
HIV
‐1 Protease Inhibitors Using (
LDHs‐g‐HMDI‐Citric
Acid), as a Green Recyclable Catalyst. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.12152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Zahra Ghiasifar
- Department of Organic Chemistry Islamic Azad University Tehran North Branch Tehran 1651153311 Iran
| | - Hafezeh Salehabadi
- Department of Medicinal Chemistry, School of Pharmacy Zanjan University of Medical Sciences Zanjan 45139‐56184 Iran
| | - Neda Adibpour
- Department of Medicinal Chemistry, School of Pharmacy Zanjan University of Medical Sciences Zanjan 45139‐56184 Iran
| | - Eskandar Alipour
- Department of Organic Chemistry Islamic Azad University Tehran North Branch Tehran 1651153311 Iran
| | - Farzad Kobarfard
- Department of Medicinal Chemistry, School of Pharmacy Shahid Beheshti University of Medical Sciences Tehran 1991953381 Iran
| | - Mohammad Reza Shoushizadeh
- Department of Medicinal Chemistry, School of Pharmacy Ahvaz Jundishapur University of Medical Sciences Ahvaz 61357‐15794 Iran
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16
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Yan L, Yu F, Zhang H, Zhao H, Wang L, Liang Z, Zhang X, Wu L, Liang H, Yang S, Tang Y, Zhang F. Transmitted and Acquired HIV-1 Drug Resistance from a Family: A Case Study. Infect Drug Resist 2020; 13:3763-3770. [PMID: 33122923 PMCID: PMC7591230 DOI: 10.2147/idr.s272232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/11/2020] [Indexed: 11/23/2022] Open
Affiliation(s)
- Liting Yan
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Fengting Yu
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Huimin Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Department of Pediatrics, Beijing Ditan Hospital, Beijing, People’s Republic of China
| | - Hongxin Zhao
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Linghang Wang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Zaiyan Liang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Xia Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Liang Wu
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Hongyuan Liang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Siyuan Yang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Yunxia Tang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Fujie Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
- Correspondence: Fujie Zhang Beijing Ditan Hospital, Capital Medical University, Beijing100015, People’s Republic of ChinaTel +86 10 84322581 Email
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Chrysostomou AC, Topcu C, Stylianou DC, Hezka J, Kostrikis LG. Development of a new comprehensive HIV-1 genotypic drug resistance assay for all commercially available reverse transcriptase, protease and integrase inhibitors in patients infected with group M HIV-1 strains. INFECTION GENETICS AND EVOLUTION 2020; 81:104243. [PMID: 32061896 DOI: 10.1016/j.meegid.2020.104243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 12/28/2022]
Abstract
Comprehensive PCR assays for the genotypic drug resistance analysis of all HIV-1 antiretroviral agents (reverse transcriptase, protease and integrase inhibitors) are increasingly in demand due to introduction of integrase inhibitors in the first line regimens and the increasing presence of non-B HIV-1 clades around the world. This study focused on the development and evaluation of a new PCR-based assay for the amplification and sequencing of the entire HIV-1 pol region of major circulating group M HIV-1 strains in Europe for genotypic drug resistance analysis. The comprehensive touchdown PCR assay developed in this study utilized HIV-1 RNA extracted from the plasma of blood samples of consenting HIV-1 infected patients in Cyprus, collected from 2017 to 2019. The HIV-1 pol region was amplified by touchdown PCR for both the primary RT-PCR and the secondary PCR steps. Successful PCR amplicons were determined by population DNA sequencing, using the Sanger method and the genotypic drug resistance analysis was performed with the Stanford University HIV Drug Resistance Database Program. The newly developed assay successfully amplified the entire HIV-1 pol region (2844 nucleotides long) of 141 out of 144 samples of group M HIV-1 subtypes and recombinant strains of the Cyprus HIV-1 Transmission Cohort Study (CHICS) isolated from 2017 to 2019 and genotypic analyses were conducted for all currently available HIV-1 reverse transcriptase, protease and integrase inhibitors. The drug resistance, epidemiological and demographic data of these study subjects will be expanded upon in the CHICS (L.G. Kostrikis et al., manuscript in preparation for publication). The newly developed HIV-1 genotypic drug resistance assay would benefit clinical settings, and research focusing on the world-wide spread of HIV-1 drug-resistant strains, especially in geographic regions characterized by polyphyletic HIV-1 infections.
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Affiliation(s)
- Andreas C Chrysostomou
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus
| | - Cicek Topcu
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus
| | - Dora C Stylianou
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus
| | - Johana Hezka
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus
| | - Leondios G Kostrikis
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia 2109, Nicosia, Cyprus.
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Günthard HF, Calvez V, Paredes R, Pillay D, Shafer RW, Wensing AM, Jacobsen DM, Richman DD. Human Immunodeficiency Virus Drug Resistance: 2018 Recommendations of the International Antiviral Society-USA Panel. Clin Infect Dis 2020; 68:177-187. [PMID: 30052811 PMCID: PMC6321850 DOI: 10.1093/cid/ciy463] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/28/2018] [Indexed: 12/16/2022] Open
Abstract
Background Contemporary antiretroviral therapies (ART) and management strategies have diminished both human immunodeficiency virus (HIV) treatment failure and the acquired resistance to drugs in resource-rich regions, but transmission of drug-resistant viruses has not similarly decreased. In low- and middle-income regions, ART roll-out has improved outcomes, but has resulted in increasing acquired and transmitted resistances. Our objective was to review resistance to ART drugs and methods to detect it, and to provide updated recommendations for testing and monitoring for drug resistance in HIV-infected individuals. Methods A volunteer panel of experts appointed by the International Antiviral (formerly AIDS) Society–USA reviewed relevant peer-reviewed data that were published or presented at scientific conferences. Recommendations were rated according to the strength of the recommendation and quality of the evidence, and reached by full panel consensus. Results Resistance testing remains a cornerstone of ART. It is recommended in newly-diagnosed individuals and in patients in whom ART has failed. Testing for transmitted integrase strand-transfer inhibitor resistance is currently not recommended, but this may change as more resistance emerges with widespread use. Sanger-based and next-generation sequencing approaches are each suited for genotypic testing. Testing for minority variants harboring drug resistance may only be considered if treatments depend on a first-generation nonnucleoside analogue reverse transcriptase inhibitor. Different HIV-1 subtypes do not need special considerations regarding resistance testing. Conclusions Testing for HIV drug resistance in drug-naive individuals and in patients in whom antiretroviral drugs are failing, and the appreciation of the role of testing, are crucial to the prevention and management of failure of ART.
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Affiliation(s)
- Huldrych F Günthard
- University Hospital Zürich and Institute of Medical Virology, University of Zurich, Switzerland
| | - Vincent Calvez
- Pierre et Marie Curie University and Pitié-Salpêtriere Hospital, Paris, France
| | - Roger Paredes
- Infectious Diseases Service and IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Badalona, Spain.,Africa Health Research Institute, KwaZulu Natal, South Africa
| | | | | | | | | | - Douglas D Richman
- Veterans Affairs San Diego Healthcare System and University of California San Diego
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19
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Chung MH, McGrath CJ, Beck IA, Levine M, Milne RS, So I, Andersen N, Dross S, Coombs RW, Chohan B, Yatich N, Kiptinness C, Sakr SR, Kiarie JN, Frenkel LM. Evaluation of the management of pretreatment HIV drug resistance by oligonucleotide ligation assay: a randomised controlled trial. Lancet HIV 2019; 7:e104-e112. [PMID: 31818716 DOI: 10.1016/s2352-3018(19)30337-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 08/14/2019] [Accepted: 08/27/2019] [Indexed: 11/30/2022]
Abstract
BACKGROUND Although experts have recommended testing for pretreatment drug resistance (PDR) before antiretroviral therapy (ART) initiation, there is little evidence to support its implementation. We aimed to establish whether an inexpensive point mutation assay can improve virological suppression by identifying PDR to guide drug selection for ART in a lower-middle income country. METHODS Investigators did an open-label, randomised controlled trial at three HIV treatment sites in Kenya: two in Nairobi and one in rural Maseno. Individuals (aged ≥2 years) were eligible to participate if they were confirmed HIV-seropositive, qualified for first-line ART, planned to reside in the area for more than 1 year, and provided informed consent. We randomly assigned participants (1:1) to either PDR testing by oligonucleotide ligation assay (OLA) to guide selection of ART or to standard of care, which did not include OLA testing. The OLA-guided therapy group had pre-ART peripheral blood mononuclear cells evaluated for drug resistance to non-nucleoside reverse transcriptase inhibitor (NNRTI) at codons Lys103Asn, Tyr181Cys, Gly190Ala, and to lamivudine at Met184Val, and when at least one drug-resistant codon was detected in a participant's pre-ART specimen, clinicians were directed to prescribe protease inhibitor-based second-line ART. Those without detected resistance and those who were randomised to standard of care received NNRTI-based first-line ART. The primary outcome was plasma HIV-1 RNA of at least 400 copies per mL at 4, 8, or 12 months after ART initiation, which defined virological failure, assessed in all participants who received treatment (data were censored for those lost-to-follow-up or who died). The study has been completed and is registered with ClinicalTrials.gov, NCT01898754. FINDINGS We screened 1198 participants between May 28, 2013, and Nov 4, 2014, of whom 991 (83%) were enrolled (492 received OLA and 495 received standard of care; four did not begin treatment). 93 participants (prevalence 9·4%) had PDR (95% CI 7·7-11·4). 34 (8·5%) of 400 participants in the OLA group had virological failure at month 12 of ART (95% CI 6·0-11·7) compared with 39 (9·7%) of 402 (7·0-13·0) in the standard-of-care group (log-rank p=0·26). Among participants with PDR, virological failure was lower in the OLA-guided therapy group than in the standard-of-care group: five (14%) of 35 compared with 13 (50%) of 26; p=0·0020). Among those prescribed NNRTI-based ART, participants given efavirenz were less likely to have virological failure than were those receiving nevirapine (odds ratio 0·37, 95% CI 0·22-0·62; p<0·0001). The OLA-guided therapy group had 39 serious non-lethal adverse events and 34 deaths. The standard-of-care group had 34 severe adverse events and 43 deaths, differences that were not significant. Adverse events judged to potentially be due to ART were few and similar between groups, with 17 (16%) in the OLA-guided therapy group and 16 (16%) in the standard-of-care group (p=0·90). INTERPRETATION Our finding that OLA testing for PDR reduced virological failure in only those with specific PDR mutations suggests that PDR poses less of a risk for virological failure than that predicted by past prevalence estimates, and that the value of PDR testing to reduce virological failure should be assessed for antiretroviral treatment regimens. FUNDING US National Institutes of Health.
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Affiliation(s)
- Michael H Chung
- Department of Global Health, University of Washington, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA
| | | | - Ingrid A Beck
- Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Molly Levine
- Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Ross S Milne
- Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Isaac So
- Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Nina Andersen
- Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Sandra Dross
- Department of Global Health, University of Washington, Seattle, WA, USA; Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Robert W Coombs
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Bhavna Chohan
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Nelly Yatich
- Department of Global Health, University of Washington, Seattle, WA, USA
| | | | | | - James N Kiarie
- Department of Obstetrics and Gynaecology, University of Nairobi, Nairobi, Kenya
| | - Lisa M Frenkel
- Department of Global Health, University of Washington, Seattle, WA, USA; Department of Laboratory Medicine, University of Washington, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA; Seattle Children's Research Institute, University of Washington, Seattle, WA, USA.
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20
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Trebelcock WL, Lama JR, Duerr A, Sanchez H, Cabello R, Gilada T, Segura P, Reisner SL, Mayer KH, Mullins J, Bender Ignacio RA. HIV pretreatment drug resistance among cisgender MSM and transgender women from Lima, Peru. J Int AIDS Soc 2019; 22:e25411. [PMID: 31773888 PMCID: PMC6880186 DOI: 10.1002/jia2.25411] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/16/2019] [Indexed: 12/29/2022] Open
Abstract
INTRODUCTION Transmitted, or any pretreatment drug resistance (TDR, PDR) can compromise efficacy of first-line antiretroviral therapy (ART). In Peru, genotypic resistance testing is not routinely performed before ART initiation, and estimated PDR prevalence prior to 2012 ranged from 1.0% to 4.7%. We aimed to update estimates of PDR prevalence in men who have sex with men (cis-MSM) and transgender women (TW). METHODS We obtained HIV sequences from three studies of ART-naïve cisgender-MSM and TW (n = 470) in Lima, Peru from 2013 to 2017, almost two-thirds of whom had acute or recent infections. Sanger sequences of HIV pol were interrogated for surveillance drug resistance mutations (SDRM) using the Stanford Calibrated Population Resistance (CPR) tool and scored for resistance to nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs) with the HIVdb programme. We calculated binomial proportions and 95% confidence intervals. χ2 and exact or trend tests were used to examine predictors of PDR. RESULTS Seventy-seven (16.4%) individuals had PDR (95% CI: 13.2 to 20.0); most resistance was likely TDR since 63% were incident infections. SDRM were present in 9.8% (7.3 to 12.9). Resistance to any NRTI was present in <1% of individuals, while efavirenz resistance was present in 10% (6.9% to 12.4%). TW were not statistically more likely than cis-MSM to have PDR (11.4% vs. 9.1%, p = 0.54). Age, incident versus prevalent infection, or residence district did not predict PDR. Prevalence of SDRM increased from 3% in 2013 to 21% 2017 within incident infections (p = 0.04), but not when including prevalent infections. CONCLUSIONS Prevalence of NNRTI resistance in three studies of ART-naïve MSM and TW in Lima, Peru reaches 10%. Because our study reports PDR in a population in which most acquired HIV recently, the overall prevalence of PDR, including previously treated persons, is likely underestimated. These results underscore the need for a nationally representative survey of PDR in Peru and consideration of non-NNRTI anchored first-line ART options. This study also represents the first evaluation of PDR in cis-MSM versus TW in South America, and demonstrates that, although TW are at higher risk of acquiring HIV, they are at similar risk of acquiring a virus with resistance mutations.
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Affiliation(s)
| | | | - Ann Duerr
- University of WashingtonSeattleWAUSA
- Fred Hutchinson Cancer Research CenterSeattleWAUSA
| | | | | | - Trupti Gilada
- Fred Hutchinson Cancer Research CenterSeattleWAUSA
- Unison Medicare and Research CentreMumbaiIndia
| | | | - Sari L Reisner
- Harvard UniversityBostonMAUSA
- The Fenway InstituteBostonMAUSA
| | - Kenneth H Mayer
- Harvard UniversityBostonMAUSA
- The Fenway InstituteBostonMAUSA
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21
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Lodi S, Günthard HF, Gill J, Phillips AN, Dunn D, Vu Q, Siemieniuk R, Garcia F, Logan R, Jose S, Bucher HC, Scherrer AU, Reiss P, van Sighem A, Boender TS, Porter K, Gilson R, Paraskevis D, Simeon M, Vourli G, Moreno S, Jarrin I, Sabin C, Hernán MA. Effectiveness of Transmitted Drug Resistance Testing Before Initiation of Antiretroviral Therapy in HIV-Positive Individuals. J Acquir Immune Defic Syndr 2019; 82:314-320. [PMID: 31609929 PMCID: PMC7830777 DOI: 10.1097/qai.0000000000002135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND For people living with HIV, major guidelines in high-income countries recommend testing for transmitted drug resistance (TDR) to guide the choice of first-line antiretroviral therapy (ART). However, individuals who fail a first-line regimen can now be switched to one of several effective regimens. Therefore, the virological and clinical benefit of TDR testing needs to be evaluated. METHODS We included individuals from the HIV-CAUSAL Collaboration who enrolled <6 months of HIV diagnosis between 2006 and 2015, were ART-naive, and had measured CD4 count and HIV-RNA. Follow-up started at the date when all inclusion criteria were first met (baseline). We compared 2 strategies: (1) TDR testing within 3 months of baseline versus (2) no TDR testing. We used inverse probability weighting to estimate the 5-year proportion and hazard ratios (HRs) of virological suppression (confirmed HIV-RNA <50 copies/mL), and of AIDS or death under both strategies. RESULTS Of 25,672 eligible individuals (82% males, 52% diagnosed in 2010 or later), 17,189 (67%) were tested for TDR within 3 months of baseline. Of these, 6% had intermediate- or high-level TDR to any antiretroviral drug. The estimated 5-year proportion virologically suppressed was 77% under TDR testing and 74% under no TDR testing; HR 1.06 (95% confidence interval: 1.03 to 1.19). The estimated 5-year risk of AIDS or death was 6% under both strategies; HR 1.03 (95% confidence interval: 0.95 to 1.12). CONCLUSIONS TDR prevalence was low. Although TDR testing improved virological response, we found no evidence that it reduced the incidence of AIDS or death in first 5 years after diagnosis.
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Affiliation(s)
- Sara Lodi
- Boston University School of Public Health, Boston, MA
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Zürich, Switzerland
| | - John Gill
- University of Calgary, Calgary, Alberta, Canada
- Southern Alberta Clinic, Calgary, Alberta, Canada
| | - Andrew N Phillips
- Institute for Global Health, University College London, London, United Kingdom
| | - David Dunn
- Institute for Global Health, University College London, London, United Kingdom
| | - Quang Vu
- University of Calgary, Calgary, Alberta, Canada
| | - Reed Siemieniuk
- Southern Alberta Clinic, Calgary, Alberta, Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
| | | | - Roger Logan
- Harvard T.H. Chan School of Public Health, Boston, MA
| | - Sophie Jose
- Institute for Global Health, University College London, London, United Kingdom
| | - Heiner C Bucher
- Basel Institute for Clinical Epidemiology and Biostatistics, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Alexandra U Scherrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Zürich, Switzerland
| | - Peter Reiss
- Stichting HIV Monitoring, Amsterdam, the Netherlands
- Division of Infectious Diseases, Department of Global Health, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands
| | | | | | - Kholoud Porter
- Institute for Global Health, University College London, London, United Kingdom
| | - Richard Gilson
- Institute for Global Health, University College London, London, United Kingdom
| | | | | | - Georgia Vourli
- National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Santiago Moreno
- Ramón y Cajal Hospital, IRYCIS, Madrid, Spain
- University of Alcalá de Henares, Madrid, Spain
| | - Inmaculada Jarrin
- Centro Nacional de Epidemiologia, Instituto de Salud Carlos III, Madrid, Spain
| | - Caroline Sabin
- Institute for Global Health, University College London, London, United Kingdom
| | - Miguel A Hernán
- Harvard T.H. Chan School of Public Health, Boston, MA
- Harvard-MIT Division of Health Sciences and Technology, Boston, MA
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22
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Rawle DJ, Li D, Wu Z, Wang L, Choong M, Lor M, Reid RC, Fairlie DP, Harris J, Tachedjian G, Poulsen SA, Harrich D. Oxazole-Benzenesulfonamide Derivatives Inhibit HIV-1 Reverse Transcriptase Interaction with Cellular eEF1A and Reduce Viral Replication. J Virol 2019; 93:e00239-19. [PMID: 30918071 PMCID: PMC6613760 DOI: 10.1128/jvi.00239-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 03/20/2019] [Indexed: 12/14/2022] Open
Abstract
HIV-1 replication requires direct interaction between HIV-1 reverse transcriptase (RT) and cellular eukaryotic translation elongation factor 1A (eEF1A). Our previous work showed that disrupting this interaction inhibited HIV-1 uncoating, reverse transcription, and replication, indicating its potential as an anti-HIV-1 target. In this study, we developed a sensitive, live-cell split-luciferase complementation assay (NanoBiT) to quantitatively measure inhibition of HIV-1 RT interaction with eEF1A. We used this to screen a small molecule library and discovered small-molecule oxazole-benzenesulfonamides (C7, C8, and C9), which dose dependently and specifically inhibited the HIV-1 RT interaction with eEF1A. These compounds directly bound to HIV-1 RT in a dose-dependent manner, as assessed by a biolayer interferometry (BLI) assay, but did not bind to eEF1A. These oxazole-benzenesulfonamides did not inhibit enzymatic activity of recombinant HIV-1 RT in a homopolymer assay but did inhibit reverse transcription and infection of both wild-type (WT) and nonnucleoside reverse transcriptase inhibitor (NNRTI)-resistant HIV-1 in a dose-dependent manner in HEK293T cells. Infection of HeLa cells was significantly inhibited by the oxazole-benzenesulfonamides, and the antiviral activity was most potent against replication stages before 8 h postinfection. In human primary activated CD4+ T cells, C7 inhibited HIV-1 infectivity and replication up to 6 days postinfection. The data suggest a novel mechanism of HIV-1 inhibition and further elucidate how the RT-eEF1A interaction is important for HIV-1 replication. These compounds provide potential to develop a new class of anti-HIV-1 drugs to treat WT and NNRTI-resistant strains in people infected with HIV.IMPORTANCE Antiretroviral drugs protect many HIV-positive people, but their success can be compromised by drug-resistant strains. To combat these strains, the development of new classes of HIV-1 inhibitors is essential and a priority in the field. In this study, we identified small molecules that bind directly to HIV-1 reverse transcriptase (RT) and inhibit its interaction with cellular eEF1A, an interaction which we have previously identified as crucial for HIV-1 replication. These compounds inhibit intracellular HIV-1 reverse transcription and replication of WT HIV-1, as well as HIV-1 mutants that are resistant to current RT inhibitors. A novel mechanism of action involving inhibition of the HIV-1 RT-eEF1A interaction is an important finding and a potential new way to combat drug-resistant HIV-1 strains in infected people.
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Affiliation(s)
- Daniel J Rawle
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, Australia
| | - Dongsheng Li
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Zhonglan Wu
- Ningxia Center for Disease Control and Prevention, Ningxia, China
| | - Lu Wang
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, Australia
| | - Marcus Choong
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- School of Biomolecular Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Mary Lor
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Robert C Reid
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - David P Fairlie
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Jonathan Harris
- School of Biomolecular Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Gilda Tachedjian
- Disease Elimination Program, Life Sciences Discipline, Burnet Institute, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Clayton, VIC, Australia
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC, Australia
| | - Sally-Ann Poulsen
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, Australia
| | - David Harrich
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
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Laker EAO, Nabaggala MS, Kaimal A, Nalwanga D, Castelnuovo B, Musubire A, Kiragga A, Lamorde M, Ratanshi RP. An observational study in an urban Ugandan clinic comparing virological outcomes of patients switched from first-line antiretroviral regimens to second-line regimens containing ritonavir-boosted atazanavir or ritonavir-boosted lopinavir. BMC Infect Dis 2019; 19:280. [PMID: 30909871 PMCID: PMC6434787 DOI: 10.1186/s12879-019-3907-5] [Citation(s) in RCA: 4] [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: 02/27/2018] [Accepted: 03/15/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The World Health Organisation approved boosted atazanavir as a preferred second line protease inhibitor in 2010. This is as an alternative to the current boosted lopinavir. Atazanavir has a lower genetic barrier than lopinavir. We compared the virological outcomes of patients during the roll out of routine viral load monitoring, who had switched to boosted second- line regimens of either atazanavir or lopinavir. METHODS This was a cross-sectional study involving adult patients at the Infectious Diseases Institute Kampala, Uganda started on a standard WHO recommended second-line regimen containing either boosted atazanavir or boosted lopinavir between 1 Dec 2014 and 31 July 2015.. Mantel -Haenszel chi square was used to test for the statistical significance of the odds of being suppressed (VL < 400 copies/ml) when on boosted atazanavir compared to boosted lopinavir after stratifying by duration on antiretroviral therapy (ART). Multivariate logistic regression analysis used to determine if the type of boosted protease inhibitor (bPI) was associated with virological outcome. RESULTS Ninety (90) % on ATV/r and 83% on LPV/r had a VL less than 1000 copies/ml. The odds of being suppressed using the same viral load cut-off while on boosted atazanavir compared to boosted lopinavir was not statistically significant after stratifying for duration on ART (p = 0.09). In a multivariate analysis the type of bPI used was not a predictor of virological outcome (p = 0.60). CONCLUSIONS Patients using the WHO recommended second-line of boosted atazanavir have comparable virological suppression to those on boosted lopinavir.
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Affiliation(s)
- Eva Agnes Odongpiny Laker
- Infectious Diseases Institute, Makerere University College of Health Sciences, P.O. Box 22418, Kampala, Uganda
| | - Maria Sarah Nabaggala
- Infectious Diseases Institute, Makerere University College of Health Sciences, P.O. Box 22418, Kampala, Uganda
| | - Arvind Kaimal
- Infectious Diseases Institute, Makerere University College of Health Sciences, P.O. Box 22418, Kampala, Uganda
| | - Damalie Nalwanga
- Infectious Diseases Institute, Makerere University College of Health Sciences, P.O. Box 22418, Kampala, Uganda
| | - Barbara Castelnuovo
- Infectious Diseases Institute, Makerere University College of Health Sciences, P.O. Box 22418, Kampala, Uganda
| | - Abdu Musubire
- Infectious Diseases Institute, Makerere University College of Health Sciences, P.O. Box 22418, Kampala, Uganda
| | - Agnes Kiragga
- Infectious Diseases Institute, Makerere University College of Health Sciences, P.O. Box 22418, Kampala, Uganda
| | - Mohammed Lamorde
- Infectious Diseases Institute, Makerere University College of Health Sciences, P.O. Box 22418, Kampala, Uganda
| | - Rosalind Parkes- Ratanshi
- Infectious Diseases Institute, Makerere University College of Health Sciences, P.O. Box 22418, Kampala, Uganda
- Institute of Public Health, University of Cambridge, Cambridge, UK
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Dong K, Ye L, Leng Y, Liang S, Feng L, Yang H, Su L, Li Y, Baloch S, He F, Yuan D, Pei X. Prevalence of HIV-1 Drug Resistance among Patients with Antiretroviral Therapy Failure in Sichuan, China, 2010-2016. TOHOKU J EXP MED 2019; 247:1-12. [PMID: 30643108 DOI: 10.1620/tjem.247.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Antiretroviral therapy (ART) has been introduced recently and has significantly impacted morbidity and mortality, but can also engender drug resistance. To identify the prevalence of HIV-1 drug resistance (HIVDR) among patients with antiretroviral therapy failure in Sichuan during the period from 2010 to 2016, we carried out a longitudinal study in Sichuan, a province with the highest HIV/AIDS prevalence in China. The data and blood samples were collected from HIV/AIDS patients who received ART for more than half a year. Overall 5,512 sequences were completed from 7,059 ART-failure patients, and 2,499 individuals were identified as drug resistant. Among those with HIVDR mutations identified, 25.37% were against non-nucleoside reverse transcriptase inhibitors (NNRTIs), and 1.60% was against nucleoside reverse transcriptase inhibitors (NRTIs). NRTI-resistant drugs were mainly lamivudine (3TC) (57.77%) and emtricitabine (FTC), while NNRTI-resistant drugs were mainly nevirapine (NVP) (91.13%) and efavirenz (EFV) (72.81%). The most common recombination subtypes of HIV-1 in sequenced samples were CRF07_BC (circulating recombinant form, CRF) (41.42%), followed by CRF01_AE (40.77%). Moreover, drug resistance rate increased with the prolongation of treatment time (χ2 = 14.758, P < 0.05). The overall prevalence of acquired drug resistance in HIV-1 infected patients in Sichuan was 5.47%, which has remained relatively stable from 2010 to 2016. HIV-1 CRF01_AE and CRF07_BC subtypes were the main epidemic strains, and the possibility of resistance was higher in CRF01_AE subtypes. The current study highlights the importance of acquired drug resistance surveillance over a long period.
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Affiliation(s)
- Ke Dong
- West China School of Public Health, No.4 West China Teaching Hospital, Sichuan University
| | - Li Ye
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention
| | - Yun Leng
- West China School of Public Health, No.4 West China Teaching Hospital, Sichuan University
| | - Shu Liang
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention
| | - Liao Feng
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention
| | - Hong Yang
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention
| | - Ling Su
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention
| | - Yiping Li
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention
| | - Saira Baloch
- West China School of Public Health, No.4 West China Teaching Hospital, Sichuan University
| | - Fangting He
- West China School of Public Health, No.4 West China Teaching Hospital, Sichuan University
| | - Dan Yuan
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention
| | - Xiaofang Pei
- West China School of Public Health, No.4 West China Teaching Hospital, Sichuan University
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Soret P, Avalos M, Wittkop L, Commenges D, Thiébaut R. Lasso regularization for left-censored Gaussian outcome and high-dimensional predictors. BMC Med Res Methodol 2018; 18:159. [PMID: 30514234 PMCID: PMC6280495 DOI: 10.1186/s12874-018-0609-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 11/02/2018] [Indexed: 12/14/2022] Open
Abstract
Background Biological assays for the quantification of markers may suffer from a lack of sensitivity and thus from an analytical detection limit. This is the case of human immunodeficiency virus (HIV) viral load. Below this threshold the exact value is unknown and values are consequently left-censored. Statistical methods have been proposed to deal with left-censoring but few are adapted in the context of high-dimensional data. Methods We propose to reverse the Buckley-James least squares algorithm to handle left-censored data enhanced with a Lasso regularization to accommodate high-dimensional predictors. We present a Lasso-regularized Buckley-James least squares method with both non-parametric imputation using Kaplan-Meier and parametric imputation based on the Gaussian distribution, which is typically assumed for HIV viral load data after logarithmic transformation. Cross-validation for parameter-tuning is based on an appropriate loss function that takes into account the different contributions of censored and uncensored observations. We specify how these techniques can be easily implemented using available R packages. The Lasso-regularized Buckley-James least square method was compared to simple imputation strategies to predict the response to antiretroviral therapy measured by HIV viral load according to the HIV genotypic mutations. We used a dataset composed of several clinical trials and cohorts from the Forum for Collaborative HIV Research (HIV Med. 2008;7:27-40). The proposed methods were also assessed on simulated data mimicking the observed data. Results Approaches accounting for left-censoring outperformed simple imputation methods in a high-dimensional setting. The Gaussian Buckley-James method with cross-validation based on the appropriate loss function showed the lowest prediction error on simulated data and, using real data, the most valid results according to the current literature on HIV mutations. Conclusions The proposed approach deals with high-dimensional predictors and left-censored outcomes and has shown its interest for predicting HIV viral load according to HIV mutations.
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Affiliation(s)
- Perrine Soret
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, Bordeaux, F-33000, France.,Inria SISTM Team, Talence, F-33405, France.,Vaccine Research Institute (VRI), Créteil, F-94000, France
| | - Marta Avalos
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, Bordeaux, F-33000, France. .,Inria SISTM Team, Talence, F-33405, France.
| | - Linda Wittkop
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, Bordeaux, F-33000, France.,Inria SISTM Team, Talence, F-33405, France.,CHU Bordeaux, Department of Public Health, Bordeaux, F-33000, France
| | - Daniel Commenges
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, Bordeaux, F-33000, France.,Inria SISTM Team, Talence, F-33405, France
| | - Rodolphe Thiébaut
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, Bordeaux, F-33000, France.,Inria SISTM Team, Talence, F-33405, France.,Vaccine Research Institute (VRI), Créteil, F-94000, France.,CHU Bordeaux, Department of Public Health, Bordeaux, F-33000, France
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26
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An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes. PLoS One 2018; 13:e0206409. [PMID: 30427878 PMCID: PMC6235296 DOI: 10.1371/journal.pone.0206409] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/14/2018] [Indexed: 01/11/2023] Open
Abstract
For many disease-causing virus species, global diversity is clustered into a taxonomy of subtypes with clinical significance. In particular, the classification of infections among the subtypes of human immunodeficiency virus type 1 (HIV-1) is a routine component of clinical management, and there are now many classification algorithms available for this purpose. Although several of these algorithms are similar in accuracy and speed, the majority are proprietary and require laboratories to transmit HIV-1 sequence data over the network to remote servers. This potentially exposes sensitive patient data to unauthorized access, and makes it impossible to determine how classifications are made and to maintain the data provenance of clinical bioinformatic workflows. We propose an open-source supervised and alignment-free subtyping method (Kameris) that operates on k-mer frequencies in HIV-1 sequences. We performed a detailed study of the accuracy and performance of subtype classification in comparison to four state-of-the-art programs. Based on our testing data set of manually curated real-world HIV-1 sequences (n = 2, 784), Kameris obtained an overall accuracy of 97%, which matches or exceeds all other tested software, with a processing rate of over 1,500 sequences per second. Furthermore, our fully standalone general-purpose software provides key advantages in terms of data security and privacy, transparency and reproducibility. Finally, we show that our method is readily adaptable to subtype classification of other viruses including dengue, influenza A, and hepatitis B and C virus.
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Abstract
OBJECTIVES An increasing prevalence of HIV pretreatment drug resistance (PDR) has been observed in Africa, which could decrease the effectiveness of antiretroviral therapy (ART) programs. We describe our experiences, the costs and challenges of implementing an oligonucleotide ligation assay (OLA) for management of PDR in Nairobi, Kenya. DESIGN An observational report of the implementation of OLA in a Kenyan laboratory for a randomized clinical trial evaluating whether onsite use of OLA in individuals initiating ART would decrease rates of virologic failure. METHODS Compared detection of mutations and proportion of mutants in participants' viral quasispecies by OLA in Kenya vs. Seattle. Reviewed records of laboratory workflow and performance of OLA. Calculated the costs of laboratory set-up and of performing the OLA based on equipment purchase receipts and supplies and labor utilization, respectively. RESULTS OLA was performed on 492 trial participants. Weekly batch-testing of median of seven (range: 2-13) specimens provided test results to Kenyan clinicians within 10-14 days of sample collection at a cost of US$ 42 per person tested. Cost of laboratory setup was US$ 32 594. Challenges included an unreliable local supply chain for reagents and the need for an experienced molecular biologist to supervise OLA performance. CONCLUSION OLA was successfully implemented in a Kenyan research laboratory. Cost was twice that projected because of fewer than predicted specimens per batch because of slow enrollment. OLA is a potential simple, low-cost method for PDR testing in resource-limited settings (RLS). Ongoing work to develop a simplified kit could improve future implementation of OLA in RLS.
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Menon RM, Polepally AR, Khatri A, Awni WM, Dutta S. Clinical Pharmacokinetics of Paritaprevir. Clin Pharmacokinet 2018; 56:1125-1137. [PMID: 28236252 DOI: 10.1007/s40262-017-0520-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Paritaprevir is a potent hepatitis C virus (HCV) nonstructural (NS) protein 3/4A protease inhibitor that is used in combination with other direct-acting antivirals (DAAs) for the treatment of chronic HCV infection. Paritaprevir is primarily metabolized by cytochrome P450 (CYP) 3A4 and is administered with a low dose of ritonavir to achieve drug concentrations suitable for once-daily dosing. Coadministration of paritaprevir with ritonavir increases the half-life of single-dose paritaprevir from approximately 3 h to 5-8 h, doubles the time to maximum plasma concentration (T max) from 2.3 to 4.7 h, and increases exposures 30-fold for maximum observed plasma concentration (C max), 50-fold for area under the plasma concentration-time curve (AUC), and >300-fold for trough concentration (C 24). Paritaprevir displays highly variable, nonlinear pharmacokinetics, with C max and AUC increasing in a greater than dose proportional manner when administered with or without ritonavir. In the presence of ritonavir, paritaprevir is excreted mostly unchanged in feces via biliary excretion. Paritaprevir exposures are higher in Japanese subjects compared with Caucasian subjects; however, no dose adjustment is needed for Japanese patients as the higher exposures are safe and well tolerated. The pharmacokinetic characteristics of paritaprevir are similar between healthy subjects and HCV-infected patients, and are not appreciably altered by mild or moderate hepatic impairment or mild, moderate, or severe renal impairment, including those on dialysis. Paritaprevir exposures are increased in patients with severe hepatic impairment. Although the presence of a low dose of ritonavir in paritaprevir-containing regimens increases the likelihood of drug-drug interactions, results from several drug interaction studies demonstrated that paritaprevir-containing regimens can be coadministered with many comedications that are commonly prescribed in HCV-infected patients.
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Affiliation(s)
- Rajeev M Menon
- Clinical Pharmacology and Pharmacometrics, AbbVie Inc., Dept. R4PK, Bldg. AP31-3, 1 North Waukegan Road, North Chicago, IL, 60064, USA.
| | - Akshanth R Polepally
- Clinical Pharmacology and Pharmacometrics, AbbVie Inc., Dept. R4PK, Bldg. AP31-3, 1 North Waukegan Road, North Chicago, IL, 60064, USA
| | - Amit Khatri
- Clinical Pharmacology and Pharmacometrics, AbbVie Inc., Dept. R4PK, Bldg. AP31-3, 1 North Waukegan Road, North Chicago, IL, 60064, USA
| | - Walid M Awni
- Clinical Pharmacology and Pharmacometrics, AbbVie Inc., Dept. R4PK, Bldg. AP31-3, 1 North Waukegan Road, North Chicago, IL, 60064, USA
| | - Sandeep Dutta
- Clinical Pharmacology and Pharmacometrics, AbbVie Inc., Dept. R4PK, Bldg. AP31-3, 1 North Waukegan Road, North Chicago, IL, 60064, USA
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29
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Zondagh J, Williams A, Achilonu I, Dirr HW, Sayed Y. Overexpression, Purification and Functional Characterisation of Wild-Type HIV-1 Subtype C Protease and Two Variants Using a Thioredoxin and His-Tag Protein Fusion System. Protein J 2018; 37:369-379. [PMID: 29869126 DOI: 10.1007/s10930-018-9779-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In recent years, various strategies have been used to overexpress and purify HIV-1 protease because it is an essential drug target in anti-retroviral therapy. Obtaining sufficient quantities of the enzyme, however, remains challenging. Overexpression of large quantities is prevented due to the enzyme's autolytic nature and its inherent cytotoxicity in Escherichia coli cells. Here, we describe a novel HIV-1 protease purification method using a thioredoxin-hexahistidine fusion system for the wild-type and two variant proteases. The fusion proteases were overexpressed in E. coli and recovered by immobilised metal ion affinity chromatography. The proteases were cleaved from the fusion constructs using thrombin. When compared to the standard overexpression and purification protocol in use in our laboratory, the expression of the fusion-derived wild-type protease was increased from 0.83 to 2.5 mg/l of culture medium. The expression levels of the two variant proteases ranged from 1.5 to 2 mg/l of culture medium. The fusion wild-type and variant proteases were inactive before the cleavage of the thioredoxin-hexahistidine fusion tag as no enzymatic activity was observed. The proteases were, however, active after cleavage of the tag. The novel thioredoxin-hexahistidine fusion system, therefore, enables the successful overexpression and purification of catalytically active HIV-1 proteases.
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Affiliation(s)
- Jake Zondagh
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, 2050, South Africa
| | - Alison Williams
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, 2050, South Africa
| | - Ikechukwu Achilonu
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, 2050, South Africa
| | - Heini W Dirr
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, 2050, South Africa
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, 2050, South Africa.
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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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Johann DJ, Steliga M, Shin IJ, Yoon D, Arnaoutakis K, Hutchins L, Liu M, Liem J, Walker K, Pereira A, Yang M, Jeffus SK, Peterson E, Xu J. Liquid biopsy and its role in an advanced clinical trial for lung cancer. Exp Biol Med (Maywood) 2018; 243:262-271. [PMID: 29405770 PMCID: PMC5813874 DOI: 10.1177/1535370217750087] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Liquid biopsy methodologies, for the purpose of plasma genotyping of cell-free DNA (cfDNA) of solid tumors, are a new class of novel molecular assays. Such assays are rapidly entering the clinical sphere of research-based monitoring in translational oncology, especially for thoracic malignancies. Potential applications for these blood-based cfDNA assays include: (i) initial diagnosis, (ii) response to therapy and follow-up, (iii) tumor evolution, and (iv) minimal residual disease evaluation. Precision medicine will benefit from cutting-edge molecular diagnostics, especially regarding treatment decisions in the adjuvant setting, where avoiding over-treatment and unnecessary toxicity are paramount. The use of innovative genetic analysis techniques on individual patient tumor samples is being pursued in several advanced clinical trials. Rather than using a categorical treatment plan, the next critical step of therapeutic decision making is providing the "right" cancer therapy for an individual patient, including correct dose and timeframe based on the molecular analysis of the tumor in question. Per the 21st Century Cures Act, innovative clinical trials are integral for biomarker and drug development. This will include advanced clinical trials utilizing: (i) innovative assays, (ii) molecular profiling with cutting-edge bioinformatics, and (iii) clinically relevant animal or tissue models. In this paper, a mini-review addresses state-of-the-art liquid biopsy approaches. Additionally, an on-going advanced clinical trial for lung cancer with novelty through synergizing liquid biopsies, co-clinical trials, and advanced bioinformatics is also presented. Impact statement Liquid biopsy technology is providing a new source for cancer biomarkers, and adds new dimensions in advanced clinical trials. Utilizing a non-invasive routine blood draw, the liquid biopsy provides abilities to address perplexing issues of tumor tissue heterogeneity by identifying mutations in both primary and metastatic lesions. Regarding the assessment of response to cancer therapy, the liquid biopsy is not ready to replace medical imaging, but adds critical new information; for instance, through a temporal assessment of quantitative circulating tumor DNA (ctDNA) assay results, and importantly, the ability to monitor for signs of resistance, via emerging clones. Adjuvant therapy may soon be considered based on a quantitative cfDNA assay. As sensitivity and specificity of the technology continue to progress, cancer screening and prevention will improve and save countless lives by finding the cancer early, so that a routine surgery may be all that is required for a definitive cure.
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Affiliation(s)
- Donald J Johann
- Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Mathew Steliga
- Surgery, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Ik Jae Shin
- Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Donghoon Yoon
- Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Konstantinos Arnaoutakis
- Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Laura Hutchins
- Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Meeiyueh Liu
- Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jason Liem
- Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Karl Walker
- Computer Science, University of Arkansas at Pine Bluff, Pine Bluff, AR 71601, USA
| | - Andy Pereira
- Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Mary Yang
- Bioinformatics, University of Arkansas at Little Rock, Little Rock, AR 72204, USA
| | - Susanne K Jeffus
- Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Erich Peterson
- Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Joshua Xu
- Bioinformatics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72709, USA
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Lodi S, Günthard HF, Dunn D, Garcia F, Logan R, Jose S, Bucher HC, Scherrer AU, Schneider MP, Egger M, Glass TR, Reiss P, van Sighem A, Boender TS, Phillips AN, Porter K, Hawkins D, Moreno S, Monge S, Paraskevis D, Simeon M, Vourli G, Sabin C, Hernán MA. Effect of immediate initiation of antiretroviral treatment on the risk of acquired HIV drug resistance. AIDS 2018; 32:327-335. [PMID: 29135583 PMCID: PMC5758415 DOI: 10.1097/qad.0000000000001692] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE We estimated and compared the risk of clinically identified acquired drug resistance under immediate initiation [the currently recommended antiretroviral therapy (ART) initiation strategy], initiation with CD4 cell count less than 500 cells/μl and initiation with CD4 cell count less than 350 cells/μl. DESIGN Cohort study based on routinely collected data from the HIV-CAUSAL collaboration. METHODS For each individual, baseline was the earliest time when all eligibility criteria (ART-naive, AIDS free, and others) were met after 1999. Acquired drug resistance was defined using the Stanford classification as resistance to any antiretroviral drug that was clinically identified at least 6 months after ART initiation. We used the parametric g-formula to adjust for time-varying (CD4 cell count, HIV RNA, AIDS, ART regimen, and drug resistance testing) and baseline (calendar period, mode of acquisition, sex, age, geographical origin, ethnicity and cohort) characteristics. RESULTS In 50 981 eligible individuals, 10% had CD4 cell count more than 500 cells/μl at baseline, and 63% initiated ART during follow-up. Of 2672 tests for acquired drug resistance, 794 found resistance. The estimated 7-year risk (95% confidence interval) of acquired drug resistance was 3.2% (2.8,3.5) for immediate initiation, 3.1% (2.7,3.3) for initiation with CD4 cell count less than 500 cells/μl, and 2.8% (2.5,3.0) for initiation with CD4 cell count less than 350 cells/μl. In analyses restricted to individuals with baseline in 2005-2015, the corresponding estimates were 1.9% (1.8, 2.5), 1.9% (1.7, 2.4), and 1.8% (1.7, 2.2). CONCLUSION Our findings suggest that the risk of acquired drug resistance is very low, especially in recent calendar periods, and that immediate ART initiation only slightly increases the risk. It is unlikely that drug resistance will jeopardize the proven benefits of immediate ART initiation.
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Affiliation(s)
- Sara Lodi
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | | | - Roger Logan
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Heiner C Bucher
- Basel Institute for Clinical Epidemiology and Biostatistics, University Hospital Basel, University of Basel, Basel
| | - Alexandra U Scherrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Marie-Paule Schneider
- Department of Ambulatory Care and Community Medicine, University of Lausanne, Lausanne
- Community Pharmacy, School of Pharmaceutical Sciences, University of Geneva, Geneva
| | - Matthias Egger
- Institute of Social and Preventive Medicine, University of Bern, Bern
| | - Tracy R Glass
- Swiss Tropical and Public Health Institute
- University of Basel, Basel, Switzerland
| | - Peter Reiss
- Stichting HIV Monitoring
- Division of Infectious Diseases, Department of Global Health, Academic Medical Centre, University of Amsterdam
- Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands
| | | | | | | | | | | | - Santiago Moreno
- IRYCIS, Ramón y Cajal Hospital
- University of Alcalá de Henares
| | - Susana Monge
- University of Alcalá de Henares
- National Centre of Epidemiology - ISCIII, Madrid, Spain
| | | | | | - Georgia Vourli
- National and Kapodistrian University of Athens Medical School, Athens
| | | | - Miguel A Hernán
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard-MIT Division of Health Sciences and Technology, Boston, Massachusetts, USA
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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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De La Mata NL, Kumarasamy N, Ly PS, Ng OT, Nguyen KV, Merati TP, Lee MP, Cuong DD, Choi JY, Ross JL, Law MG. Growing challenges for HIV programmes in Asia: clinic population trends, 2003-2013. AIDS Care 2017; 29:1243-1254. [PMID: 28132544 PMCID: PMC5534184 DOI: 10.1080/09540121.2017.1282108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The scale-up of antiretroviral therapy (ART) has led to a substantial change in the clinical population of HIV-positive patients receiving care. We describe the temporal trends in the demographic and clinical characteristics of HIV-positive patients initiating ART in 2003-13 within an Asian regional cohort. All HIV-positive adult patients that initiated ART between 2003 and 2013 were included. We summarized ART regimen use, age, CD4 cell count, HIV viral load, and HIV-related laboratory monitoring rates during follow-up by calendar year. A total of 16 962 patients were included in the analysis. Patients in active follow-up increased from 695 patients at four sites in 2003 to 11,137 patients at eight sites in 2013. The proportion of patients receiving their second or third ART regimen increased over time (5% in 2003 to 29% in 2013) along with patients aged ≥50 years (8% in 2003 to 18% in 2013). Concurrently, CD4 monitoring has remained stable in recent years, whereas HIV viral load monitoring, although varied among the sites, is increasing. There have been substantial changes in the clinical and demographic characteristics of HIV-positive patients receiving ART in Asia. HIV programmes will need to anticipate the clinical care needs for their aging populations, expanded viral load monitoring, and, the eventual increase in second and third ART regimens that will lead to higher costs and more complex drug procurement needs.
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Affiliation(s)
| | | | - Penh Sun Ly
- National Center for HIV/AIDS, Dermatology & STDs, Phnom Penh, Cambodia
| | | | | | | | - Man Po Lee
- Queen Elizabeth Hospital, Hong Kong SAR, China
| | | | - Jun Yong Choi
- Department of Internal Medicine and AIDS Research Institute, Yonsei University College of Medicine, Severance Hospital, Seoul, South Korea
| | - Jeremy L. Ross
- TREAT Asia, amfAR - The Foundation for AIDS Research, Bangkok, Thailand
| | - Matthew G. Law
- The Kirby Institute, UNSW Australia, Sydney, NSW, Australia
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Tambe J, Aves T, Siemieniuk R, Mbuagbaw L. Antiretroviral resistance testing in people living with HIV. Hippokratia 2017. [DOI: 10.1002/14651858.cd006495.pub4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Joshua Tambe
- Yaoundé Central Hospital; Centre for the Development of Best Practices in Health (CDBPH); Yaoundé Cameroon
| | - Theresa Aves
- McMaster University; Department of Health Research Methods, Evidence, and Impact; 1280 Main St W Hamilton Ontario Canada L8S 4L8
| | - Reed Siemieniuk
- McMaster University; Department of Health Research Methods, Evidence, and Impact; 1280 Main St W Hamilton Ontario Canada L8S 4L8
| | - Lawrence Mbuagbaw
- Yaoundé Central Hospital; Centre for the Development of Best Practices in Health (CDBPH); Yaoundé Cameroon
- McMaster University; Department of Health Research Methods, Evidence, and Impact; 1280 Main St W Hamilton Ontario Canada L8S 4L8
- South African Medical Research Council; South African Cochrane Centre; Tygerberg South Africa
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Multimethod Longitudinal HIV Drug Resistance Analysis in Antiretroviral-Therapy-Naive Patients. J Clin Microbiol 2017; 55:2785-2800. [PMID: 28659324 DOI: 10.1128/jcm.00634-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 06/27/2017] [Indexed: 11/20/2022] Open
Abstract
The global intensification of antiretroviral therapy (ART) can lead to increased rates of HIV drug resistance (HIVDR) mutations in treated and also in ART-naive patients. ART-naive HIV-1-infected patients from Cameroon were subjected to a multimethod HIVDR analysis using amplification-refractory mutation system (ARMS)-PCR, Sanger sequencing, and longitudinal next-generation sequencing (NGS) to determine their profiles for the mutations K103N, Y181C, K65R, M184V, and T215F/Y. We processed 66 ART-naive HIV-1-positive patients with highly diverse subtypes that underlined the predominance of CRF02_AG and the increasing rate of F2 and other recombinant forms in Cameroon. We compared three resistance testing methods for 5 major mutation sites. Using Sanger sequencing, the overall prevalence of HIVDR mutations was 7.6% (5/66) and included all studied mutations except K65R. Comparing ARMS-PCR with Sanger sequencing as a reference, we obtained a sensitivity of 100% (5/5) and a specificity of 95% (58/61), caused by three false-positive calls with ARMS-PCR. For 32/66 samples, we obtained NGS data and we observed two additional mismatches made up of minority variants (7% and 18%) that might not be clinically relevant. Longitudinal NGS analyses revealed changes in HIVDR mutations in all five positive subjects that could not be attributed to treatment. In one of these cases, superinfection led to the temporary masking of a resistant virus. HIVDR mutations can be sensitively detected by ARMS-PCR and sequencing methods with comparable performances. Longitudinal changes in HIVDR mutations have to be considered even in the absence of treatment.
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Saravanan S, Kausalya B, Gomathi S, Sivamalar S, Pachamuthu B, Selvamuthu P, Pradeep A, Sunil S, Mothi SN, Smith DM, kantor R. Etravirine and Rilpivirine Drug Resistance Among HIV-1 Subtype C Infected Children Failing Non-Nucleoside Reverse Transcriptase Inhibitor-Based Regimens in South India. AIDS Res Hum Retroviruses 2017; 33:567-574. [PMID: 27869478 DOI: 10.1089/aid.2016.0133] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We have analyzed reverse transcriptase (RT) region of HIV-1 pol gene from 97 HIV-infected children who were identified as failing first-line therapy that included first-generation non-nucleoside RT inhibitors (Nevirapine and Efavirenz) for at least 6 months. We found that 54% and 65% of the children had genotypically predicted resistance to second-generation non-nucleoside RT inhibitors drugs Etravirine (ETR) and Rilpivirine, respectively. These cross-resistance mutations may compromise future NNRTI-based regimens, especially in resource-limited settings. To complement these investigations, we also analyzed the sequences in Stanford database, Monogram weighted score, and DUET weighted score algorithms for ETR susceptibility and found almost perfect agreement between the three algorithms in predicting ETR susceptibility from genotypic data.
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Affiliation(s)
- Shanmugam Saravanan
- Y.R. Gaitonde Centre for AIDS Research and Education (YRG CARE), Chennai, India
| | - Bagavathi Kausalya
- Y.R. Gaitonde Centre for AIDS Research and Education (YRG CARE), Chennai, India
| | - Selvamurthi Gomathi
- Y.R. Gaitonde Centre for AIDS Research and Education (YRG CARE), Chennai, India
| | | | | | | | - Amrose Pradeep
- Y.R. Gaitonde Centre for AIDS Research and Education (YRG CARE), Chennai, India
| | - Solomon Sunil
- Y.R. Gaitonde Centre for AIDS Research and Education (YRG CARE), Chennai, India
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Davey M. Smith
- University of California, San Diego, San Diego, California
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Dennis AM, Hué S, Learner E, Sebastian J, Miller WC, Eron JJ. Rising prevalence of non-B HIV-1 subtypes in North Carolina and evidence for local onward transmission. Virus Evol 2017; 3:vex013. [PMID: 28567304 PMCID: PMC5442504 DOI: 10.1093/ve/vex013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1 diversity is increasing in North American and European cohorts which may have public health implications. However, little is known about non-B subtype diversity in the southern United States, despite the region being the epicenter of the nation's epidemic. We characterized HIV-1 diversity and transmission clusters to identify the extent to which non-B strains are transmitted locally. We conducted cross-sectional analyses of HIV-1 partial pol sequences collected from 1997 to 2014 from adults accessing routine clinical care in North Carolina (NC). Subtypes were evaluated using COMET and phylogenetic analysis. Putative transmission clusters were identified using maximum-likelihood trees. Clusters involving non-B strains were confirmed and their dates of origin were estimated using Bayesian phylogenetics. Data were combined with demographic information collected at the time of sample collection and country of origin for a subset of patients. Among 24,972 sequences from 15,246 persons, the non-B subtype prevalence increased from 0% to 3.46% over the study period. Of 325 persons with non-B subtypes, diversity was high with over 15 pure subtypes and recombinants; subtype C (28.9%) and CRF02_AG (24.0%) were most common. While identification of transmission clusters was lower for persons with non-B versus B subtypes, several local transmission clusters (≥3 persons) involving non-B subtypes were identified and all were presumably due to heterosexual transmission. Prevalence of non-B subtype diversity remains low in NC but a statistically significant rise was identified over time which likely reflects multiple importation. However, the combined phylogenetic clustering analysis reveals evidence for local onward transmission. Detection of these non-B clusters suggests heterosexual transmission and may guide diagnostic and prevention interventions.
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Affiliation(s)
- Ann M Dennis
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Stephane Hué
- London School of Hygiene & Tropical Medicine, London, UK
| | - Emily Learner
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Joseph Sebastian
- Laboratory Corporation of America, Research Triangle Park, NC, USA
| | - William C Miller
- Department of Epidemiology, Ohio State University, Columbus, OH, USA
| | - Joseph J Eron
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA.,Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
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39
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Praparattanapan J, Tragoolpua Y, Wongtrakul J, Kotarathitithum W, Chaiwarith R, Nuntachit N, Sirisanthana T, Supparatpinyo K. Comparison of in-house HIV-1 genotypic drug resistant test with commercial HIV-1 genotypic test kit. ASIAN BIOMED 2017. [DOI: 10.5372/1905-7415.0502.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Abstract
Background: The use of combination antiretroviral therapy (cART) has become a standard of care in the treatment of HIV infection. However, antiretroviral drug resistance occurs in a substantial number of patients. In resource-limited settings, genotypic resistance assay using a commercial kit is costly.
Objective: Focus on the validation of an in-house HIV-1 specific genotypic drug resistance assay in Thai patients failing cART.
Materials and methods: Results of HIV-1 genotypic drug resistance assay was evaluated by comparing an inhouse method to a commercial test. The TRUGENE HIV-1 genotyping kit was used in 79 plasma specimens (49 from HIV patients failing cART therapy and 30 from proficiency testing panels).
Results: The results from the in-house assay were comparable to those obtained from the TRUGENE HIV-1 genotyping kit with >99.0% codon-to-codon agreement. The lower limit of detection by the in-house assay was approximately 100 copies/mL of HIV-1 RNA. In addition, this in-house assay would allow testing of samples from patients infected with HIV-1 subtype other than B.
Conclusion: The in-house HIV-1 genotypic drug resistance assay may be used as an alternative to commercial kits, particularly in resource limited settings.
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Affiliation(s)
- Jutarat Praparattanapan
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand Thailand
- Department of Medicine, Faculty of Medicine; Chiang Mai University, Chiang Mai 50200, Thailand
| | - Yingmanee Tragoolpua
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jeerang Wongtrakul
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Wilai Kotarathitithum
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Romanee Chaiwarith
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nontakan Nuntachit
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Thira Sirisanthana
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Khuanchai Supparatpinyo
- Correspondence to: Department of Medicine, Faculty of Medicine Chiang Mai University, Chiang Mai 50200, Thailand Thailand
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
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40
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41
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Drugs for HIV Infection. Infect Dis (Lond) 2017. [DOI: 10.1016/b978-0-7020-6285-8.00152-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
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42
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Gill VC, Lynch T, Ramazani S, Krentz HB. Reporting on the prevalence of antiretroviral drug resistance in a regional HIV population over 20 years: a word of caution. Antivir Ther 2016; 22:277-286. [PMID: 27805572 DOI: 10.3851/imp3105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Failure to achieve complete viral suppression with antiretroviral drugs (ARV) may lead to uncontrolled HIV replication, ARV resistance and negative outcomes. Monitoring and reporting of HIV resistance trends is important but problematic. We examined prevalent resistance rates in an HIV population over 20 years and document how rates may appear to vary greatly based solely on which parameters are utilized. METHODS We determined the annual use of genotypic antiretroviral resistance testing (GART) from 1995 to 2014 for all patients receiving HIV care in southern Alberta, Canada, and the presence of resistance mutations in those tested. The impact on prevalent resistance rates of using cumulative or latest GART was also determined. RESULTS Between 1995 and 2014, the number of patients with GART increased from <1% to 71%. Prevalent resistance in patients with GART decreased from a high of 52% in 2003 to 25.8% in 2014. However, if prevalence rates were reported using all active patients as denominator, including those without GART, prevalence increased from 0.7% to 18.5%. Prevalence rates were 7% to 9% higher in any given year if cumulative GART rather than latest GART results were used. CONCLUSIONS While prevalence resistance rates are decreasing, the precise rates being reported may vary due to increasing number of patients tested annually, using either the entire population as denominator or only patients with GART, and using either last or cumulative GART. Defining these parameters is critical if prevalence is to be compared over time or between HIV populations.
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Affiliation(s)
| | - Tarah Lynch
- Southern Alberta Clinic, Calgary, AB, Canada.,Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Hartmut B Krentz
- Southern Alberta Clinic, Calgary, AB, Canada.,Department of Medicine, University of Calgary, Calgary, AB, Canada
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43
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Kesselring S, Cescon A, Colley G, Osborne C, Zhang W, Raboud JM, Hosein SR, Burchell AN, Cooper C, Klein MB, Loutfy M, Machouf N, Montaner J, Rachlis A, Tsoukas C, Hogg RS, Lima VD. Quality of initial HIV care in Canada: extension of a composite programmatic assessment tool for HIV therapy. HIV Med 2016; 18:151-160. [PMID: 27385643 DOI: 10.1111/hiv.12409] [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] [Accepted: 03/17/2016] [Indexed: 11/29/2022]
Abstract
OBJECTIVES To document the quality of initial HIV care in Canada using the Programmatic Compliance Score (PCS), to explore the association of the PCS with mortality, and to identify factors associated with higher quality of care. METHODS We analysed data from the Canadian Observational Cohort Collaboration (CANOC), a multisite Canadian cohort of HIV-positive adults initiating combination antiretroviral therapy (ART) from 2000 to 2011. PCS indicators of noncompliance with HIV treatment guidelines include: fewer than three CD4 count tests in the first year of ART; fewer than three viral load tests in the first year of ART; no drug resistance testing before initiation; baseline CD4 count < 200 cells/mm3 ; starting a nonrecommended ART regimen; and not achieving viral suppression within 6 months of initiation. Indicators are summed for a score from 0 to 6; higher scores indicate poorer care. Cox regression was used to assess the association between PCS and mortality and ordinal logistic regression was used to explore factors associated with higher quality of care. RESULTS Of the 7460 participants (18% female), the median score was 1.0 (Q1-Q3 1.0-2.0); 21% scored 0 and 8% scored ≥ 4. In multivariable analysis, compared with a score of 0, poorer PCS was associated with mortality for scores > 1 [score = 2: adjusted hazard ratio (AHR) 1.64; 95% confidence interval (CI) 1.13-2.36; score = 3: AHR 2.02; 95% CI 1.38-2.97; score ≥ 4: AHR 2.14; 95% CI 1.43-3.21], after adjustments for age, sex, province, ART start year, hepatitis C virus (HCV) coinfection, and baseline viral load. Women, individuals with HCV coinfection, younger people, and individuals starting ART earlier (2000-2003) had poorer scores. CONCLUSIONS Our findings further validate the PCS as a predictor of all-cause mortality. Disparities identified suggest that further efforts are needed to ensure that care is equitably accessible.
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Affiliation(s)
- S Kesselring
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - A Cescon
- Northern Ontario School of Medicine, Sudbury, ON, Canada
| | - G Colley
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - C Osborne
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - W Zhang
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - J M Raboud
- Toronto General Research Institute, University Health Network, Toronto, ON, Canada.,University of Toronto, Toronto, ON, Canada
| | | | - A N Burchell
- University of Toronto, Toronto, ON, Canada.,Ontario HIV Treatment Network, Toronto, ON, Canada
| | - C Cooper
- University of Ottawa, Ottawa, ON, Canada
| | - M B Klein
- McGill University, Montreal, QC, Canada
| | - M Loutfy
- University of Toronto, Toronto, ON, Canada.,Women's College Research Institute, Toronto, ON, Canada.,Maple Leaf Medical Clinic, Toronto, ON, Canada
| | - N Machouf
- Clinique médicale l'Actuel, Montreal, QC, Canada
| | - Jsg Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,University of British Columbia, Vancouver, BC, Canada
| | - A Rachlis
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - C Tsoukas
- McGill University, Montreal, QC, Canada
| | - R S Hogg
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Simon Fraser University, Burnaby, BC, Canada
| | - V D Lima
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,University of British Columbia, Vancouver, BC, Canada
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Court R, Gordon M, Cohen K, Stewart A, Gosnell B, Wiesner L, Maartens G. Random lopinavir concentrations predict resistance on lopinavir-based antiretroviral therapy. Int J Antimicrob Agents 2016; 48:158-62. [PMID: 27345268 DOI: 10.1016/j.ijantimicag.2016.04.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/13/2016] [Accepted: 04/30/2016] [Indexed: 10/21/2022]
Abstract
Considering that most patients who experience virological failure (VF) on lopinavir-based antiretroviral therapy (ART) fail due to poor adherence rather than resistance, an objective adherence measure could limit costs by rationalising the use of genotype antiretroviral resistance testing (GART) in countries with access to third-line ART. A cross-sectional study was conducted in a resource-limited setting at two large clinics in Kwazulu-Natal, South Africa, in patients experiencing VF (HIV-RNA > 1000 copies/mL) on lopinavir-based ART who had undergone GART. Associations between major protease inhibitor (PI) resistance mutations and random plasma lopinavir concentrations were explored. A total of 134 patients, including 31 children, were included in the analysis. The prevalence of patients with major PI resistance mutations was 20.9% (n = 28). A random lopinavir concentration above the recommended minimum trough of 1 µg/mL [adjusted odds ratio (aOR) = 5.81, 95% confidence interval (CI) 2.04-16.50; P = 0.001] and male sex (aOR = 3.19, 95% CI 1.22-8.33; P = 0.018) were predictive of the presence of at least one major PI resistance mutation. Random lopinavir concentrations of <1 µg/mL had a negative predictive value of 91% for major PI resistance mutations. Random lopinavir concentrations are strongly associated with the presence of major PI resistance mutations. Access to costly GART in patients experiencing VF on second-line ART could be restricted to patients with lopinavir concentrations above the recommended minimum trough of 1 µg/mL or, in areas where GART is unavailable, could be used as a criterion to empirically switch to third-line ART.
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Affiliation(s)
- Richard Court
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa.
| | - Michelle Gordon
- Department of Virology, Nelson R. Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Karen Cohen
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Annemie Stewart
- Clinical Research Centre, University of Cape Town, Cape Town, South Africa
| | - Bernadett Gosnell
- Department of Infectious Diseases, Nelson R. Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Lubbe Wiesner
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Gary Maartens
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
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Menon RM, Klein CE, Podsadecki TJ, Chiu YL, Dutta S, Awni WM. Pharmacokinetics and tolerability of paritaprevir, a direct acting antiviral agent for hepatitis C virus treatment, with and without ritonavir in healthy volunteers. Br J Clin Pharmacol 2016; 81:929-40. [PMID: 26710243 PMCID: PMC4834602 DOI: 10.1111/bcp.12873] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 12/17/2015] [Accepted: 12/21/2015] [Indexed: 12/11/2022] Open
Abstract
AIMS Paritaprevir is a direct acting antiviral agent for use as part of a multidrug hepatitis C virus infection treatment regimen. To characterize the pharmacokinetics, safety, and tolerability of paritaprevir and determine an optimal dosing regimen for subsequent evaluations, clinical studies were conducted with paritaprevir alone or with ritonavir, a cytochrome P450 3A4 inhibitor anticipated to increase paritaprevir exposure. METHODS Two phase 1, double-blind, placebo-controlled, parallel group studies were conducted in healthy volunteers (NCT00850044 and NCT00931281). Single dose study participants (n = 87) were randomized to one time administration of either paritaprevir or placebo, or paritaprevir with ritonavir or placebo. Participants (n = 38) enrolled in the multiple dose study received paritaprevir with ritonavir or placebo once or twice daily for 14 days. Pharmacokinetics, safety and tolerability were assessed throughout the study treatment periods. RESULTS After single or multiple dose administration, paritaprevir displayed non-linear pharmacokinetics, with maximum plasma concentration and area under the plasma concentration-time curve increasing in a greater than dose proportional manner. Concomitant administration of 100 mg ritonavir increased paritaprevir exposure from a 300 mg dose approximately 30- to 50-fold and extended paritaprevir half-life. The tolerability of paritaprevir was similar with or without ritonavir. Asymptomatic, transient increases in bilirubin were observed but were not associated with abnormalities in other liver function tests. CONCLUSIONS Paritaprevir exhibits non-linear pharmacokinetics with greater than dose proportional increases in exposure after single or multiple dosing. Co-administration with ritonavir increases paritaprevir exposure and half-life without adversely influencing tolerability.
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Affiliation(s)
- R M Menon
- Clinical Pharmacokinetics and Pharmacodynamics, AbbVie, 1 North Waukegan Road, AP31-3, North Chicago, Illinois, 60064
| | - C E Klein
- Clinical Pharmacokinetics and Pharmacodynamics, AbbVie, 1 North Waukegan Road, AP31-3, North Chicago, Illinois, 60064
| | - T J Podsadecki
- Infectious Diseases, R48U, AP-30, AbbVie, 1 North Waukegan Road, North Chicago, Illinois, 60064
| | - Y-L Chiu
- Department of Biometrics, AbbVie, 1 North Waukegan Road, AP31-2, North Chicago, Illinois, 60064
| | - S Dutta
- Clinical Pharmacokinetics and Pharmacodynamics, AbbVie, 1 North Waukegan Road, AP31-3, North Chicago, Illinois, 60064
| | - W M Awni
- Clinical Pharmacology and Pharmacometrics, AbbVie, 1 North Waukegan Road, R4PD AP31-3, North Chicago, IL, 60064, USA
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46
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Phylogeny and drug resistance of HIV PR gene among HIV patients receiving RT inhibitors in Iran. Asian Pac J Trop Biomed 2016. [DOI: 10.1016/j.apjtb.2015.12.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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47
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Deep Sequencing of HIV-1 RNA and DNA in Newly Diagnosed Patients with Baseline Drug Resistance Showed No Indications for Hidden Resistance and Is Biased by Strong Interference of Hypermutation. J Clin Microbiol 2016; 54:1605-1615. [PMID: 27076656 DOI: 10.1128/jcm.00030-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/01/2016] [Indexed: 12/29/2022] Open
Abstract
Deep sequencing of plasma RNA or proviral DNA may be an interesting alternative to population sequencing for the detection of baseline transmitted HIV-1 drug resistance. Using a Roche 454 GS Junior HIV-1 prototype kit, we performed deep sequencing of the HIV-1 protease and reverse transcriptase genes on paired plasma and buffy coat samples from newly diagnosed HIV-1-positive individuals. Selection was based on the outcome of population sequencing and included 12 patients with either a revertant amino acid at codon 215 of the reverse transcriptase or a singleton resistance mutation, 4 patients with multiple resistance mutations, and 4 patients with wild-type virus. Deep sequencing of RNA and DNA detected 6 and 43 mutations, respectively, that were not identified by population sequencing. A subsequently performed hypermutation analysis, however, revealed hypermutation in 61.19% of 3,188 DNA reads with a resistance mutation. The removal of hypermutated reads dropped the number of additional mutations in DNA from 43 to 17. No hypermutation evidence was found in the RNA reads. Five of the 6 additional RNA mutations and all additional DNA mutations, after full exclusion of hypermutation bias, were observed in the 3 individuals with multiple resistance mutations detected by population sequencing. Despite focused selection of patients with T215 revertants or singleton mutations, deep sequencing failed to identify the resistant T215Y/F or M184V or any other resistance mutation, indicating that in most of these cases there is no hidden resistance and that the virus detected at diagnosis by population sequencing is the original infecting variant.
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Abstract
The virally encoded protease is an important drug target for AIDS therapy. Despite the potency of the current drugs, infections with resistant viral strains limit the long-term effectiveness of therapy. Highly resistant variants of HIV protease from clinical isolates have different combinations of about 20 mutations and several orders of magnitude worse binding affinity for clinical inhibitors. Strategies are being explored to inhibit these highly resistant mutants. The existing inhibitors can be modified by introducing groups with the potential to form new interactions with conserved protease residues, and the flexible flaps. Alternative strategies are discussed, including designing inhibitors to bind to the open conformation of the protease dimer, and inhibition of the protease-catalyzed processing of the Gag-Pol precursor.
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Scherrer AU, von Wyl V, Yang WL, Kouyos RD, Böni J, Yerly S, Klimkait T, Aubert V, Cavassini M, Battegay M, Furrer H, Calmy A, Vernazza P, Bernasconi E, Günthard HF, Aubert V, Battegay M, Bernasconi E, Böni J, Braun DL, Bucher HC, Burton-Jeangros C, Calmy A, Cavassini M, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Gorgievski M, Günthard H, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Kahlert C, Kaiser L, Keiser O, Klimkait T, Kouyos R, Kovari H, Ledergerber B, Martinetti G, Martinez de Tejada B, Marzolini C, Metzner K, Müller N, Nadal D, Nicca D, Pantaleo G, Rauch A, Regenass S, Rudin C, Schöni-Affolter F, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Vernazza P, Weber R, Yerly S. Emergence of Acquired HIV-1 Drug Resistance Almost Stopped in Switzerland: A 15-Year Prospective Cohort Analysis. Clin Infect Dis 2016; 62:1310-1317. [PMID: 26962075 DOI: 10.1093/cid/ciw128] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/05/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Drug resistance is a major barrier to successful antiretroviral treatment (ART). Therefore, it is important to monitor time trends at a population level. METHODS We included 11 084 ART-experienced patients from the Swiss HIV Cohort Study (SHCS) between 1999 and 2013. The SHCS is highly representative and includes 72% of patients receiving ART in Switzerland. Drug resistance was defined as the presence of ≥1 major mutation in a genotypic resistance test. To estimate the prevalence of drug resistance, data for patients with no resistance test was imputed based on the patient's risk of harboring drug-resistant viruses. RESULTS The emergence of new drug resistance mutations declined dramatically from 401 to 23 patients between 1999 and 2013. The upper estimated prevalence limit of drug resistance among ART-experienced patients decreased from 57.0% in 1999 to 37.1% in 2013. The prevalence of 3-class resistance decreased from 9.0% to 4.4% and was always <0.4% for patients who initiated ART after 2006. Most patients actively participating in the SHCS in 2013 with drug-resistant viruses initiated ART before 1999 (59.8%). Nevertheless, in 2013, 94.5% of patients who initiated ART before 1999 had good remaining treatment options based on Stanford algorithm. CONCLUSIONS Human immunodeficiency virus type 1 drug resistance among ART-experienced patients in Switzerland is a well-controlled relic from the era before combination ART. Emergence of drug resistance can be virtually stopped with new potent therapies and close monitoring.
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Affiliation(s)
- Alexandra U Scherrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology
| | - Viktor von Wyl
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich
| | - Wan-Lin Yang
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology
| | | | - Sabine Yerly
- Laboratory of Virology, Division of Infectious Diseases
| | | | | | | | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel
| | - Hansjakob Furrer
- Department of Infectious Diseases, Berne University Hospital and University of Berne
| | - Alexandra Calmy
- HIV/AIDS Unit, Infectious Disease Service, Geneva University Hospital
| | - Pietro Vernazza
- Division of Infectious Diseases, Cantonal Hospital St Gallen
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology
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50
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St. John EP, Simen BB, Turenchalk GS, Braverman MS, Abbate I, Aerssens J, Bouchez O, Gabriel C, Izopet J, Meixenberger K, Di Giallonardo F, Schlapbach R, Paredes R, Sakwa J, Schmitz-Agheguian GG, Thielen A, Victor M, Metzner KJ, Däumer MP. A Follow-Up of the Multicenter Collaborative Study on HIV-1 Drug Resistance and Tropism Testing Using 454 Ultra Deep Pyrosequencing. PLoS One 2016; 11:e0146687. [PMID: 26756901 PMCID: PMC4710461 DOI: 10.1371/journal.pone.0146687] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/21/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Ultra deep sequencing is of increasing use not only in research but also in diagnostics. For implementation of ultra deep sequencing assays in clinical laboratories for routine diagnostics, intra- and inter-laboratory testing are of the utmost importance. METHODS A multicenter study was conducted to validate an updated assay design for 454 Life Sciences' GS FLX Titanium system targeting protease/reverse transcriptase (RTP) and env (V3) regions to identify HIV-1 drug-resistance mutations and determine co-receptor use with high sensitivity. The study included 30 HIV-1 subtype B and 6 subtype non-B samples with viral titers (VT) of 3,940-447,400 copies/mL, two dilution series (52,129-1,340 and 25,130-734 copies/mL), and triplicate samples. Amplicons spanning PR codons 10-99, RT codons 1-251 and the entire V3 region were generated using barcoded primers. Analysis was performed using the GS Amplicon Variant Analyzer and geno2pheno for tropism. For comparison, population sequencing was performed using the ViroSeq HIV-1 genotyping system. RESULTS The median sequencing depth across the 11 sites was 1,829 reads per position for RTP (IQR 592-3,488) and 2,410 for V3 (IQR 786-3,695). 10 preselected drug resistant variants were measured across sites and showed high inter-laboratory correlation across all sites with data (P<0.001). The triplicate samples of a plasmid mixture confirmed the high inter-laboratory consistency (mean% ± stdev: 4.6 ±0.5, 4.8 ±0.4, 4.9 ±0.3) and revealed good intra-laboratory consistency (mean% range ± stdev range: 4.2-5.2 ± 0.04-0.65). In the two dilutions series, no variants >20% were missed, variants 2-10% were detected at most sites (even at low VT), and variants 1-2% were detected by some sites. All mutations detected by population sequencing were also detected by UDS. CONCLUSIONS This assay design results in an accurate and reproducible approach to analyze HIV-1 mutant spectra, even at variant frequencies well below those routinely detectable by population sequencing.
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Affiliation(s)
| | - Birgitte B. Simen
- 454 Life Sciences, A Roche Company, Branford, CT, United States of America
| | | | | | - Isabella Abbate
- National Institute for Infectious Diseases “L. Spallanzani, Rome, Italy
| | - Jeroen Aerssens
- Janssen Infectious Diseases—Diagnostics bvba, Beerse, Belgium
| | - Olivier Bouchez
- Plateforme Génomique Toulouse/Laboratoire Génétique Cellulaire, Toulouse, France
| | | | | | | | - Francesca Di Giallonardo
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, University of Zurich, ETH Zurich, Zurich, Switzerland
| | - Roger Paredes
- Institut de Recerca de la SIDA–IrsiCaixa, Badalona, Spain
| | - James Sakwa
- Technology Innovation Agency-National Genomics Platform, Durban, South Africa
| | | | | | | | - Karin J. Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- * E-mail:
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